A MINIMAL GENE SET FOR CELLULAR LIFE DERIVED BY COMPARISON OF COMPLETE BACTERIAL GENOMES

The recently sequenced genome of the parasitic bacterium Mycoplasma ge nitalium contains only 468 identified protein-coding genes that have b een dubbed a minimal gene complement [Fraser, C. M., Gocayne, J. D., W hite, O., Adams, M. D., Clayton, R. A., et al. (1995) Science 270, 397 -403]. Although the M. genitalium gene complement is indeed the smalle st among known cellular life forms, there is no evidence that it is th e minimal self-sufficient gene set, To derive such a set, we compared the 468 predicted M. genitalium protein sequences with the 1703 protei n sequences encoded by the other completely sequenced small bacterial genome, that of Haemophilus influenzae. M. genitalium and H. influenza e belong to two ancient bacterial lineages, i.e., Gram-positive and Gr am-negative bacteria, respectively. Therefore, the genes that are cons erved in these two bacteria are almost certainly essential for cellula r function. It is this category of genes that is most likely to approx imate the minimal gene set. We found that 240 M. genitalium genes have orthologs among the genes of H. influenzae. This collection of genes falls short of comprising the minimal set as some enzymes responsible for intermediate steps in essential pathways are missing. The apparent reason for this is the phenomenon that we call nonorthologous gene di splacement when the same function is fulfilled by nonorthologous prote ins in two organisms. We identified 22 nonorthologous displacements an d supplemented the set of orthologs with the respective M. genitalium genes. After examining the resulting List of 262 genes for possible fu nctional redundancy and for the presence of apparently parasite-specif ic genes, 6 genes were removed. We suggest that the remaining 256 gene s are close to the minimal gene set that is necessary and sufficient t o sustain the existence of a modern-type cell. Most of the proteins en coded by the genes from the minimal set have eukaryotic or archaeal ho mologs but seven key proteins of DNA replication do not. We speculate that the last common ancestor of the three primary kingdoms had an RNA genome. Possibilities are explored to further reduce the minimal set to model a primitive cell that might have existed at a very early stag e of life evolution.