- Assistant Professor, Molecular and Cellular Biology
Betul Kacar is an Assistant Professor in the Molecular and Cellular Biology and Astronomy Departments at the University of Arizona. She received her PhD from the Departments of Chemistry and Biochemistry at Emory Medical School, studying the structure–function relationship of monoamine oxidases. She was a NASA Postdoctoral Fellow of the NASA Astrobiology Institute and a Research Group Leader at Harvard University Department of Organismic and Evolutionary Biology before joining Arizona in 2017 where she focused on reconstructing key enzymatic intermediates between biological activity and global geochemical reservoirs throughout the Earth's deep history through molecular evolution, biochemistry and genomics. The overall goal of Betul's research group is to assess the possible environmental impacts of ancient enzymes on global-scale signatures that record biological activity.
Betul Kacar serves as a Co-PI on NASA Astrobiology Institute's Reliving the Past (CAN7) node. She is an Associate-PI with the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology and one of the founders of the first and only online astrobiology network SAGANet (saganet.org).
- Way Cool Scientist
- Science Club for Girls, Winter 2016
- Big Questions in Life Sciences
- John Templeton Foundation, Fall 2016
- VWR Distinguished Postdoctoral Award
- Georgia Institute of Technology, Fall 2015
- NASA Postdoctoral Fellowship
- NASA, Fall 2012
- NASA Astrobiology Young Investigator Award
- NASA, Spring 2011
- NSF K12 Teaching Fellow
- Emory University, Summer 2006
- Summer Undergraduate Research Fellowship
- Howard Hughes Medical Institute Emory University, Summer 2003
astrobiology, molecular biology, evolution
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- , S. I., , W. B., , L. C., , S. D., , S. D., , S. D., , B. K., , N. Y., , A. L., , C. T., , W. M., , E. W., , E. L., & , H. B. (2018). Exoplanet Biosignatures: Future Directions.More infoExoplanet science promises a continued rapid accumulation of new observationsin the near future, energizing a drive to understand and interpret theforthcoming wealth of data to identify signs of life beyond our Solar System.The large statistics of exoplanet samples, combined with the ambiguity of ourunderstanding of universal properties of life and its signatures, necessitate aquantitative framework for biosignature assessment Here, we introduce aBayesian framework for guiding future directions in life detection, whichpermits the possibility of generalizing our search strategy beyondbiosignatures of known life. The Bayesian methodology provides a language todefine quantitatively the conditional probabilities and confidence levels offuture life detection and, importantly, may constrain the prior probability oflife with or without positive detection. We describe empirical and theoreticalwork necessary to place constraints on the relevant likelihoods, includingthose emerging from stellar and planetary context, the contingencies ofevolutionary history and the universalities of physics and chemistry. Wediscuss how the Bayesian framework can guide our search strategies, includingdetermining observational wavelengths or deciding between targeted searches orlarger, lower resolution surveys. Our goal is to provide a quantitativeframework not entrained to specific definitions of life or its signatures,which integrates the diverse disciplinary perspectives necessary to confidentlydetect alien life.[Journal_ref: ]
- Kacar, B., Garmendia, E., Tuncbag, N., Andersson, D. I., & Hughes, D. (2017). Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs. mBio, 8(4).More infoGenes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 billion years ago (bya). Our results demonstrate that all of the foreign tuf genes are transferable to the E. coli genome, provided that an additional copy of the EF-Tu gene, tufB, remains present in the E. coli genome. However, when the tufB gene was removed, only the variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth which demonstrates the limited functional interchangeability of E. coli tuf with its homologs. Relative bacterial fitness correlated with the evolutionary distance of the extant tuf homologs inserted into the E. coli genome. This reduced fitness was associated with reduced levels of EF-Tu and reduced rates of protein synthesis. Increasing the expression of tuf partially ameliorated these fitness costs. In summary, our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.IMPORTANCE Horizontal gene transfer (HGT) is a fundamental driving force in bacterial evolution. However, whether essential genes can be acquired by HGT and whether they can be acquired from distant organisms are very poorly understood. By systematically replacing tuf with ancestral homologs and homologs from distantly related organisms, we investigated the constraints on HGT of a highly conserved gene with multiple interaction partners. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 bya. Only variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth, demonstrating the limited functional interchangeability of E. coli tuf with its homologs. Our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.
- Kacar, B., Ge, X., Sanyal, S., & Gaucher, E. A. (2017). Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein. Journal of molecular evolution, 84(2-3), 69-84.More infoThe ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. While the ancient homolog was not lethal to the cell, it did cause a twofold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2000 generations in the laboratory and examined the adaptive response via fitness assays, whole genome sequencing, proteomics, and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by upregulation of protein production. Our results suggest that an ancient-modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.
- 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).More infoTwo datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction.This article is part of the themed issue 'Reconceptualizing the origins of life'.
- Kacar, B., Hanson-Smith, V., Adam, Z. R., & Boekelheide, N. (2017). Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. Geobiology, 15(5), 628-640.More infoRibulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen-sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem-bearing, oxygen-evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen-sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.
- Domagal-Goldman, S. D., Wright, K. E., Adamala, K., Arina de la Rubia, L., Bond, J., Dartnell, L. R., Goldman, A. D., Lynch, K., Naud, M. E., Paulino-Lima, I. G., Singer, K., Walter-Antonio, M., Abrevaya, X. C., Anderson, R., Arney, G., Atri, D., Azúa-Bustos, A., Bowman, J. S., Brazelton, W. J., , Brennecka, G. A., et al. (2016). The Astrobiology Primer v2.0. Astrobiology, 16(8), 561-653.
