Publications

2023

Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago.

Hoshino Y, Nettersheim BJ, Gold DA, Hallmann C, Vinnichenko G, van Maldegem LM, Bishop C, Brocks JJ, Gaucher EA.Nat Ecol Evol. 2023 Oct 26. doi: 10.1038/s41559-023-02223-5. Online ahead of print.PMID: 37884688

Protection of Catalytic Cofactors by Polypeptides as a Driver for the Emergence of Primordial Enzymes.

Gutierrez-Rus LI, Gamiz-Arco G, Gavira JA, Gaucher EA, Risso VA, Sanchez-Ruiz JM.Mol Biol Evol. 2023 Jun 1;40(6):msad126. doi: 10.1093/molbev/msad126.PMID: 37235753

Oral Delivery of Nanoparticles Carrying Ancestral Uricase Enzyme Protects against Hyperuricemia in Knockout Mice.

Tran L, Das S, Zhao L, Finn MG, Gaucher EA.Biomacromolecules. 2023 May 8;24(5):2003-2008. doi: 10.1021/acs.biomac.2c01388. Epub 2023 Apr 26.PMID: 37126604

2022

Johnson RJ, Sánchez-Lozada LG, Nakagawa T, Rodriguez-Iturbe B, Tolan D, Gaucher EA, Andrews P, Lanaspa MA.Obesity (Silver Spring). 2022 Oct;30(10):1917-1926. doi: 10.1002/oby.23540.PMID: 36150210 Review.

Li Z, Hoshino Y, Tran L, Gaucher EA.Mol Biol Evol. 2022 Jan 7;39(1):msab312. doi: 10.1093/molbev/msab312.PMID: 34718698

2021

Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis.

Hoshino Y, Gaucher EA.Proc Natl Acad Sci U S A. 2021 Jun 22;118(25):e2101276118. doi: 10.1073/pnas.2101276118.PMID: 34131078

Molecular coevolution of coagulation factor VIII and von Willebrand factor.

Zakas PM, Coyle CW, Brehm A, Bayer M, Solecka-Witulska B, Radford CE, Brown C, Nesbitt K, Dwyer C, Kannicht C, Spencer HT, Gaucher EA, Doering CB, Lillicrap D.Blood Adv. 2021 Feb 9;5(3):812-822. doi: 10.1182/bloodadvances.2020002971.PMID: 33560395

Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.
Gamiz-Arco G, Gutierrez-Rus LI, Risso VA, Ibarra-Molero B, Hoshino Y, Petrović D, Justicia J, Cuerva JM, Romero-Rivera A, Seelig B, Gavira JA, Kamerlin SCL, Gaucher EA, Sanchez-Ruiz JM.Nat Commun. 2021 Jan 15;12(1):380. doi: 10.1038/s41467-020-20630-1.PMID: 33452262

Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond.

Selberg AGA, Gaucher EA, Liberles DA.J Mol Evol. 2021 Apr;89(3):157-164. doi: 10.1007/s00239-021-09993-1. Epub 2021 Jan 24.PMID: 33486547

Combining Ancestral Reconstruction with Folding-Landscape Simulations to Engineer Heterologous Protein Expression.

Gamiz-Arco G, Risso VA, Gaucher EA, Gavira JA, Naganathan AN, Ibarra-Molero B, Sanchez-Ruiz JM.J Mol Biol. 2021 Dec 3;433(24):167321. doi: 10.1016/j.jmb.2021.167321. Epub 2021 Oct 21.PMID: 34687715

CRISPR-Cas9-mediated reactivation of the uricase pseudogene in human cells prevents acute hyperuricemia.
de Lima Balico L, Gaucher EA.Mol Ther Nucleic Acids. 2021 Aug 19;25:578-584. doi: 10.1016/j.omtn.2021.08.002. eCollection 2021 Sep 3.PMID: 34589279

Identification of coagulation factor IX variants with enhanced activity through ancestral sequence reconstruction.

