Journal Covers
Some of our recent research papers!
Klos, A., Sobol, M., Boden, J. S., Stueeken, E. E., Anderson, R. E., Kurt O, K., & Kacar, B. (2025). Biological molybdenum usage stems back to 3.4 billion years ago. bioRxiv, 2025-04. https://www.biorxiv.org/content/10.1101/2025.04.02.646658v1 PDF
Cuevas-Zuviría, B., Detemple, F., Amritkar, K., Garcia, A. K., Seefeldt, L. C., Einsle, O., & Kaçar, B. (2025). Nitrogenase structural evolution across Earth’s history. eLife, 14. https://elifesciences.org/reviewed-preprints/105613 PDF
Fer, E., Yao, T., McGrath, K. M., Goldman, A. D., & Kaçar, B. (2025). The origins and evolution of translation factors. Trends in Genetics. https://www.cell.com/trends/genetics/fulltext/S0168-9525(25)00045-9 PDF
Amritkar, K., Cuevas-Zuviría, B., & Kaçar, B. (2025). Evolutionary Dynamics of RuBisCO: Emergence of the Small Subunit and its Impact Through Time. Molecular Biology and Evolution, 42(1), msae268. https://academic.oup.com/mbe/article/42/1/msae268/7934943 PDF
Kaçar, B. (2024). Reconstructing early microbial life. Annual Review of Microbiology, 78. https://www.annualreviews.org/content/journals/10.1146/annurev-micro-041522-103400 PDF
Evans, G. N., Ji, S., Kaçar, B., Anbar, A. D., & Seyfried Jr, W. E. (2024). Transition metals in alkaline Lost City vent fluids are sufficient for early-life metabolisms. Geochimica et Cosmochimica Acta, 385, 61-73. https://www.sciencedirect.com/science/article/pii/S0016703724004241 PDF
Rico, K. I., Garcia, A. K., Saito, M. A., Kaçar, B., & Anbar, A. D. (2024). Mysteries of metallome evolution: Integrating insights from the Earth and life sciences. In Treatise on Geochemistry, Third Edition, 8 Volume Set (pp. V5-337). Elsevier. https://www.sciencedirect.com/science/article/abs/pii/B9780323997621001431?via%3Dihub PDF
Harris, D. F., Rucker, H. R., Garcia, A. K., Yang, Z. Y., Chang, S. D., Feinsilber, H., ... & Seefeldt, L. C. (2024). Ancient nitrogenases are ATP dependent. Mbio, 15(7), e01271-24. https://journals.asm.org/doi/full/10.1128/mbio.01271-24 PDF
Cuevas-Zuviría, B., Garcia, A. K., Rivier, A. J., Rucker, H. R., Carruthers, B. M., & Kaçar, B. (2024). Emergence of an orphan nitrogenase protein following atmospheric oxygenation. Molecular Biology and Evolution, 41(4), msae067. https://doi.org/10.1093/molbev/msae067 PDF
Russell, S. J., Garcia, A. K., & Kaçar, B. (2024). A CRISPR interference system for engineering biological nitrogen fixation. Msystems, 9(3), e00155-24. https://journals.asm.org/doi/full/10.1128/msystems.00155-24 PDF
McGrath, K. M., Russell, S. J., Fer, E., Garmendia, E., Hosgel, A., Baltrus, D. A., & Kaçar, B. (2024). Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background. Journal of Bacteriology, 206(2), e00329-23. https://journals.asm.org/doi/full/10.1128/jb.00329-23 PDF
Rucker, H. R., & Kaçar, B. (2024). Enigmatic evolution of microbial nitrogen fixation: insights from Earth’s past. Trends in Microbiology, 32(6), 554-564. Trends in Microbiology. https://www.cell.com/trends/microbiology/fulltext/S0966-842X(23)00091-4 PDF
Marshall, B., Amritkar, K., Wolfe, M., Kaçar, B., & Landick, R. (2023). Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway. Frontiers in Microbiology, 14, 1286626. https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1286626/full PDF
Peng, Z., Adam, Z. R., Fahrenbach, A. C., & Kaçar, B. (2023). Assessment of stoichiometric autocatalysis across element groups. Journal of the American Chemical Society, 145(41), 22483-22493. https://pubs.acs.org/doi/full/10.1021/jacs.3c07041 PDF
Cuevas-Zuviría, B., Fer, E., Adam, Z. R., & Kaçar, B. (2023). The modular biochemical reaction network structure of cellular translation. npj Systems Biology and Applications, 9(1), 52. https://www.nature.com/articles/s41540-023-00315-3 PDF
Rivier, A. J., Myers, K. S., Garcia, A. K., Sobol, M. S., & Kaçar, B. (2023). Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii. Microbiology Spectrum, 11(5), e02815-23. https://journals.asm.org/doi/full/10.1128/spectrum.02815-23 PDF
Cuevas-Zuviría, B., Adam, Z. R., Goldman, A. D., & Kaçar, B. (2023). Informatic capabilities of translation and its implications for the origins of life. Journal of Molecular Evolution, 91(5), 567-569. https://link.springer.com/article/10.1007/s00239-023-10125-0 PDF
Goldman, A. D., & Kaçar, B. (2023). Very early evolution from the perspective of microbial ecology. Environmental Microbiology, 25(1), 5-10. https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.16144 PDF
Garcia, A. K., Kędzior, M., Taton, A., Li, M., Young, J. N., & Kaçar, B. (2023). Effects of RuBisCO and CO2 concentration on cyanobacterial growth and carbon isotope fractionation. Geobiology, 21(3), 390-403. https://onlinelibrary.wiley.com/doi/full/10.1111/gbi.12543 PDF
