[Frontiers in Bioscience 4657-4666, May 1, 2008]

[Frontiers in Bioscience 4657-4666, May 1, 2008]

Gene content of LUCA, the last universal common ancestor

Stowers Institute for Medical Research, 1000 E 50^th St., Kansas City, Missouri 64110, and Department of Microbiology, Molecular Genetics and Immunology, Kansas University Medical Center, Kansas City, Kansas, 66160, USA

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. The data: genome tree, gene trees, lists of orthologs and phyletic vectors
4. Ancestral state inference: gene loss to gene gain ratio is a crucial parameter
5. Which genes are in LUCA and which are not
6. The effects of tree topology and of horizontal gene transfer
7. Ancestral genes and "LUCA-likeness" of the present-day genomes
8. LUCAS instead of LUCA?
9. Conclusions
10. Acknowledgments
11. References

1. ABSTRACT

Comparative genomics and modern phylogenetic approaches allow us to infer the gene content of LUCA, the Last Universal Common Ancestor of all known currently living cellular organisms. Most of the estimates produce a putative LUCA with 500-1000 protein-coding genes and biochemically coherent metabolism, if the average rates of gene gains (gene emergence plus horizontal gene transfer) and gene losses per family are allowed to be close to each other. This estimate is not strongly sensitive to the topology of the Tree of Life, but the identity of the genes that are placed in LUCA may depend on the position of the deep branches and the root of the tree.