Gustavo Caetano-Anolles

Professor

Dr. Caetano-Anollés explores molecular diversity and how molecular structure determines biological function in plants, animals, fungi and microbes of significance to agriculture. He studies the origin, structure, and evolution of genomes, proteomes, RNomes, and functionomes for applications including bioengineering, biomedicine, and systems biology.

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)