Thursday, March 25, 2010

Compensatory gene amplification restores fitness after inter-species gene replacement.

Lind P.A., C. Tobin, O.G. Berg, C.G. Kurland, and D.I. Andersson (2010) Mol. Microbiol. 75: 1078-1089.

Transfer of genes to organisms can occur in various ways especially in microorganisms. Introduction of foreign genes follows one of the three fates: insertion to replacement of an existing homologous gene locus, uncertain locations on chromosome, or inactivation. If the transferred genes are neutral or deleterious to bacteria, they are likely to be lost over time (Berg and Kurland, 2002). Because of this reason, there have been few examples of experimental evidence for evolution of horizontally transferred genes.

To examine whether and how horizontally transferred genes evolve, the authors replaced the ribosomal protein genes of Salmonella typhimuriums with homologous genes of foreign origin and evolved the strain by repeating serial batch culture transfer. Since the ribosomal protein gene is essential in bacteria, the transferred gene will not be lost and the gene needs to adapt to the new host to allow the cell to grow more efficiently (to increase fitness). Low fitness of the six constructed strains was observed as expected, because the transferred gene and its product do not initially fit the new host for many reasons; for example, difference in codon usage causes translational problem. However, within 25-200 generation of growth, adaptive mutations did overcome the fitness defects of the strains.

An interesting finding was that all genetic changes observed in the six evolved strains were not directly related to the changes in the replaced protein coding sequence, but resulted in increased expression of the introduced gene product. It is known that protein concentration imbalance can cause fitness problems for several reasons (Papp and Pai et al. 2003). The increase in protein expression was required because the introduced alien protein was inefficiently expressed due to the differences in codon usage, or because the alien protein did not have sufficient affinities to the partner molecules (RNA and proteins) to reconstitute an effective ribosome complex. All observed mutations were duplication of DNA segments containing the introduced ribosomal protein gene. This indicates that the rate of beneficial mutations in the protein coding sequence, which can change codon usage or the function of the alien protein, is much lower than the rate of recombination event that results in increase in protein expression level. The former mutation can happen, and could eventually be fixed in the population if you kept evolving the strains for long time, but such beneficial mutations were not fixed in the population within 250 generations of growth of this bacterium.

This study support the hypothesis that gene paralogs and orthologs arise upon horizontal gene transfer in the presence of selection for the gene. Although gene duplication under selection is not a rare event (Reams and Neidle, 2004; Kugelberg and Kofoid et al, 2006), the hypothesis is attractive because bioinformatics analysis revealed that duplication is more common in laterally transferred genes than in indigenous genes (Hooper and Berg, 2003).
By the way, how long does it take for the changes in the coding sequence to be fixed? It depends on selection and population size. Ask mathematicians!

Lind P.A., C. Tobin, O.G. Berg, C.G. Kurland, and D.I. Andersson (2010) Compensatory gene amplification restores fitness after inter-species gene replacement. Mol. Microbiol. 75: 1078-1089

Papp B., C. Pai, and L.D. Hurst (2003)
Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.

Berg O.D. and C.G. Kurland. (2002)
Evolution of microbial genomes: Sequence acquisition and loss. Mol. Biol. Evol. 19:2265–2276

Hooper S.D. and O.D. Berg. (2003)
Duplication is more common among laterally transferred genes than among indigenous genes. Genome Biol. 4: R48

Reams A.B. and E.L. Neidle (2004)
Gene amplification involves site-specific short homology-independent illegitimate recombination in Acinetobacter sp. strain ADP1. J. Mol. Biol. 338:643-656

Kugelberg E, E. Kofoid, A.B. Reams, D.I. Andersson, J.R. Roth (2006)
Multiple pathways of selected gene amplification during adaptive mutation. Proc. Natl. Acad. Sci. USA 103:17319-17324

H. Yano, University of Idaho