Gustavo Caetano-Anolles

Summary

Affiliation: University of Illinois
Country: USA

Publications

  1. ncbi request reprint Origins and evolution of modern biochemistry: insights from genomes and molecular structure
    Gustavo Caetano-Anolles
    Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
    Front Biosci 13:5212-40. 2008
  2. doi request reprint The origin, evolution and structure of the protein world
    Gustavo 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
  3. pmc NOBAI: a web server for character coding of geometrical and statistical features in RNA structure
    Vegeir Knudsen
    Department of Crop Sciences, University of Illinois at Urbana Champaign, IL 61801, USA
    Nucleic Acids Res 36:W85-90. 2008
  4. pmc Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code
    Feng Jie Sun
    Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS ONE 3:e2799. 2008
  5. pmc Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses
    Feng Jie Sun
    Department of Crop Sciences, University of Illinois Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Comput Biol 4:e1000018. 2008
  6. pmc Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism
    Kelsey Caetano-Anollés
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS ONE 8:e59300. 2013
  7. doi request reprint The origin and evolution of modern metabolism
    Gustavo Caetano-Anolles
    Department of Crop Sciences, University of Illinois, Urbana, IL 61801, United States
    Int J Biochem Cell Biol 41:285-97. 2009
  8. doi request reprint 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 function
    Gustavo Caetano-Anolles
    Department of Crop Sciences, University of Illinois, Urbana, IL, USA
    Bioessays 32:655-8. 2010
  9. pmc The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture
    Gustavo 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
  10. pmc An evolutionarily structured universe of protein architecture
    Gustavo Caetano-Anolles
    Vital NRG, Knoxville, Tennessee 37919, USA
    Genome Res 13:1563-71. 2003

Collaborators

Detail Information

Publications46

  1. ncbi request reprint Origins and evolution of modern biochemistry: insights from genomes and molecular structure
    Gustavo Caetano-Anolles
    Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
    Front Biosci 13:5212-40. 2008
    ....
  2. doi request reprint The origin, evolution and structure of the protein world
    Gustavo 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...
  3. pmc NOBAI: a web server for character coding of geometrical and statistical features in RNA structure
    Vegeir 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...
  4. pmc Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code
    Feng 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...
  5. pmc Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses
    Feng 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...
  6. pmc Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism
    Kelsey Caetano-Anollés
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS ONE 8:e59300. 2013
    ..The simultaneous appearance of purine biosynthesis and the ribosome probably fulfilled the expanding matter-energy and processing needs of genomic information...
  7. doi request reprint The origin and evolution of modern metabolism
    Gustavo 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...
  8. doi request reprint 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 function
    Gustavo 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...
  9. pmc The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture
    Gustavo 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...
  10. pmc An evolutionarily structured universe of protein architecture
    Gustavo 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...
  11. ncbi request reprint Universal sharing patterns in proteomes and evolution of protein fold architecture and life
    Gustavo 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
    ....
  12. ncbi request reprint Grass evolution inferred from chromosomal rearrangements and geometrical and statistical features in RNA structure
    Gustavo Caetano-Anolles
    Department of Crop Sciences, University of Illinois, Urbana Champaign, 61801, USA
    J Mol Evol 60:635-52. 2005
    ....
  13. pmc Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
    Minglei 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...
  14. doi request reprint Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen
    Kyung 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...
  15. pmc Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility
    Gustavo Caetano-Anolles
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
    PLoS ONE 8:e72225. 2013
    ..These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure. ..
  16. ncbi request reprint Global phylogeny determined by the combination of protein domains in proteomes
    Minglei Wang
    Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Mol Biol Evol 23:2444-54. 2006
    ..Results suggest strongly that the process of domain combination is not random but curved by evolution, rejecting the null hypothesis of domain modules combining in the absence of natural selection or an optimality criterion...
  17. doi request reprint Proteome evolution and the metabolic origins of translation and cellular life
    Derek 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...
  18. doi request reprint The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis
    Gustavo 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...
  19. pmc The ancient history of the structure of ribonuclease P and the early origins of Archaea
    Feng 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...
  20. pmc Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya
    Arshan 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...
  21. doi request reprint The evolutionary history of the structure of 5S ribosomal RNA
    Feng 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...
  22. doi request reprint Phylogenomics supports a cellularly structured urancestor
    Manfredo J Seufferheld
    Department of Crop Sciences, University of Illinois, Urbana, IL 61801, 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...
  23. doi request reprint The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm
    Gustavo Caetano-Anolles
    Department of Crop Sciences, University of Illinois, Urbana, IL 61801, 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...
  24. pmc Tracing the evolution of RNA structure in ribosomes
    Gustavo 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...
  25. pmc The proteomic complexity and rise of the primordial ancestor of diversified life
    Kyung 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...
  26. doi request reprint A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
    Minglei 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...
  27. doi request reprint Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data
    Kyung 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...
  28. pmc Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes
    Syed Abbas Bukhari
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
    PLoS Comput Biol 9:e1003009. 2013
    ..Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable...
  29. pmc MANET: tracing evolution of protein architecture in metabolic networks
    Hee 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...
  30. pmc The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms
    Kyung 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...
  31. ncbi request reprint The origin and evolution of tRNA inferred from phylogenetic analysis of structure
    Feng 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...
  32. ncbi request reprint Common evolutionary trends for SINE RNA structures
    Feng 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...
  33. pmc Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome
    Manfredo 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...
  34. doi request reprint The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
    Minglei Wang
    Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Structure 17:66-78. 2009
    ....
  35. pmc A general framework of persistence strategies for biological systems helps explain domains of life
    Liudmila 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...
  36. pmc Ribosomal history reveals origins of modern protein synthesis
    Ajith 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...
  37. doi request reprint The origin of modern 5S rRNA: a case of relating models of structural history to phylogenetic data
    Feng 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...
  38. ncbi request reprint Transfer RNA and the origins of diversified life
    Feng Jie Sun
    Department of Crop Sciences, University of Illinois, Urbana Champaign, IL 61801, USA
    Sci Prog 91:265-84. 2008
    ....
  39. doi request reprint Comparative genomic and phylogenetic analyses reveal the evolution of the core two-component signal transduction systems in enterobacteria
    Mingsheng Qi
    Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    J Mol Evol 70:167-80. 2010
    ....
  40. pmc Reductive evolution of proteomes and protein structures
    Minglei 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...
  41. doi request reprint Global patterns of protein domain gain and loss in superkingdoms
    Arshan Nasir
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America Illinois Informatics Institute, University of Illinois, Urbana, Illinois, United States of America
    PLoS Comput Biol 10:e1003452. 2014
    ..This dynamics highlights ongoing secondary evolutionary adaptations in akaryotic microbes, especially Archaea. ..
  42. pmc 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...
  43. pmc Biphasic patterns of diversification and the emergence of modules
    JAY MITTENTHAL
    Department of Cell and Developmental Biology, University of Illinois Urbana Champaign, IL, USA
    Front Genet 3:147. 2012
    ....
  44. doi request reprint Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification
    Arshan Nasir
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, and Illinois Informatics Institute, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
    Archaea 2013:648746. 2013
    ....
  45. pmc Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus
    Liudmila S Yafremava
    Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA National Center for Supercomputing Applications, Urbana, IL 61801, USA
    Archaea 2013:680436. 2013
    ....
  46. pmc Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals
    Ulrike 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...