Origins and evolution of modern biochemistry: insights from genomes and molecular structure.

The survey of components in living systems at different levels of organization enables an evolutionary exploration of patterns and processes in macromolecules, networks, and genomic repertoires. Here we discuss how phylogenetic strategies that generate intrinsically rooted phylogenies impact the evolutionary study of RNA and protein components of the macromolecular machinery that is responsible for biological function. We used these methods to generate timelines of discovery of components in systems, such as substructures in RNA molecules, architectures in proteomes, domains in multi-domain proteins, enzymes in metabolic networks, and protein architectures in proteomes. These timelines unfolded remarkable patterns of origin and evolution of molecules, repertoires and networks, showing episodes of both functional specialization (e.g., rise of domains with specialized functions) and molecular simplification (e.g., reductive tendencies in molecules and proteomes). These observations have important evolutionary implications for origins of translation, the genetic code, modules in the protein world, and diversification of life, and suggest early evolution of modern biochemistry was driven by recruitment of both RNA and protein catalysts in an ancient community of complex organisms.published or submitted for publicationis peer reviewe

Additional file 1: Table S1. of Genomic characterization of plant cell wall degrading enzymes and in silico analysis of xylanses and polygalacturonases of Fusarium virguliforme

CAZy of Fusarium virguliforme. (XLSX 480 kb

Correlation analysis of ATAF1 vs. PAO expression.

<p>Using Pearson correlation analysis it was found that ATAF1 correlates positively and significantly with PAO at the P<0.05 level in all three microarray datasets. Information about the genetics and physiology of the data sets were also provided.</p