Adler R. Dillman and Dr. Byron J. Adams, Microbiology and Molecular Biology
Introduction
The process of horizontal or lateral gene transfer involves the movement of genetic information in a lateral fashion from one organism to another, regardless of phylogenetic distance. Horizontal gene transfer (HGT) is a major mechanism of prokaryotic evolution while its role in eukaryotic evolution remains undecided, with many claims of genes being laterally transferred from prokaryotes to eukaryotes being subsequently refuted [1,2]. Recently, 12 genes of the plant parasite M. incognita have been proposed as being good candidates of HGT. Because certain rhizobial bacteria occupy a very similar niche both inside and out of the plant, and use many of the same kinds of enzymes to break down the cellulose of plant cell walls, researchers have hypothesized that nematodes could have acquired some of these genes from rhizobial bacteria via HGT. If this sort of transfer occurred it would represent a wholesale acceleration of Darwinian gradualism.
We first looked to better establish these 12 candidates as bonafide examples of HGT . There are several hallmarks that can be viewed as evidence of HGT: phylogenetic incongruency, anomalous nucleotide composition, gene organization, and transfer vestige [3,4,5]. In our study we focused on nucleotide composition and G+C content. All organisms exhibit a wide range of variation in the overall G+C content of their genomes and each organism experiences a specific set of directional mutation pressures that affects the genome in different ways. Genes within a particular genome are similar in base composition, codon bias, and nucleotide frequencies [5]. These characteristics have been helpful in phylogenetic and systematic studies and can be used to identify putative candidates of laterally acquired genes. It is expected that recently acquired genes will have anomalous G+C content in the host genome, as it should reflect the G+C content of the donor. This is not the case for the 12 genes we examined. It has been suggested that these genes have been more anciently transferred and then subsequently ameliorated: the laterally acquired genes have been under the codon bias and mutational pressure of the new host and over time will reflect the DNA composition of the host genome rather than the donor. We assess the third position codon usage and compare the mutational bias of these putative HGT candidate genes in the M. incognita genome to detect the possible evidence of amelioration.
Material and Methods
We did a BLASTX search using the consensus sequences of the expressed sequence tags (ESTs) for the 12 HGT candidates to determine relevant sequence similarity and to have the most current information possible. As more eukaryotic sequences are being added to GenBank we get increasingly more eukaryotic matches than our last BLASTX search with those same consensus sequences.
In order to examine the prevalence of silent substitutions and the effect of amelioration on these candidates we used the EST consensus sequences and the program prot4EST to obtain the protein translations [7]. Using those translations we aligned the amino acid (AA) strings of the nematode ESTs with the top five prokaryotic matches found in our BLASTX searches with ClustalX [8]. The nucleotide strings of these same taxa were then aligned according to the AA alignment using MacClade [9]. We were able to then look at the G+C content of these genes in the various taxa and look for codons that had made silent substitutions in the nematode sequences that would lower or raise the G+C content of each individual gene.
Results and Discussion
Our BLASTX search for similar prokaryotic sequences turned up several donor candidates for 4 of the proposed 12 genes. The remaining genes did not give us search results that favored the HGT hypothesis. Often the consensus ESTs we BLASTed had equally high and sometimes higher similarity with eukaryotic sequences. For the cellulases and pectinases there were plenty of eukaryotic matches with high similarity and we feel that there is no need to examine these genes any further for signs of HGT. Instead these results seem to support the null hypothesis that these genes arose via convergent evolution due to selective pressure. For the four genes with high sequence similarity to rhizobial matches there seemed reason to look for signs of amelioration.
The Big Idea
The G+C content of the nematode gene sequences compared to the most similar rhizobial donor of each gene suggested that the majority of the time, mutations occurred favoring the G+C content of the recipient genome (amelioration). The next step would be to see if these same changes occur in a host genome when non-beneficial genes are inserted. Our overall results are consistent with the HGT hypothesis and show evidence of amelioration. However, they still do not strongly reject the null hypothesis of convergent evolution because functional constraints on the nematode genes may require deviation from the mean G+C content of its overall genome. Therefore, a body of additional research is needed to establish multiple robust tests that can reject the null hypothesis, and pave the way for furthering the development of this as a model for studying natural insertion events.
References
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