Knight KA, Coyle CW, Radford CE, Parker ET, Fedanov A, Shields JM, Szlam F, Purchel A, Chen M, Denning G, Sniecinski RM, Lollar P, Spencer HT, Gaucher EA, Doering CB.Blood Adv. 2021 Sep 14;5(17):3333-3343. doi: 10.1182/bloodadvances.2021004742.PMID: 34477814

Brief report: The uricase mutation in humans increases our risk for cancer growth.

Fini MA, Lanaspa MA, Gaucher EA, Boutwell B, Nakagawa T, Wright RM, Sanchez-Lozada LG, Andrews P, Stenmark KR, Johnson RJ.Cancer Metab. 2021 Sep 15;9(1):32. doi: 10.1186/s40170-021-00268-3.PMID: 34526149

2020

Stabilization of Near-Infrared Fluorescent Proteins by Packaging in Virus-like Particles.
Das S, Zhao L, Crooke SN, Tran L, Bhattacharya S, Gaucher EA, Finn MG.Biomacromolecules. 2020 Jun 8;21(6):2432-2439. doi: 10.1021/acs.biomac.0c00362. Epub 2020 May 22.PMID: 32441521

Fructose metabolism as a common evolutionary pathway of survival associated with climate change, food shortage and droughts.

Johnson RJ, Stenvinkel P, Andrews P, Sánchez-Lozada LG, Nakagawa T, Gaucher E, Andres-Hernando A, Rodriguez-Iturbe B, Jimenez CR, Garcia G, Kang DH, Tolan DR, Lanaspa MA.J Intern Med. 2020 Mar;287(3):252-262. doi: 10.1111/joim.12993. Epub 2019 Oct 31.PMID: 31621967

2019

Non-conservation of folding rates in the thioredoxin family reveals degradation of ancestral unassisted-folding.

Gamiz-Arco G, Risso VA, Candel AM, Inglés-Prieto A, Romero-Romero ML, Gaucher EA, Gavira JA, Ibarra-Molero B, Sanchez-Ruiz JM.Biochem J. 2019 Dec 12;476(23):3631-3647. doi: 10.1042/BCJ20190739.PMID: 31750876

DeLey Cox VE, Cole MF, Gaucher EA.ACS Synth Biol. 2019 Feb 15;8(2):287-296. doi: 10.1021/acssynbio.8b00305. Epub 2019 Jan 15.PMID: 30609889

2018

Hoshino Y, Gaucher EA.Mol Biol Evol. 2018 Sep 1;35(9):2185-2197. doi: 10.1093/molbev/msy120.PMID: 29905874

Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus.

Okafor CD, Pathak MC, Fagan CE, Bauer NC, Cole MF, Gaucher EA, Ortlund EA.Structure. 2018 Jan 2;26(1):118-129.e3. doi: 10.1016/j.str.2017.11.018. Epub 2017 Dec 21.PMID: 29276038

2017

De novo active sites for resurrected Precambrian enzymes.

Risso VA, Martinez-Rodriguez S, Candel AM, Krüger DM, Pantoja-Uceda D, Ortega-Muñoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM.Nat Commun. 2017 Jul 18;8:16113. doi: 10.1038/ncomms16113.PMID: 28719578

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein.

Kacar B, Ge X, Sanyal S, Gaucher EA.J Mol Evol. 2017 Mar;84(2-3):69-84. doi: 10.1007/s00239-017-9781-0. Epub 2017 Feb 23.PMID: 28233029 Free PMC article.

Zakas PM, Brown HC, Knight K, Meeks SL, Spencer HT, Gaucher EA, Doering CB.Nat Biotechnol. 2017 Jan;35(1):35-37. doi: 10.1038/nbt.3677. Epub 2016 Sep 26.PMID: 27669166

2016

2015

Molecular Evolution Directs Protein Translation Using Unnatural Amino Acids.

Cox VE, Gaucher EA.Curr Protoc Chem Biol. 2015 Dec 2;7(4):223-228. doi: 10.1002/9780470559277.ch150115.PMID: 26629613 Review.

Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

Risso VA, Manssour-Triedo F, Delgado-Delgado A, Arco R, Barroso-delJesus A, Ingles-Prieto A, Godoy-Ruiz R, Gavira JA, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM.Mol Biol Evol. 2015 Feb;32(2):440-55. doi: 10.1093/molbev/msu312. Epub 2014 Nov 12.PMID: 25392342

2014

Kratzer JT, Lanaspa MA, Murphy MN, Cicerchi C, Graves CL, Tipton PA, Ortlund EA, Johnson RJ, Gaucher EA.Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3763-8. doi: 10.1073/pnas.1320393111. Epub 2014 Feb 18.PMID: 24550457

STRAD pseudokinases regulate axogenesis and LKB1 stability.

Veleva-Rotse BO, Smart JL, Baas AF, Edmonds B, Zhao ZM, Brown A, Klug LR, Hansen K, Reilly G, Gardner AP, Subbiah K, Gaucher EA, Clevers H, Barnes AP.Neural Dev. 2014 Mar 4;9:5. doi: 10.1186/1749-8104-9-5.PMID: 24594058

Engineering proteins by reconstructing evolutionary adaptive paths.

Cox VE, Gaucher EA.Methods Mol Biol. 2014;1179:353-63. doi: 10.1007/978-1-4939-1053-3_24.PMID: 25055790

Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins.

Risso VA, Gavira JA, Gaucher EA, Sanchez-Ruiz JM.Proteins. 2014 Jun;82(6):887-96. doi: 10.1002/prot.24575. Epub 2014 Apr 18.PMID: 24710963

Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

Risso VA, Manssour-Triedo F, Delgado-Delgado A, Arco R, Barroso-delJesus A, Ingles-Prieto A, Godoy-Ruiz R, Gavira JA, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM.Mol Biol Evol. 2015 Feb;32(2):440-55. doi: 10.1093/molbev/msu312. Epub 2014 Nov 12.PMID: 25392342

Uric acid-dependent inhibition of AMP kinase induces hepatic glucose production in diabetes and starvation: evolutionary implications of the uricase loss in hominids.

Cicerchi C, Li N, Kratzer J, Garcia G, Roncal-Jimenez CA, Tanabe K, Hunter B, Rivard CJ, Sautin YY, Gaucher EA, Johnson RJ, Lanaspa MA.FASEB J. 2014 Aug;28(8):3339-50. doi: 10.1096/fj.13-243634. Epub 2014 Apr 22.PMID: 24755741

2013

Experimental evolution of protein-protein interaction networks.

Kaçar B, Gaucher EA.Biochem J. 2013 Aug 1;453(3):311-9. doi: 10.1042/BJ20130205.PMID: 23849056

Conservation of protein structure over four billion years.

Ingles-Prieto A, Ibarra-Molero B, Delgado-Delgado A, Perez-Jimenez R, Fernandez JM, Gaucher EA, Sanchez-Ruiz JM, Gavira JA.Structure. 2013 Sep 3;21(9):1690-7. doi: 10.1016/j.str.2013.06.020. Epub 2013 Aug 8.PMID: 23932589

Hydrophobic environment is a key factor for the stability of thermophilic proteins.

Gromiha MM, Pathak MC, Saraboji K, Ortlund EA, Gaucher EA.Proteins. 2013 Apr;81(4):715-21. doi: 10.1002/prot.24232. Epub 2013 Jan 15.PMID: 23319168

Secondary structure and domain architecture of the 23S and 5S rRNAs.

Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD.Nucleic Acids Res. 2013 Aug;41(15):7522-35. doi: 10.1093/nar/gkt513. Epub 2013 Jun 14.PMID: 23771137

Reconstructing evolutionary adaptive paths for protein engineering.

Cole MF, Cox VE, Gratton KL, Gaucher EA.Methods Mol Biol. 2013;978:115-25. doi: 10.1007/978-1-62703-293-3_8.PMID: 23423892

Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases.

Risso VA, Gavira JA, Mejia-Carmona DF, Gaucher EA, Sanchez-Ruiz JM.J Am Chem Soc. 2013 Feb 27;135(8):2899-902. doi: 10.1021/ja311630a. Epub 2013 Feb 14.PMID: 23394108

Interchanging functionality among homologous elongation factors using signatures of heterotachy.

