Bioinformatics 2005, 21:3797–3800.CrossRef 17. Tcherepanov V, Ehlers A, Upton C: Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome. BMC Genomics 2006, 7:150.CrossRefPubMed Authors’ contributions PM conceived the study, designed the analytical procedure and wrote the software. The paper was written by PM, JM, and MR. All authors read and approved the final manuscript.”
“Background

Neisseria gonorrhoeae (GC) is an obligate human pathogen. In order to manifest the diversity of diseases that it is able to cause, GC must produce a variety of cell surface antigens such that the appropriate find more antigen(s) is (are) expressed in the appropriate environment at the appropriate PHA-848125 solubility dmso time. Since each of the anatomical sites that GC can infect has unique physiological properties, its success in establishing itself in a new niche requires that it rapidly adapt to its new environment. To do this, it has evolved a variety of

genetic mechanisms that result in high frequency antigenic variation of its surface components. These include: intramolecular recombination for pili antigenic variation [1]; changes in the number of pentameric DNA repeat sequences for Opa expression [2]; and changes in the length of a polyguanine tract for a variety of genes, including LOS variation [3, 4], pilin glycosylation [5], pilC expression [6] and iron utilization [7, 8]. Bioinformatic analysis of the GC genome has identified a variety of additional genes that may be subject to phase variation that is mediated by some form of transient DNA mispairing [9]. Since DNA mispairings, including insertions and deletions,

will arise as an intermediate in the phase variation process, and the frequency of phase variation is so high, it suggests that this pathogen should be defective in mismatch repair. However, studies in the meningococcus indicate that this organism contains a functional mismatch PLX3397 supplier repair system [10], and homologs of Loperamide all of the identified genes are present in the FA1090 genome [11]. In addition to the presence of a mismatch repair system, GC possesses homologs to genes that encode the proteins for recombinational repair [12], very short patch repair (DCS, unpublished observations), excision repair [13] and oxidative damage repair [14]. This indicates that GC is capable of dealing with most errors that might arise during DNA metabolism. Previous studies on GC DNA repair indicate that GC lacks error prone and photoreactivation repair systems [15, 16]. Homologs to genes associated with error-prone repair and photoreactivation are not present. For complete review of DNA repair capacities, see review by Kline et. al. [11] or Ambur et. al. [17]. Nitroreductases have been identified in a wide variety of microorganisms [18–22].