Garcia, A. K., Harris, D. F., Rivier, A. J., Carruthers, B. M., Pinochet-Barros, A., Seefeldt, L. C., & Kaçar, B. (2023). Nitrogenase resurrection and the evolution of a singular enzymatic mechanism. Elife, 12, e85003. https://elifesciences.org/articles/85003 PDF
Kędzior, M., Garcia, A. K., Li, M., Taton, A., Adam, Z. R., Young, J. N., & Kaçar, B. (2022). Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time. Cell reports, 39(4). https://www.sciencedirect.com/science/article/pii/S2211124722004879 PDF
Schwartz, S. L., Garcia, A. K., Kaçar, B., & Fournier, G. P. (2022). Early nitrogenase ancestors encompassed novel active site diversity. Molecular Biology and Evolution, 39(11), msac226. https://academic.oup.com/mbe/article/39/11/msac226/6763667 PDF
Fer, E., McGrath, K. M., Guy, L., Hockenberry, A. J., & Kaçar, B. (2022). Early divergence of translation initiation and elongation factors. Protein Science, 31(9), e4393. https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4393 PDF
Sephus, C. D., Fer, E., Garcia, A. K., Adam, Z. R., Schwieterman, E. W., & Kacar, B. (2022). Earliest photic zone niches probed by ancestral microbial rhodopsins. Molecular Biology and Evolution, 39(5), msac100. https://academic.oup.com/mbe/article/39/5/msac100/6582242 PDF
Garcia, A. K., Kolaczkowski, B., & Kaçar, B. (2022). Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins. Genome Biology and Evolution, 14(3), evac031. https://academic.oup.com/gbe/article/14/3/evac031/6531971 PDF
Garcia, A. K., Fer, E., Sephus, C., & Kacar, B. (2022). An integrated method to reconstruct ancient proteins. In Environmental Microbial Evolution: Methods and Protocols (pp. 267-281). New York, NY: Springer US. https://link.springer.com/protocol/10.1007/978-1-0716-2691-7_13 PDF
Garcia, A. K., Cavanaugh, C. M., & Kacar, B. (2021). The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution. The ISME Journal, 15(8), 2183-2194. https://academic.oup.com/ismej/article/15/8/2183/7474499 PDF
Goldman, A. D., & Kacar, B. (2021). Cofactors are remnants of life’s origin and early evolution. Journal of Molecular Evolution, 89(3), 127-133. https://link.springer.com/article/10.1007/S00239-020-09988-4 PDF
Venkataram, S., Monasky, R., Sikaroodi, S. H., 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, 117(31), 18582-18590. https://www.pnas.org/doi/abs/10.1073/pnas.1921881117 PDF
Garcia, A. K., McShea, H., Kolaczkowski, B., & Kaçar, B. (2020). Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization. Geobiology, 18(3), 394-411. https://onlinelibrary.wiley.com/doi/full/10.1111/gbi.12381 PDF
Kacar, B., Garcia, A. K., & Anbar, A. D. (2021). Evolutionary history of bioessential elements can guide the search for life in the universe. ChemBioChem, 22(1), 114-119. https://doi.org/10.1002/cbic.202000500 PDF
Liberles, D. A., Chang, B., Geiler-Samerotte, K., Goldman, A., Hey, J., Kaçar, B., ... & Storfer, A. (2020). Emerging frontiers in the study of molecular evolution. Journal of molecular evolution, 88, 211-226. https://link.springer.com/article/10.1007/s00239-020-09932-6 PDF
Garcia, A. K., & Kaçar, B. (2019). How to resurrect ancestral proteins as proxies for ancient biogeochemistry. Free Radical Biology and Medicine, 140, 260-269. https://www.sciencedirect.com/science/article/pii/S0891584918315831 PDF
Ginsberg, A. D., Chieza, N., Kaçar, B., Womack, Y., & Vilutis, J. (2018). Future shaped by pasts that could have been. Journal of Design and Science. https://doi.org/10.21428/5e41a54a PDF
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. https://onlinelibrary.wiley.com/doi/full/10.1111/gbi.12243 PDF
Kacar, B., Guy, L., Smith, E., & Baross, J. (2017). Resurrecting ancestral genes in bacteria to interpret ancient biosignatures. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 375(2109), 20160352. https://royalsocietypublishing.org/doi/full/10.1098/rsta.2016.0352 PDF
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, 69-84. https://link.springer.com/article/10.1007/S00239-017-9781-0 PDF
Kacar, B. (2016). Rolling the dice twice: evolving reconstructed ancient proteins in extant organisms. Chance in evolution, 264-276. doi.org/10.7208/9780226401911-013 PDF
Kaçar, B., & Gaucher, E. A. (2013). Experimental evolution of protein–protein interaction networks. Biochemical Journal, 453(3), 311-319. https://doi.org/10.1042/BJ20130205 PDF
Kacar, B., & Gaucher, E. A. (2012, July). Towards the recapitulation of ancient history in the laboratory: combining synthetic biology with experimental evolution. In Artificial Life Conference Proceedings (pp. 11-18). One Rogers Street, Cambridge, MA 02142-1209, USA journals-info@ mit. edu: MIT Press. https://doi.org/10.1162/978-0-262-31050-5-ch002 PDF