RECENT PUBLICATIONS

Sun F-J and G Caetano-Anollés (2009) The evolutionary significance of the long variable arm in transfer RNA. Complexity, in press

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

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)

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

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) The origin and evolution of tRNA inferred from phylogenetic analysis of structure. Journal of Molecular Evolution 66: 21-35. (abstract)

Wang ML, LS Yafremava, D. Caetano-Anollés G, 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. (abstract) (pdf) Press release: Census of protein architectures offers new view of history of life

Caetano-Anollés G, SH Kim and JE Mittenthal (2007) The origins of modern metabolic networks inferred from phylogenomic analysis of protein structure. Proceeding of the National Academy of Sciences USA 10: 9358-9363. (abstract) (pdf) Press release: Study of protein folds offers insight into metabolic evolution

Martin N, EA Ruedi, R LeDuc, F-J 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. (abstract)(pdf)

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. (abstract)

TEACHING

CPSC 569 / ANSC 542: APPLIED BIOINFORMATICS
CPSC 567 / IB 505: BIOINFORMATICS 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

BIG BANG IN THE PROTEIN WOLRD: Most proteins consist of one or more domains, tightly folded segments of the polypeptide chain that act as structural, functional, and evolutionary units. Domains sometimes combine with each other or excise to produce new proteins and this process is non-random and highly conserved in evolution. Wang and Caetano-Anollés (2009) reconstruct genome-based phylogenetic trees that define timelines of discovery of domains and domain combinations and describe an explosive combinatorial game that is vastly responsible for the complexity of the protein world. This ‘big bang’ of protein discovery occured during early stages of diversified life and its explosive appearance in the world is here illustrated as a cosmic event that features in the foreground several domain combinations of the membrane-associated guanylate kinase (MAGUK) family. From January 2009 issue of the journal Structure (abstract).

My current reseach program focuses on creative ways to mine, visualize and integrate data from structural and functional genomic research. I am particularly interested in the evolution of macromolecular structure and networks in biology, the reconstruction of phylogenetic history, and the incorporation of evolutionary considerations in genomic research. Research relates to the ‘mapping’ of genotype, phenotype, function and fitness to each other, and how this mapping can be used to study origins of molecular diversification, biological systems, processes that are linked to co-evolutionary phenomena (such as pathogenesis and symbiosis), and levels and patterns of genome-wide muation.

Evolution of macromolecular structure and genomic demography: Most functional constraints on the evolutionary divergence of molecules operate at the level of tertiary structure. Consequently, three-dimensional structures are generally more evolutionary conserved than sequences. We have therefore chosen to reconstruct phylogenetic history directly from the structure of proteins and nucleic acids. In these studies, structure, function, and genomic demography are embedded directly into phylogenetic analysis and molecules and genomes compared at a wide range of evolutionary levels, from the subspecies analysis of a fungal plant pathogen to the universal tree of life. This phylogenetic approach can be used to unravel evolutionary processes and uncover functional relationships in RNA molecules, proteomes, and protein architectures. Current studies: (1) compare systematically the structure of proteins and nucleic acids at different evolutionary levels, (2) establish which are the ‘contextual’ constraints imposed by the function and inherent properties of these molecules, and (3) delimit a structural morphospace for phylogenomic analysis.

RECENT REVIEW ARTICLES

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).

Sun F-J and G Caetano-Anollés (2009) Transfer RNA and the origins of diversified life. Science Progress 91: 265-284. (abstract)

Caetano-Anollés G, LS Yafremava, H Gee, D Caetano-Anollés, and JE Mittenthal (2008) The origin and evolution of modern metabolism. International J Biochemistry & Cell Biology 41: 285-297. (abstract)(advance access: 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)

View Gustavo Caetano-Anollés' publications at the National Library of Medicine (PubMed)

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