The phylogenetic distribution of divergently related protein families into the three domains of life (archaea, bacteria and eukaryotes) can signify the presence or absence of entire cellular processes in these domains and their ancestors. We can thus study the emergence of the major transitions during cellular evolution, and resolve some of the controversies surrounding the evolutionary status of archaea and the origins of the eukaryotic cell. In view of the ongoing projects that sequence the complete genomes of several Archaea, this work forms a testable prediction when the genome sequences become available. Using the presence of the protein families as taxonomic traits, and linking them to biochemical pathways, we are able to reason about the presence of the corresponding cellular processes in the last universal ancestor of contemporary cells. The analysis shows that metabolism was already a complex network of reactions which included amino acid, nucleotide, fatty acid, sugar and coenzyme metabolism. In addition, genetic processes such as translation are conserved and close to the original form. However, other processes such as DNA replication and repair or transcription are exceptional and seem to be associated with the stru...Continue Reading
Modular organization of related Archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum
Histone-encoding genes from Pyrococcus: evidence for members of the HMf family of archaeal histones in a non-methanogenic Archaeon
Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins
Reverse interpretation: a hypothetical selection mechanism for adaptive mutagenesis based on autoregulated mRNA stability
The topology of the bacterial co-conserved protein network and its implications for predicting protein function.
Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.
Structural and functional perturbation of Giardia lamblia triosephosphate isomerase by modification of a non-catalytic, non-conserved region
Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey
A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective
The comparative metabolism of the mollicutes (Mycoplasmas): the utility for taxonomic classification and the relationship of putative gene annotation and phylogeny to enzymatic function in the smallest free-living cells
Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins
Exploring Proteomic Drug Targets, Therapeutic Strategies and Protein - Protein Interactions in Cancer: Mechanistic View
Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families
Comparative metabolic modeling of multiple sulfate-reducing prokaryotes reveals versatile energy conservation mechanisms.
Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.