Cacan E, Kratzer JT, Cole MF, Gaucher EA.J Mol Evol. 2013 Feb;76(1-2):4-12. doi: 10.1007/s00239-013-9540-9. Epub 2013 Jan 31.PMID: 23370546

2012

Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components.

Zhou Y, Asahara H, Gaucher EA, Chong S.Nucleic Acids Res. 2012 Sep;40(16):7932-45. doi: 10.1093/nar/gks568. Epub 2012 Jun 20.PMID: 22723376

2011

Utilizing natural diversity to evolve protein function: applications towards thermostability.
Cole MF, Gaucher EA.Curr Opin Chem Biol. 2011 Jun;15(3):399-406. doi: 10.1016/j.cbpa.2011.03.005. Epub 2011 Apr 4.PMID: 21470898

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes.

Perez-Jimenez R, Inglés-Prieto A, Zhao ZM, Sanchez-Romero I, Alegre-Cebollada J, Kosuri P, Garcia-Manyes S, Kappock TJ, Tanokura M, Holmgren A, Sanchez-Ruiz JM, Gaucher EA, Fernandez JM.Nat Struct Mol Biol. 2011 May;18(5):592-6. doi: 10.1038/nsmb.2020. Epub 2011 Apr 3.PMID: 21460845

Exploiting models of molecular evolution to efficiently direct protein engineering.

Cole MF, Gaucher EA.J Mol Evol. 2011 Feb;72(2):193-203. doi: 10.1007/s00239-010-9415-2. Epub 2010 Dec 4.PMID: 21132281

The evolutionary history of the catenin gene family during metazoan evolution.

Zhao ZM, Reynolds AB, Gaucher EA.BMC Evol Biol. 2011 Jul 8;11:198. doi: 10.1186/1471-2148-11-198.PMID: 21740572

Uric acid: a danger signal from the RNA world that may have a role in the epidemic of obesity, metabolic syndrome, and cardiorenal disease: evolutionary considerations.

Johnson RJ, Lanaspa MA, Gaucher EA.Semin Nephrol. 2011 Sep;31(5):394-9. doi: 10.1016/j.semnephrol.2011.08.002.PMID: 22000645

2010

Deep phylogeny–how a tree can help characterize early life on Earth.
Gaucher EA, Kratzer JT, Randall RN.Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a002238. doi: 10.1101/cshperspect.a002238.PMID: 20182607

The molecular evolution of the p120-catenin subfamily and its functional associations.

Carnahan RH, Rokas A, Gaucher EA, Reynolds AB.PLoS One. 2010 Dec 31;5(12):e15747. doi: 10.1371/journal.pone.0015747.PMID: 21209830

Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection.

Chen F, Gaucher EA, Leal NA, Hutter D, Havemann SA, Govindarajan S, Ortlund EA, Benner SA.Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1948-53. doi: 10.1073/pnas.0908463107. Epub 2010 Jan 11.PMID: 20080675

2009

Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy.

Perez-Jimenez R, Li J, Kosuri P, Sanchez-Romero I, Wiita AP, Rodriguez-Larrea D, Chueca A, Holmgren A, Miranda-Vizuete A, Becker K, Cho SH, Beckwith J, Gelhaye E, Jacquot JP, Gaucher EA, Sanchez-Ruiz JM, Berne BJ, Fernandez JM.Nat Struct Mol Biol. 2009 Aug;16(8):890-6. doi: 10.1038/nsmb.1627. Epub 2009 Jul 13.PMID: 19597482

2008

The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease.

Johnson RJ, Gaucher EA, Sautin YY, Henderson GN, Angerhofer AJ, Benner SA.Med Hypotheses. 2008;71(1):22-31. doi: 10.1016/j.mehy.2008.01.017. Epub 2008 Mar 10.PMID: 18331782

Palaeotemperature trend for Precambrian life inferred from resurrected proteins.

Gaucher EA, Govindarajan S, Ganesh OK.Nature. 2008 Feb 7;451(7179):704-7. doi: 10.1038/nature06510.PMID: 18256669

2007

Molecular paleoscience: systems biology from the past.

