Gustavo Caetano-Anolles

Professor

Research Interests

  • Evolution of macromolecular structure
  • Function and structure in proteins and ncRNA
  • Evolution of biological networks
  • The spontaneous mutation process
  • Interaction of plants and microbes

Selected Articles in Journals

  • Martin N, EA Ruedi, R LeDuc, F Sun and G Caetano-Anollés (2007) Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: Are they proof of an ancient genome duplication event? Biology Direct 2: 23.
  • Sun F-J, S Fleurdepine, C Bousquet-Antonelli, G Caetano-Anollés and J-M Deragon (2007) Common evolutionary trends for tRNA-derived SINE RNA structures. Trends in Genetics 23: 26-33.
  • Wang M, LS Yafremava, D Caetano-Anollés, JE Mittenthal and G Caetano-Anollés (2007) Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Research 17: 1572-1585.
  • Caetano-Anollés G, HS Kim and JE Mittenthal (2007) The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proceedings of the National Academy of Sciences USA 104: 9358-9363.
  • Sun F-J and G Caetano-Anollés (2008) The origin and evolution of tRNA inferred from phylogenetic analysis of structure. Journal of Molecular Evolution 66: 21-35. (abstract)

  • Knudsen V and G Caetano-Anollés (2008) NOBAI: a web server for character coding of geometrical and statistical features in RNA structure. Nucleic Acids Research 36: 85-90 (abstract)(pdf)
  • Sun F-J and G Caetano-Anollés (2008) Evolutionary patterns in the sequence and structure of transfer RNA: early origins of Archaea and viruses. PLoS Computational Biology 4: e1000018. (abstract) (pdf) Press release: Researchers see history of life in the structure of transfer RNA

  • Sun F-J and G Caetano-Anollés (2008) Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code. PLoS ONE 3: e2799 (abstract)(pdf) Press release: Study reveals surprising details of the evolution of protein translation

  • Kim KM, S Sung, G Caetano-Anollés, JY Han, and H Kim (2008) An approach to orthology detection from homologous sequences under minimum evolution. Nucleic Acids Research 36(17): e10 (abstract) (pdf)

  • Caetano-Anollés G, Sun F-J, ML, Wang, LS Yafremava, A Harish, HS Kim, V Knudsen, D. Caetano-Anollés G and JE Mittenthal (2008) Origins and evolution of modern biochemistry: insights from genomes and molecular structure. Frontiers in Bioscience 13: 5212-5240. (abstract)(pdf)

  • Sun F-J and G Caetano-Anollés (2008) Transfer RNA and the origins of diversified life. Science Progress 91: 265-284. (abstract)

  • Wang M and G Caetano-Anollés (2009) The evolutionary mechanics of domain organization in proteomes and the rise of moduarity in the protein world. Structure 17: 66-78 (abstract) Press release: Study of protein structures reveals key events in evolutionary history

  • Sun F-J and G Caetano-Anollés (2009) The evolutionary significance of the long variable arm in transfer RNA. Complexity14:26-39 (abstract).

  • Sun F-J and G Caetano-Anollés (2009) The evolutionary history of the structure of 5S ribosomal RNA. Journal of Molecular Evolution 69:430-443 (abstract).

  • Caetano-Anollés G, LS Yafremava, H Gee, D Caetano-Anollés, and JE Mittenthal (2009) The origin and evolution of modern metabolism. International J Biochemistry & Cell Biology 41: 285-297. (abstract)(advance access: pdf)
  • Caetano-Anollés G, M Wang, D Caetano-Anollés, and JE Mittenthal (2009) The origin, evolution and structure of the protein world. Biochemical Journal 417: 621-637 (abstract)(pdf).

  • Caetano-Anollés G, and JE Mittenthal (2010) Exploring the interplay of stability and function in protein evolution. BioEssays 32(8): 655-658 (abstract)
  • Caetano-Anollés D, KM Kim and G Caetano-Anollés (2010) Proteome evolution and the metabolic origins of translation and cellular life. Journal of Molecular Evolution 72: 14-32 (abstract)

  • Sun F-J and G Caetano-Anollés (2010) The origin of modern 5S rRNA: A case of relating models of structural history to phylogenetic data. Journal of Molecular Evolution 71(1): 3-5 (abstract)

