Research Topics
| Gustavo Caetano-AnollesSummaryAffiliation: University of Illinois Country: USA Publications
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Detail Information
Publications
Origins and evolution of modern biochemistry: insights from genomes and molecular structureGustavo Caetano-Anolles
Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
Front Biosci 13:5212-40. 2008....
The origin, evolution and structure of the protein worldGustavo Caetano-Anolles
Department of Crop Sciences, University of Illinois at Urbana Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
Biochem J 417:621-37. 2009..These observations have important implications for origins of modern biochemistry and diversification of life...- The origin and evolution of modern metabolismGustavo Caetano-Anolles
Department of Crop Sciences, University of Illinois, Urbana, IL 61801, United States
Int J Biochem Cell Biol 41:285-97. 2009..Remarkably, recruitment occurred in a layered system reminiscent of Morowitz's prebiotic shells, supporting the notion that modern metabolism represents a palimpsest of ancient metabolic chemistries... 
An evolutionarily structured universe of protein architectureGustavo Caetano-Anolles
Vital NRG, Knoxville, Tennessee 37919, USA
Genome Res 13:1563-71. 2003..Lastly, we traced the total number of enzymatic functions associated with folds in the trees and show that there is a general link between structure and enzymatic function...- Universal sharing patterns in proteomes and evolution of protein fold architecture and lifeGustavo Caetano-Anolles
Department of Crop Sciences, University of Illinois, 332 NSRC, 1101 West Peabody Drive, Urbana, IL, 61801, USA
J Mol Evol 60:484-98. 2005.... - Grass evolution inferred from chromosomal rearrangements and geometrical and statistical features in RNA structureGustavo Caetano-Anolles
Department of Crop Sciences, University of Illinois, Urbana Champaign, 61801, USA
J Mol Evol 60:635-52. 2005.... - The origin of modern metabolic networks inferred from phylogenomic analysis of protein architectureGustavo Caetano-Anolles
Departments of Crop Sciences and Cell and Developmental Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Proc Natl Acad Sci U S A 104:9358-63. 2007..Consequently, the first enzymatic takeover of an ancient biochemistry or prebiotic chemistry was related to the synthesis of nucleotides for the RNA world... - Exploring the interplay of stability and function in protein evolution: new methods further elucidate why protein stability is necessarily so tenuous and stability-increasing mutations compromise biological functionGustavo Caetano-Anolles
Department of Crop Sciences, University of Illinois, Urbana, IL, USA
Bioessays 32:655-8. 2010..Non-equilibrium thermodynamics provides crucial concepts, e.g., cells as emergent energy-dissipating entities that do work and build their own parts, and a framework to study the sculpting role of evolution at different scales... - Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygenKyung Mo Kim
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
Structure 20:67-76. 2012..The evolutionary patterns we uncover in molecules and chemistries provide strong support for the coevolution of biochemistry and geochemistry... - Proteome evolution and the metabolic origins of translation and cellular lifeDerek Caetano-Anolles
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, 332 NSRC, 1101 W Peabody Drive, Urbana, IL 61801, USA
J Mol Evol 72:14-33. 2011..Our results explain how the generation of structure in the protein world and the concurrent crystallization of translation and diversified cellular life created further opportunities for proteomic diversification... - The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesisGustavo Caetano-Anolles
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
J Mol Evol 74:1-34. 2012..The model explains how the generation of protein structures acted as scaffold for nucleic acids and resulted in crystallization of modern translation... - The ancient history of the structure of ribonuclease P and the early origins of ArchaeaFeng Jie Sun
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
BMC Bioinformatics 11:153. 2010..It represents an important macromolecular complex and model system that is universally distributed in life. Its putative origins have inspired fundamental hypotheses, including the proposal of an ancient RNA world... - Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and virusesFeng Jie Sun
Department of Crop Sciences, University of Illinois Urbana Champaign, Urbana, Illinois, United States of America
PLoS Comput Biol 4:e1000018. 2008..Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world... - Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and EukaryaArshan Nasir
Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
BMC Evol Biol 12:156. 2012..Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life... - Tracing the evolution of RNA structure in ribosomesGustavo Caetano-Anolles
Laboratory of Molecular Ecology and Evolution and Division of Molecular Biology, Department of Biology, University of Oslo, N 0316 Oslo, Norway and Vital NRG, Knoxville, TN, USA
Nucleic Acids Res 30:2575-87. 2002..Overall results provide a rare insight into the evolution of ribosomal structure... - The evolutionary history of the structure of 5S ribosomal RNAFeng Jie Sun
Department of Crop Sciences, University of Illinois at Urbana Champaign, 332 National Soybean Research Center, 1101 West Peabody Drive, Urbana, IL 61801, USA
J Mol Evol 69:430-43. 2009..The molecule therefore represents a late evolutionary addition to the ribosomal ensemble that occurred prior to the early diversification of Archaea... - MANET: tracing evolution of protein architecture in metabolic networksHee Shin Kim
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
BMC Bioinformatics 7:351. 2006..Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolism, using information derived from structural genomics... - The proteomic complexity and rise of the primordial ancestor of diversified lifeKyung Mo Kim
Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, USA
BMC Evol Biol 11:140. 2011..However, most of these studies were based on molecular sequences, which are fast evolving and of limited value for deep evolutionary explorations... - The origin and evolution of tRNA inferred from phylogenetic analysis of structureFeng Jie Sun
