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. 2010 Mar;59(2):212-25.
doi: 10.1093/sysbio/syp104. Epub 2010 Jan 15.

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes

Adi Stern  1 , Itay Mayrose, Osnat Penn, Shaul Shaul, Uri Gophna, Tal Pupko
Affiliations

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes

Adi Stern et al. Syst Biol. 2010 Mar.

Abstract

Thymidylate synthases (Thy) are key enzymes in the synthesis of deoxythymidylate, 1 of the 4 building blocks of DNA. As such, they are essential for all DNA-based forms of life and therefore implicated in the hypothesized transition from RNA genomes to DNA genomes. Two evolutionally unrelated Thy enzymes, ThyA and ThyX, are known to catalyze the same biochemical reaction. Both enzymes are sporadically distributed within each of the 3 domains of life in a pattern that suggests multiple nonhomologous lateral gene transfer (LGT) events. We present a phylogenetic analysis of the evolution of the 2 enzymes, aimed at unraveling their entangled evolutionary history and tracing their origin back to early life. A novel probabilistic evolutionary model was developed, which allowed us to compute the posterior probabilities and the posterior expectation of the number of LGT events. Simulation studies were performed to validate the model's ability to accurately detect LGT events, which have occurred throughout a large phylogeny. Applying the model to the Thy data revealed widespread nonhomologous LGT between and within all 3 domains of life. By reconstructing the ThyA and ThyX gene trees, the most likely donor of each LGT event was inferred. The role of viruses in LGT of Thy is finally discussed.

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Figures

F<sc>IGURE</sc> 1.
FIGURE 1.
Mapping of the thymidylate synthase enzymes ThyA and ThyX onto the species tree. Posterior probabilities of an LGT event are coded onto the edges. A black line represents a probability of LGT higher than 0.75, and a dashed line represents a probability between 0.5 and 0.75. The states at the extant organisms are color coded onto the tips of the tree as follows: ThyA in red, ThyX in blue, and cases in which an organism codes both ThyA and ThyX simultaneously are in violet. Colored arrows represent an LGT event, with the color of the arrow standing for the gained gene. The tree is presented using the FigTree software (http://tree.bio.ed.ac.uk/) as a cladogram, and edge lengths are not shown to scale. Cren, Crenarchaeota; Nano, Nanoarchaeota.
F<sc>IGURE</sc> 2.
FIGURE 2.
Unrooted collapsed ML gene tree of ThyA. Collapsed clades are color-coded according to their phylogenetic inclusion: blue, red, and orange stand for Bacteria, Eukarya, and Archaea, respectively. Node supports are presented as percentage of support out of 100 bootstrap iterations. One edge length unit is equivalent to an average of one substitution per site. An example of LGT involving Bacillus subtilis and the bacillus infecting phages φ-3T and β-22 is boxed in black. The tree is presented using the FigTree software (http://tree.bio.ed.ac.uk/). The full tree is available as part of the online supplementary material.
F<sc>IGURE</sc> 3.
FIGURE 3.
Unrooted collapsed ML gene tree of ThyX. Collapsed clades are color-coded according to their phylogenetic inclusion: blue, red, and orange stand for Bacteria, Eukarya, and Archaea, respectively. Node supports are presented as percentage of support out of 100 bootstrap iterations. One edge length unit is equivalent to an average of one substitution per site. The tree is presented using the FigTree software (http://tree.bio.ed.ac.uk/). The full tree is available as part of the online supplementary material.
F<sc>IGURE</sc> A1.
FIGURE A1.
An example tree used to illustrate the computation of posterior probabilities.
F<sc>IGURE</sc> A2.
FIGURE A2.
A schematic representation of a continuous-time Markov chain. Circles represent different states represented by different colors, and t1–t4 represent the waiting times.
See this image and copyright information in PMC

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