Horizontal Gene Transfer Between Host Eukaryotes and Their Bacterial Endosymbionts: Analyses and Problems
—Jared Haynes, University Writing Program
Horizontal gene transfer (HGT) is the direct acquisition of novel genetic material from another organism, as opposed to the vertical transfer of DNA from a parent. HGT can provide an alternative pathway for evolution, allowing organisms to acquire new genetic functions. Because of its evolutionary significance to biological and ecological innovation, HGT should interest anyone curious about adaptation in living organisms. Regardless of the functional activity of transferred genetic material, HGT should also be a concern for those hoping to use DNA sequence data to reconstruct phylogenies, as lateral gene transfer can easily obscure phylogenetic relationships between both closely and distantly related species.
Between bacteria, HGT is rampant, and its mechanisms have been studied extensively and are fairly well understood. The spread of antibiotic resistance among pathogenic bacteria is a prime example. Though not as common as transfers between bacteria, HGTs involving eukaryotes do occur. Recent developments in genome sequencing and computational techniques are allowing researchers to understand these events more deeply than ever before. Symbiotic associations between host eukaryotes and intracellular bacteria have been particularly good systems for studying these rare events because of the proximity of the host’s nuclear genome to the bacterial genome. Recent surveys of these host-symbiont relationships have provided many new insights into the patterns and processes of interdomain HGT between eukaryotes and prokaryotes. However, analysis of HGT events can be misleading because of many factors, and care must be taken when attempting to elucidate the details of such events. This article offers a brief review of recent work done on interdomain HGTs between eukaryotic hosts and their bacterial symbionts, and provides a synopsis of the multifarious problems affecting their detection and annotation.
Horizontal Gene Transfers Between Host-Endosymbiont Associations
Endosymbiotic bacteria that reside in the germ-line cells of their hosts are usually transmitted vertically each generation to the host’s offspring. This close reproductive and physical association between the host and symbiont genomes provides ample opportunities for both the occurrence and subsequent study of HGT.
Transfers from bacteria to eukaryotes
The lateral transfer of genes from bacterium to eukaryote appears to be quite widespread in endosymbiotic relationships. To look for evidence of HGT, Dunning Hotopp et al. (2007) conducted a survey of genomic data involving the endosymbiont Wolbachia pipientis, an intracellular bacterium that infects many species of arthropods and filarial nematodes. The study documented numerous occurrences of HGTs from bacteria to host, ranging in size from the transfer of single genes into host genomes to the insertion of the entire Wolbachia genome in Drosophila ananassae. Similarly, in the beetle Callosobruchus chinensis, around 30% of the Wolbachia genome has been transferred to the host beetle genome (Nikoh et al. 2008). Although most of the genes observed in these two studies appear nonfunctional and show signs of mutational decay, approximately 2% of the transferred genes in the D. ananassae genome show evidence of being actively transcribed (Dunning Hotopp et al. 2007), illustrating that HGT from a bacterial symbiont to its host can, in fact, provide novel funtions.
Eukaryotic organelles provide another illuminating example of HGT from symbionts to their hosts. It is now widely accepted that genome-containing organelles, like mitochondria and chloroplasts, originated as ancient endosymbionts of early eukaryotic cells. These organellar genomes are highly reduced in size, as many unnecessary genes have been lost over time. However, it has been shown that many genes have actually been transferred from organelle genomes to their host genomes (Timmis et al. 2004), where they are actively transcribed under the control of the host. Furthermore, recent analyses of genomic data support the hypothesis that organellar HGT to host genomes is still regularly occurring in many eukaryotic lineages (Timmis et al. 2004).
Transfers from eukaryotes to bacteria
Although horizontal gene transfers from eukaryotes to bacteria are much less common, the recent genomic explorations of endosymbiotic relationships has shed some light on this particular path of HGT and has shown that transfers in this direction do occur. An ancient HGT between mosquitoes and the intracellular bacterium Wolbachia was recently discovered by Woolfit et al. (2009). The study revealed that a gene coding for a salivary gland surface protein was transferred from the mosquito genome to its intracellular symbiont, is currently under purifying selection, and is being actively transcribed in the novel bacterial genome. This work illustrates two important concepts: 1) genetic material from eukaryotes can be transferred and incorporated into bacterial genomes; and 2) these transferred genes can be functional in the newly acquired genome, allowing for unique and perhaps evolutionarily significant innovation in bacterial species (Woolfit et al. 2009).
