Fusobacterium nucleatum
We identified several candidate genes in Fusobacterium nucleatum which may have resulted from horizontal gene transfer. Three of these genes were corroborated with DarkHorse, HMPREF9094_2765, an Amino Acid-Polyamine-Organocation (APC) family arginine/ornithine antiporter, HMPREF9094_2777, a dipeptide/tripeptide permease, and HMPREF9094_2752, a MarR family transcriptional regulator.
The arginine/ornithine antiporter had a z-score for GC content of 8.39 (enriched in GC), which was highly unlikely to occured by chance. DarkHorse contained an entry of this gene from Clostridium perfrigens which displayed phylogenetic discrepancies with a similar gene in Burkholderia xenovorans (normalized LPI score of 0.458). Similarly, the permease was enriched in GC (z-score 8.88) and was matched to a gene in the DarkHorse database from Clostridium perfringens. This gene displayed phylogenetic discrepancies with the same gene in Chlamydophila felis (normalized LPI score of 0.484). Finally, the MarR family transcriptional regulator was enriched in GC (z-score 8.12) and was matched by DarkHorse to a gene in Clostridium acetobutylicum, which displayed phylogenetic discrepancies with the gene in Vibrio fischeri. In summary, these three genes (arginine/ornithine antiporter, permease, and MarR family transcriptional regulator) both showed unusual GC content, and were associated with genes which were indicated by phylogenetic analysis to be implicated in horizontal gene transfer. These results from two separate methods of analysis makes it highly likely that these genes originated in F. nucleatum by horizontal gene transfer.
F. nucleatum has been identified in the literature as an organism that has likely undergone significant horizontal gene transfer in its evolutionary history. In a phylogenetic analysis of the F. nucleatum genome, 35-56% of genes appear to have origins from a variety of other bacterial phyla (F. nucleatum is of the phylum Fusobacteria) including bacteroidetes, proteobacteria, spirochetes and Firmicutes (to which Clostridium perfringens belongs)[1]. A separate study identified a subspecies of F. nucleatum which was particularly amenable to horizontal gene transfer, and identified a large number of genes across many different functions that may have been resulting from other organisms[2].
F. nucleatum is a human oral bacterium, and is a key component in periodontal plaque, where it is able to coaggregate with other species. This in particular makes it evolutionarily favorable for adaptive genes to be transferred between organisms. In particular, it is suggested that key components of organisms, such as cell wall properties and metabolism, might be mixed and matched in order to create desirable qualities[1]. The genes which we identified as potential horizontal gene transfer candidates fit well into this context. The arginine/ornithine antiporter and permease both are involved in the transport of nutrients and other molecules across the cell membrane, and the MarR family transcriptional regulator has been implicated in antibiotic resistance[3]. All of these could represent genes which would be beneficial for F. nucleatum to have in its environment.
1. Mira A, Pushker R, Legault BA, Moreira D, RodrÃguez-Valera F (2004) Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol Biol, 4(50).
2.Karpathy SE, Qin X, Gioia J, Jiang HY, Liu Y, et al (2007) Genome Sequence of Fusobacterium nucleatum Subspecies Polymorphum — a Genetically Tractable Fusobacterium. PLoS ONE 2(8): e659. doi:10.1371/journal.pone.0000659
3. Thirumananseri Kumarevel (2012). The MarR Family of Transcriptional Regulators - A Structural Perspective, Antibiotic Resistant Bacteria - A Continuous Challenge in the New Millennium, Dr. Marina Pana