  • Dupont CL, A Butcher, RE Valas, PE Bourne, and G Caetano-Anollés (2010) History of biological metal utilization inferred through phylogenomic analysis of protein structure. Proceedings of the National Academy of Sciences USA 107 (23): 10567-10572 (abstract)
  • Dupont CL and G Caetano-Anollés (2010) Reply to Mulkidjanian and Galperin: Zn may have constrained evolution during the Proterozoic but not the Archean. Proceedings of the National Academy of Sciences USA 107: E138.
  • Kim KM and G Caetano-Anollés (2010) Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data. Molecular Biology and Evolution 27 (7): 1710-1733 (abstract)
  • Sun F-J and G Caetano-Anollés (2010) The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics 11:153 (abstract)

  • Qi M, F-J Sun, G Caetano-Anollés, and Y Zhao (2010) Comparative genomic and phylogenetic analysis of two-component signal transduction systems in Erwinia amylovora and related enterobacteria. Journal of Molecular Evolution 70:167-180 (abstract)
  • Twizeyimana M, PS Ojiambo, JS Haudenshield, G Caetano-Anollés, KF Pedeley, R Bandyopadhyay and GL Hartman (2011) Genetic structure and diversity of Phakopsora pachyrhizi isolates from soyabean. Plant Pathology 60:719-729.
  • Wang M, YY Jiang, KM Kim, G Qu, HF Ji, JE Mittenthal, HY Zhang and G Caetano-Anollés (2011) A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Molecular Biology and Evolution 28: 567-582 (abstract)
  • Caetano-Anollés D, KM Kim and G Caetano-Anollés (2011) Proteome evolution and the metabolic origins of translation and cellular life. Journal of Molecular Evolution 72: 14-32.
  • Kim KM and G Caetano-Anollés (2011) The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evolutionary Biology 11:140 (abstract) (pdf)
  • Wang M, CG Kurland and G Caetano-Anollés (2011) Reductive evolution of proteomes and protein structures. Proceedings of the National Academy of Sciences USA 108: 11954-11958.(abstract) (pdf)
  • Nasir A, A Naeem, MJ Kahn, HD Lopez Nicora and G Caetano-Anollés (2011) Annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. Genes 2:869-911.(pdf)
  • Kim KM, T Qin, Y-Y Jiang, L-L Chen, M Xiong, D Caetano-Anollés, H-Y Zhang and G Caetano-Anollés (2012) Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygenation. Structure 20:67-76 (abstract) Press release: Researchers identify molecular culprit in rise of planetary oxygen
  • Kim KM and G Caetano-Anollés (2012) The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. BMC Evolutionary Biology 12:13 (abstract)
  • Harish A and G Caetano-Anollés (2012) Ribosomal history reveals the origin of modern protein synthesis. PLoS ONE 7: e32776 (abstract)
  • Zhang H-Y, T Qin, Y-Y Jiang and G Caetano-Anollés (2012) Structural phylogenomics uncovers the early and concurrent origins of Cysteine biosynthesis and Iron-Sulfur proteins. Journal of Biomolecular Structure and Dynamics 30: 542-545 (abstract)
  • Caetano-Anollés G, KM Kim and D Caetano-Anollés (2012) The phylogenomic roots of modern biochemistry: Origins of proteins, cofactors and protein biosynthesis. Journal of Molecular Evolution 74: 1-34 (abstract)
  • Caetano-Anollés G and A Nasir (2012) Benefits of using molecular structure and abundance in phylogenomic analysis. Frontiers in Genetics 3: 172 (abstract)
  • Mittenthal JE, D Caetano-Anollés and G Caetano-Anollés (2012) Biphasic patterns of diversification and the emergence of modules. Frontiers in Genetics 3: 147 (abstract)
  • Nasir A, KM Kim and G Caetano-Anollés (2012) Giant viruses coexisted with cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evolutionary Biology 15: 156 (abstract)
  • Nasir A, KM Kim and G Caetano-Anollés (2012) Viral evolution: Primordial cellular origins and late adaptation to parasitism. Mobile Genetic Elements 2: 1-6
  • Debes C, M Wang, G Caetano-Anollés and F Gräter (2013) Folding rate evolution of protein domain structure. PLoS Computational Biology 9:e1002861 (abstract)
  • Aziz F, P Chan, J Osorio, BF Minhas, V Parekat and G Caetano-Anollés (2012) Stress induces biphasic-rewiring and modularization in the metabolomics networks of Escherichia coli. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Conference Publication, pp. 593-597. (abstract)