Abstract
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 genome composed of 187 elements expressing a virtually living organism, Virtual Cell (ViCe), that exhibits homeostatic capabilities and produces biomass. Moreover, the steady-state distribution of the concentrations of virtual metabolites that resulted was similar to that experimentally measured in bacteria. We conclude then that ViCe is able to “live in silico.”
Highlights
The search for LUCA, the Last Unknown Common Ancestor, is an open problem in evolutionary theory, which has been addressed using many different approaches
We shall examine how such a simplified organism can be inferred by a comparative genomics approach, following Mushegian and Koonin [3]
The final result of this work was the so-called Minimal Gene Set (MGS), made of 254 singular genes. This hypothetical minimal genome was claimed to specify for a very essential prokaryote, but no argument was provided to address the fundamental question of whether a cell equipped with MGS is able to live or not
Summary
Comparative genomics usually involves managing the functional aspects of genomes, by comparing gene-bygene functions Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal Gene Set (MGS), aiming for a possible oldest ancestor genome. We 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. These genes encode for enzymes involved in critical nodes of the metabolic network These modifications led to a genome composed of 187 elements expressing a virtually living organism, Virtual Cell (ViCe), that exhibits homeostatic capabilities and produces biomass. PLoS Comput Biol 3(9): e174. doi:10.1371/journal. pcbi.0030174
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have