a computational approach to the functional screening of genomes计算基因组的功能筛选方法.pdfVIP

A Computational Approach to the Functional Screening of Genomes 1 2 2* Davide Chiarugi , Pierpaolo Degano , Roberto Marangoni ` ` 1 Dipartimento di Matematica e Informatica, Universita di Siena, Siena, Italy, 2 Dipartimento di Informatica, Universita di Pisa, Pisa, Italy Comparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene-by- gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained MGS by comparing the genomes of two simple bacteria and eliminating duplicated or functionally identical genes. The authors raised the fundamental question of whether a hypothetical organism possessing MGS is able to live or not. We attacked this viability problem specifying in silico the metabolic pathways of the MGS-based prokaryote. We then performed a dynamic simulation of cellular metabolic activities in order to check whether the MGS-prokaryote reaches some equilibrium state and produces the necessary biomass. We assumed these two conditions to be necessary for a living organism. Our simulations clearly show that the MGS does not express an organism that is able to live. We then iteratively proceeded with functional replacements in order to obtain a genome composition that gives rise to equilibrium. We ruled out 76 of the original 254 genes in the MGS, because they resulted in duplication from a functional point of view. We also added seven genes not present in the MGS. These genes encode for enzymes involved in critical nodes of the metabolic network. These modifications led to a