Phylogenomic analysis of the uracil-DNA glycosylase superfamily

Abstract

The spontaneous deamination of cytosine produces uracil mispaired with guanine in DNA, which will produce a mutation, unless repaired. In all domains of life, uracil-DNA glycosylases (UDGs) are responsible for the elimination of uracil from DNA. Thus, UDGs contribute to the integrity of the genetic information and their loss results in mutator phenotypes. We are interested in understanding the role of UDG genes in the evolutionary variation of the rate and the spectrum of spontaneous mutations. To this end, we determined the presence or absence of the five main UDG families in more than 1,000 completely sequenced genomes and analyzed their patterns of gene loss and gain in eubacterial lineages. We observe nonindependent patterns of gene loss and gain between UDG families in Eubacteria, suggesting extensive functional overlap in an evolutionary timescale. Given that UDGs prevent transitions at G:C sites, we expected the loss of UDG genes to bias the mutational spectrum toward a lower equilibrium G + C content. To test this hypothesis, we used phylogenetically independent contrasts to compare the G + C content at intergenic and 4-fold redundant sites between lineages where UDG genes have been lost and their sister clades. None of the main UDG families present in Eubacteria was associated with a higher G + C content at intergenic or 4-fold redundant sites. We discuss the reasons of this negative result and report several features of the evolution of the UDG superfamily with implications for their functional study. uracil-DNA glycosylase, mutation rate evolution, mutational bias, GC content, DNA repair, mutator gene.

FIG. 1.

Conditional spontaneous base substitution rates per base per generation for Drosophila melanogaster (white, Keightley et al. 2009), Caenorhabditis elegans (pattern, Denver et al. 2009), and Arabidopsis thaliana (black, Ossowski et al. 2010). Horizontal lines indicate total mutation rates for each species with their standard errors in grey. Total mutation rates are equal to the average of the sum of mutation rates at A:T sites and the sum of mutation rates at G:C sites, weighted by the proportion of each kind of sites in the genome. Data for D. melanogaster and for C. elegans were derived from the original publications assuming that the proportion of A:T sites surveyed is the same as the genomic proportion of A + T. Data for D. melanogaster were not corrected for a small downward bias described in Keightley et al. (2009).

FIG. 2.

ML phylogenies of the main UDG families, and the sequence logos of their most conserved homologous motif. The branch color indicates eubacterial (black), archaeal (green), or eukaryotic (red) sequences. A putative family 6, not functionally described in the literature, is indicated with a question mark.

FIG. 3.

Summary of values of the Michaelis constant ($K_M$) and the rate of uracil excision ($k_{cat}$; see text for details) from U:A pairs by family 1 UDGs of different species found in the literature (see raw data and references in the Supplementary table S4, Supplementary Material online). Boxes are interquartile ranges; horizontal lines within the boxes are medians; whiskers extend to the most extreme data points that are no more than 1.5 times the interquartile range away from the box; data points further than 1.5 times the interquartile range from the box are drawn as empty circles. Horizontal lines without a box represent single values.

FIG. 4.

Posterior distributions of the rates of loss of UDG family 1 and of extended family 4, in the absence or presence of families 2 or 1. The meanings of boxes, whiskers, and empty circles are the same as in figure 3.