- Kaçar, B., & Gaucher, E. A. (2013). Experimental evolution of protein-protein interaction networks. The Biochemical journal, 453(3), 311-9.More infoThe 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.
- Kacar, B. (2012). Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution. Artificial Life XIII: Proceedings of the Thirteenth International Conference on the Synthesis and Simulation of Living Systems. pp, 11-18.More infoOne way to understand the role history plays on evolutionary trajectories isby giving ancient life a second opportunity to evolve. Our ability toempirically perform such an experiment, however, is limited by currentexperimental designs. Combining ancestral sequence reconstruction withsynthetic biology allows us to resurrect the past within a modern context andhas expanded our understanding of protein functionality within a historicalcontext. Experimental evolution, on the other hand, provides us with theability to study evolution in action, under controlled conditions in thelaboratory. Here we describe a novel experimental setup that integrates twodisparate fields - ancestral sequence reconstruction and experimentalevolution. This allows us to rewind and replay the evolutionary history ofancient biomolecules in the laboratory. We anticipate that our combination willprovide a deeper understanding of the underlying roles that contingency anddeterminism play in shaping evolutionary processes.[Journal_ref: Artificial Life XIII: Proceedings of the Thirteenth International Conference on the Synthesis and Simulation of Living Systems. pp 11-18. Cambridge, MA: MIT Press 2012]
- Kacar, B., Aldeco, M., & Edmondson, D. E. (2011). Catalytic and inhibitor binding properties of zebrafish monoamine oxidase (zMAO): comparisons with human MAO A and MAO B. Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology, 159(2), 78-83.More infoA comparative investigation of substrate specificity and inhibitor binding properties of recombinant zebrafish (Danio rerio) monoamine oxidase (zMAO) with those of recombinant human monoamine oxidases A and B (hMAO A and hMAO B) is presented. zMAO oxidizes the neurotransmitter amines (serotonin, dopamine and tyramine) with k(cat) values that exceed those of hMAO A or of hMAO B. The enzyme is competitively inhibited by hMAO A selective reversible inhibitors with the exception of d-amphetamine where uncompetitive inhibition is exhibited. The enzyme is unreactive with most MAO B-specific reversible inhibitors with the exception of chlorostyrylcaffeine. zMAO catalyzes the oxidation of para-substituted benzylamine analogs exhibiting (D)k(cat) and (D)(k(cat)/K(m)) values ranging from 2 to 8. Structure-activity correlations show a dependence of log k(cat) with the electronic factor σ(p) with a ρ value of +1.55±0.34; a value close to that for hMAO A but not with MAO B. zMAO differs from hMAO A or hMAO B in benzylamine analog binding correlations where an electronic effect (ρ=+1.29±0.31) is observed. These data demonstrate zMAO exhibits functional properties similar to hMAO A as well as exhibits its own unique behavior. These results should be useful for studies of MAO function in zebrafish models of human disease states.
- Kacar, B., Boyd, E. S., Dolci, W. W., Dodson, K. E., Boldt, M. S., & Pilcher, C. B. (2011). Workshops Without Walls: broadening access to science around the world. PLoS biology, 9(8), e1001118.More infoThe National Aeronautics and Space Administration (NASA) Astrobiology Institute (NAI) conducted two "Workshops Without Walls" during 2010 that enabled global scientific exchange--with no travel required. The second of these was on the topic "Molecular Paleontology and Resurrection: Rewinding the Tape of Life." Scientists from diverse disciplines and locations around the world were joined through an integrated suite of collaborative technologies to exchange information on the latest developments in this area of origin of life research. Through social media outlets and popular science blogs, participation in the workshop was broadened to include educators, science writers, and members of the general public. In total, over 560 people from 31 US states and 30 other nations were registered. Among the scientific disciplines represented were geochemistry, biochemistry, molecular biology and evolution, and microbial ecology. We present this workshop as a case study in how interdisciplinary collaborative research may be fostered, with substantial public engagement, without sustaining the deleterious environmental and economic impacts of travel.
- Kacar, B., & Edmondson, D. E. (2010). Expression of zebrafish (Danio rerio) monoamine oxidase (MAO) in Pichia pastoris: purification and comparison with human MAO A and MAO B. Protein expression and purification, 70(2), 290-7.More infoThe expression, purification and characterization of zebrafish monoamine oxidase (zMAO) using the methylotropic yeast Pichia pastoris expression system is described. A 1L fermentation culture of Pichia pastoris containing the gene encoding zMAO under control of the methanol oxidase promotor expresses approximately 200mg of zMAO exhibiting 300 U of total activity. The enzyme is found in the mitochondrial fraction of the expression host and is purified in a 30% yield as a homogenous species with a M(r) of approximately 60,000 on SDS-PAGE and a mass of 58,525+/-40 Da from MALDI-TOF measurements. The zMAO preparation contains one mole of covalent flavin cofactor per mole of enzyme and exhibits >80% functionality. The covalent flavin exhibits fluorescence and EPR spectral properties consistent with known properties of 8 alpha-S-cysteinyl FAD. Chemical degradation of the flavin peptide results in the liberation of FAD. zMAO exhibits no immuno-chemical cross-reactivity with polyclonal anti-sera raised against human MAO A. The enzyme preparation exhibits reasonable thermostability up to a temperature of 30 degrees C. Benzylamine is oxidized with a k(cat) value of 4.7+/-0.1 min(-1) (K(m)=82+/-9 microM) and the enzyme oxidizes phenylethylamine with a k(cat) value of 204 min(-1) (K(m)=86+/-13 microM). The K(m) (O(2)) values determined for zMAO using either benzylamine or phenylethylamine as substrates ranges from 108(+/-5) to 140(+/-21)microM. The functional behavior of this teleost MAO relative to human MAO A and MAO B is discussed.