Computational Biology

Simulating a Bacteriophage

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Science  19 May 2000:
Vol. 288, Issue 5469, pp. 1137
DOI: 10.1126/science.288.5469.1137a

Progress in determining the genome sequences of complex organisms has reinforced the idea that much will become clear (although there still will be much biology to be studied). An idea of what will become possible can be gleaned from studies of the bacteriophage T7, which is known to contain 39,937 bp of DNA, encoding 59 proteins that together serve to hijack Escherichia coli into making more T7 particles.

Endy et al. constructed a simulation of the life cycle of T7 and used this model to compute the synthetic rates of T7 proteins and the overall growth rate (virus.molsci.org/t7). These compared reasonably well with the observed values for wild-type phage and for some, but not all, mutants in which the gene for T7 RNA polymerase had been repositioned. They then randomly permuted the T7 genome and found that less than 5% of these simulated phages displayed a computational growth rate faster than that of the wild type, revealing that this descendant of a laboratory isolate from half a century ago is quite fit indeed.—GJC

Proc. Natl. Acad. Sci. U.S.A.97, 5379 (2000).

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