“Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution” by Dagan et al. (2008)
A horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the process by which genetic material is transferred between distinct evolutionary lineages, through (plasmid-mediated) conjugation, (virus-mediated) transduction, and transformation (extracellular DNA uptake). Although HGT may occur at the cellular level frequently, transferred genes cannot be always inherited to the subsequent generations.
Generally, a gene is thought to be acquired by HGT if gene tree conflicts or unusual nucleotide composition is observed. The major caveat of these approaches is that the observations can also be explained by other reasons, such as inaccurate phylogenetic reconstruction methods, gene loss in multiple lineages, novel sequences arising from the divergence of gene duplications, and varying mutation rates for different proteins (Kechris et al., 2006).
HGT is an important source of genetic diversity among microorganisms, but the degree of its contribution on microbial genome evolution is still debated. Dagan et al. (2008) conducted a network analysis of shared gene content across prokaryotic genomes to estimate the contribution of HGT to microbial evolution. Their result suggests that on average, 81 ± 15% of the genes in each genome were involved in HGT at some point in their history. Once acquired, genes can be vertically inherited within a group, and their result suggests that this has occurred for the vast majority of genes.
The Dagan's work have inspired us to estimate relative contributions of different mechanisms (conjugation, transduction, and transformation) on horizontal gene transfer among prokaryotes.
Dagan T, Artzy-Randrup Y, Martin W. Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10039-44. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution.
Choi IG, Kim SH. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4489-94. Global extent of horizontal gene transfer.
Dagan T, Martin W. Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):870-5. Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.
Kechris KJ, Lin JC, Bickel PJ, Glazer AN. Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9584-9. Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study.
Beiko RG, Harlow TJ, Ragan MA. Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14332-7. Highways of gene sharing in prokaryotes.
Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. Genome Res. 2005 Jul;15(7):954-9. The net of life: reconstructing the microbial phylogenetic network.
Dr. Haruo Suzuki
University of Idaho