The use of genome annotation data and its impact on biological conclusions

To the editor:

We were interested to read the recent paper by Nakamura et al.¹ describing a new technique to identify horizontally acquired genes in bacterial genomes. But we were surprised to see that NMB0066, a gene from the Neisseria meningitidis MC58 genome, was used as an example of horizontal transfer. In fact, NMB0066 is part of an artificial erythromycin resistance cassette that was inserted into the capsule gene siaD (NMB0067) to disrupt it, rendering the MC58 strain less virulent and therefore less hazardous to manipulate in the laboratory. The annotation of NMB0066 submitted to the public databases clearly indicates that it is foreign: “NMB0066 rRNA adenine N-6-methyltransferase (ErmC); foreign cassette inserted to disrupt NMB0067 (SiaD) to reduce virulence.” This gene may be a good positive control for the in silico approach used by Nakamura et al., but it is biologically irrelevant in the context of this genome. Therefore, the further discussion on how this gene and the capsule locus in which it is inserted were horizontally transferred from Staphylococcus aureus is meaningless. The capsule locus probably was recently acquired by MC58 but probably not directly from S. aureus.

This example highlights the importance of not taking the output of any bioinformatics program at face value; the results should always be interpreted in the biological context of the organism or sequence under study, and the relevant literature should be thoroughly examined. In this case, however, reading the literature may not have helped; in the original sequence paper² the gene NMB0066 was mentioned as being within an island of horizontal transfer (the capsule locus), but, due to an oversight, the specific reason for its presence was not spelled out. Notwithstanding the fact that this was described in the annotation submitted to the public databases, this may have been misleading for the casual reader, for which we apologize. This serves to underscore the need to be rigorous in interpreting data, both one's own and those from other groups.