Similarly, the transfer of a Calvin-cycle gene encoding for fructose bisphosphate aldolase (FBA) has been observed between red algae and cyanobacteria (Rogers, Patron, and Keeling 2007). Although this transfer did not involve an endosymbiont and its host, the study documents a clear and well-supported HGT from a eukaryote to a prokaryote, and the details of its history will be helpful in understanding similar transfers within endosymbiotic relationships. Quite interestingly, Rogers, Patron, and Keeling (2007) found that the eukaryotic FBA gene has been inserted directly upstream of its analogous gene in the cyannobacterial genome. This analogous FBA gene performs the same function as its eukaryotic counterpart, but is evolutionarily unrelated to the eukaryotic gene (Rogers, Patron, and Keeling 2007). Such an apparently non-random insertion of the transferred gene suggests that the location of transferred genes in their novel genomes may be of importance to the evolutionary fate of laterally transferred genes (Rogers, Patron, and Keeling 2007).
Problems With Analyzing Horizontal Gene Transfer Events
Ancestral vs. laterally transferred genes
There are many problems with inferring HGTs from sequence data. One question that must be addressed is whether lateral transfer actually took place, or if the homologous sequences in separate taxa represent ancestral genes that have been passed vertically from parent to offspring since the splitting of their lineages. Answering this question can be complicated by the lack of available sequence data for taxa that might help reveal whether the gene is ancestral or laterally transferred. Furthermore, even when genomic data are available, the gene phylogeny may be sporadic due to loss of the gene within particular clades and retention of the gene in others. As more data become available, researchers may be forced to reevaluate previously held beliefs about the presence or absence of HGTs. Until recently, for example, the existence of SET domain genes in bacteria was thought to be a prime example of HGT from eukaryotes to bacteria. A major factor supporting that hypothesis was that the genes are known to chemically modify chromatin (Rea et al. 2000). Because bacteria do not have chromatin, it seemed unreasonable that they would contain SET domain genes independently, so it was proposed that they obtained the genes laterally from eukaryotes (Stephens et al. 1998). However, a recent study by Alvarez-Venegas et al. (2007) indicates that no HGT occurred, and that the SET domain genes are in fact ancestral and have been evolving separately from their eukaryotic homologs, thus illustrating how difficult and misleading it can be to determine a HGT event.
Direction of transfer
Researchers are also often interested in the direction of these lateral transfer events. Gene characteristics such as gene size, the presence of introns or promoter regions, G+C content, and predicted (or known) gene functions can provide clues that help elucidate the direction of transfer. However, these characteristics are not always dependable and at times may be misleading. As seen with the SET domain genes, gene function has been a major source of error in the annotation of HGTs (Alvarez-Venegas et al. 2007). Other characteristics may be merely uninformative. For instance, although G+C content of the transferred gene should be representative of the genome of origin, enough time may have passed since the occurrence of the transfer event that the G+C content of the gene has equilibrated to the new genome (Woolfit et al. 2009) and, as such, would be uninformative as to the specific genome in which the gene originated.
Contamination in sequencing efforts
Yet arguably one of the biggest difficulties pertaining to HGT analysis is obtaining correct data in the first place. Detection of HGTs occurs entirely through analyses of sequence data, and as such, the quality of one’s data can have profound effects on any subsequent inferences made. Contamination during sequencing efforts complicates the investigation of HGTs and is particularly troublesome for cases of host-endosymbiont associations, as it may not be possible to physically separate the DNA before sequencing (Wu et al. 2006). Published genomes, particularly those from studies not concerned with host-symbiont genome evolution, may simply discard any sequence data that appears bacterial in origin on the assumption that the bacterial sequence is an artifact of the sequencing procedure (Dunning Hotopp et al. 2007).
Analysis of HGTs, especially those between bacteria, has come a long way in recent years because of an increase in genomic data, faster and more intelligent bioinformatics algorithms, and a deeper understanding of the underlying biology. However, a large gap still remains in our understanding of HGTs involving eukaryotes because of both the rarity of such events and the variety of complications associated with these analyses. Host-endosymbiont associations have helped bridge this gap to some degree, but more work is needed to fully understand HGT and its role in shaping the evolutionary history of distantly related organisms.
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