Complete Prokaryotic Genomes: Reading and Comprehension

Abstract The windfall of complete genomic sequences in the past ten years has dramatically changed the face of biology, which has started to lose its purely descriptive character. Instead, biology is gradually becoming a quantitative discipline that deals with firmly established numerical values and can be realistically described by mathematical models. Indeed, we now know that, for example, the bacteriumMycoplasma genitalium has a single chromosome which consists of 580,074 base pairs and carries genes for three ribosomal RNAs (5S, 16S, and 23S), 36 tRNAs, and 478 proteins [1,2]. We also know that about a hundred of the protein-coding genes can be disrupted without impairing the ability of this bacterium to grow on a synthetic peptide-rich broth containing the necessary nutrients [3], suggesting that the truly minimal gene set necessary for the cell life might be even smaller, in the 300–350 gene range [4–6]. Furthermore, we know that the cell ofAquifex aeolicus with its 1521 protein-coding genes is capable of autonomous, autotrophic existence in the environment, requiring for growth only hydrogen, oxygen, carbon dioxide, and mineral salts [7]. These observations bring us to the brink of finally answering the 60-year-old question posed by Erwin Schrödinger’s “What is Life?” Furthermore, although the descriptions of greatly degraded organelle-like cells likeBuchnera aphidicola[8,9] and giant cell-like mimiviruses [10] necessarily complicate the picture, analysis of these genomes allows an even better understanding of what is necessary and what is dispensable for cellular life.