Department of Crop Sciences, University of Illinois at Urbana Champaign, 332 NSRC, 1101 West Peabody Drive, Urbana, IL 61801, USA
J Mol Evol 66:21-35. 2008..The DHU arm was then incorporated into the resulting three-stemmed structure to form a proto-cloverleaf structure. The variable region was the last structural addition to the molecular repertoire of evolving tRNA substructures... - Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological dataKyung Mo Kim
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana Champaign, IL, USA
Mol Biol Evol 27:1710-33. 2010..The approach uncovers patterns in the morphing of function that are unprecedented and necessary for systematic views in biology... - A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenationMinglei Wang
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana Champaign, USA
Mol Biol Evol 28:567-82. 2011..The clock also extends the standard concept that was specific to molecules and their timescales and turns it into a universal timescale-generating tool... - The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdomsKyung Mo Kim
Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, IL 61801, USA
BMC Evol Biol 12:13. 2012..In contrast, protein structures are evolutionary modules that are highly conserved and diverse enough to enable deep historical exploration... - Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic codeFeng Jie Sun
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
PLoS ONE 3:e2799. 2008..These histories were probably curbed by co-options and important take-overs during early diversification of the living world... - Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisomeManfredo J Seufferheld
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
Biol Direct 6:50. 2011..Volutin granules and acidocalcisomes have been found in organisms as diverse as bacteria and humans... - Transfer RNA and the origins of diversified lifeFeng Jie Sun
Department of Crop Sciences, University of Illinois, Urbana Champaign, IL 61801, USA
Sci Prog 91:265-84. 2008.... - The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein worldMinglei Wang
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Structure 17:66-78. 2009.... - Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite worldMinglei Wang
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
Genome Res 17:1572-85. 2007..Our analysis also suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya... - A general framework of persistence strategies for biological systems helps explain domains of lifeLiudmila S Yafremava
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana, IL, USA
Front Genet 4:16. 2013..Protista occupy a saddle manifold separating akaryotes from multicellular organisms. Plants and the more flexible Fungi share an economic stratum, and Metazoa are locked in a positive feedback loop toward flexibility... - Ribosomal history reveals origins of modern protein synthesisAjith Harish
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana Champaign, Illinois, United States of America
PLoS ONE 7:e32776. 2012..Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world... - The origin of modern 5S rRNA: a case of relating models of structural history to phylogenetic dataFeng Jie Sun
Department of Crop Sciences, University of Illinois at Urbana Champaign, 332 National Soybean Research Center, 1101 W Peabody Drive, Urbana, IL 61801, USA
J Mol Evol 71:3-5. 2010..When combined with additional data, such as the age of protein domains that interact with RNA substructures, these trees can be used to falsify unlikely hypotheses... - NOBAI: a web server for character coding of geometrical and statistical features in RNA structureVegeir Knudsen
Department of Crop Sciences, University of Illinois at Urbana Champaign, IL 61801, USA
Nucleic Acids Res 36:W85-90. 2008..The NOBAI web server is accessible at 'http://www.manet.uiuc.edu/nobai/nobai.php'. This web site is free and open to all users and there is no login requirement... - Comparative genomic and phylogenetic analyses reveal the evolution of the core two-component signal transduction systems in enterobacteriaMingsheng Qi
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
J Mol Evol 70:167-80. 2010.... - Reductive evolution of proteomes and protein structuresMinglei Wang
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
Proc Natl Acad Sci U S A 108:11954-8. 2011..Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not... - Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?Nicolas Martin
Department of Crop Sciences, University of Illinois at Urbana Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
Biol Direct 2:23. 2007..We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization... - Biphasic patterns of diversification and the emergence of modulesJAY MITTENTHAL
Department of Cell and Developmental Biology, University of Illinois Urbana Champaign, IL, USA
Front Genet 3:147. 2012.... - Common evolutionary trends for SINE RNA structuresFeng Jie Sun
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Trends Genet 23:26-33. 2007..Based on these results, we propose a general multistep model for the evolution of tRNA-related SINEs in eukaryotes... - The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigmGustavo Caetano-Anolles
Department of Crop Sciences, University of Illinois, Urbana, Ill, USA
J Mol Microbiol Biotechnol 23:152-77. 2013..This changes the perception we have of the rise of modern biochemistry and prompts further analysis of the emergence of biological complexity in an ever-expanding coevolving world of macromolecules... - Phylogenomics supports a cellularly structured urancestorManfredo J Seufferheld
Department of Crop Sciences, University of Illinois, Urbana, Ill, USA
J Mol Microbiol Biotechnol 23:178-91. 2013..4 billion years ago. Results highlight the centrality of the cellular compartment and bioenergetics in the early evolutionary stages of life... - Extensive and specific responses of a eukaryote to bacterial quorum-sensing signalsUlrike Mathesius
Genomic Interactions Group, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra ACT 2601, Australia
Proc Natl Acad Sci U S A 100:1444-9. 2003..Our results indicate that eukaryotes have an extensive range of functional responses to AHLs that may play important roles in the beneficial or pathogenic outcomes of eukaryote-prokaryote interactions...