Benner SA, Sassi SO, Gaucher EA.Adv Enzymol Relat Areas Mol Biol. 2007;75:1-132, xi. doi: 10.1002/9780471224464.ch1.PMID: 17124866 Review.

2006

The diverse biological functions of phosphatidylinositol transfer proteins in eukaryotes.

Phillips SE, Vincent P, Rizzieri KE, Schaaf G, Bankaitis VA, Gaucher EA.Crit Rev Biochem Mol Biol. 2006 Jan-Feb;41(1):21-49. doi: 10.1080/10409230500519573.PMID: 16455519 Review.

Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family.

Gaucher EA, De Kee DW, Benner SA.BMC Genomics. 2006 Mar 7;7:44. doi: 10.1186/1471-2164-7-44.PMID: 16522197

Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics.

Li T, Chamberlin SG, Caraco MD, Liberles DA, Gaucher EA, Benner SA.BMC Evol Biol. 2006 Mar 20;6:25. doi: 10.1186/1471-2148-6-25.PMID: 16545144 Free

2005

Resurrecting ancestral alcohol dehydrogenases from yeast.

Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP, Benner SA.Nat Genet. 2005 Jun;37(6):630-5. doi: 10.1038/ng1553. Epub 2005 May 1.PMID: 15864308

A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous.

Gaucher EA, Miyamoto MM.Mol Phylogenet Evol. 2005 Dec;37(3):928-31. doi: 10.1016/j.ympev.2005.03.027.PMID: 16291095 No abstract available.

2004

Cytoplasmic glycosylation of protein-hydroxyproline and its relationship to other glycosylation pathways.
West CM, Van Der Wel H, Sassi S, Gaucher EA.Biochim Biophys Acta. 2004 Jul 6;1673(1-2):29-44. doi: 10.1016/j.bbagen.2004.04.007.PMID: 15238247 Review.

The planetary biology of cytochrome P450 aromatases.

Gaucher EA, Graddy LG, Li T, Simmen RC, Simmen FA, Schreiber DR, Liberles DA, Janis CM, Benner SA.BMC Biol. 2004 Aug 17;2:19. doi: 10.1186/1741-7007-2-19.PMID: 15315709

2003

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins.

Gaucher EA, Thomson JM, Burgan MF, Benner SA.Nature. 2003 Sep 18;425(6955):285-8. doi: 10.1038/nature01977.PMID: 13679914

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein.

Gaucher EA, Miyamoto MM, Benner SA.Genetics. 2003 Apr;163(4):1549-53. doi: 10.1093/genetics/163.4.1549.PMID: 12702697

2002

Gaucher EA, Gu X, Miyamoto MM, Benner SA.Trends Biochem Sci. 2002 Jun;27(6):315-21. doi: 10.1016/s0968-0004(02)02094-7.PMID: 12069792 Review.

Planetary biology–paleontological, geological, and molecular histories of life.

Benner SA, Caraco MD, Thomson JM, Gaucher EA.Science. 2002 May 3;296(5569):864-8. doi: 10.1126/science.1069863.PMID: 11988562 Review.

Complex glycosylation of Skp1 in Dictyostelium: implications for the modification of other eukaryotic cytoplasmic and nuclear proteins.

West CM, van der Wel H, Gaucher EA.Glycobiology. 2002 Feb;12(2):17R-27R. doi: 10.1093/glycob/12.2.17r.PMID: 11886837 Review.

The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors.

Gaucher EA, Das UK, Miyamoto MM, Benner SA.Mol Biol Evol. 2002 Apr;19(4):569-73. doi: 10.1093/oxfordjournals.molbev.a004113.PMID: 11919299 No abstract available.

2001

Evolution, language and analogy in functional genomics.

Benner SA, Gaucher EA.Trends Genet. 2001 Jul;17(7):414-8. doi: 10.1016/s0168-9525(01)02320-4.PMID: 11418223

Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors.
Gaucher EA, Miyamoto MM, Benner SA.Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):548-52. doi: 10.1073/pnas.98.2.548.PMID: 11209054

1998

SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein.

Laten HM, Majumdar A, Gaucher EA.Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6897-902. doi: 10.1073/pnas.95.12.6897.PMID: 9618510