ABSTRACT: In this work, proteomes of seven Treponema pallidum subsp. pallidum (TPA) strains including Nichols-like strains (DAL-1, Haiti B, Madras) and SS14-like strains (SS14, Philadelphia 1, Grady, Mexico A), grown under in vitro conditions, were analyzed in biological triplicates. Digestion peptides during proteome analyses (LC-MS/MS) were detected with different annotation algorithms (DFAST, PGAP, Prodigal, Prokka, RAST, GeneMarkS, and a manual GenBank annotation) of the corresponding genomes. In addition, ORFfinder was used to predict all ORFs encoding polypeptides longer than 50 amino acid residues. Altogether, 10,823 unique peptides of treponemal origin were detected during analyses. The number of detected peptides per strain varied between 2117 and 7455 with the highest number of detected peptides found for TPA DAL-1 strain. To determine the extent of detected proteins, seven different annotations of seven TPA strains were combined together and only unique protein annotations were kept. Altogether, 1216 predicted protein sequences were searched in the database of detected peptides and 911 individual proteins were identified (74.9%). From individual annotation algorithms, the highest percentage coverage of annotated proteins was detected by GeneMarkS algorithm reaching up to 88.9% of detected proteins out of GeneMarkS-annotated proteins in TPA Haiti B. The support for detected proteins was quite robust with 85.5% of detected proteins identified by two or more peptides and almost three quarters of proteins identified by three and more peptides (72.4%). Altogether, a set of 51 proteins out of 1,053 RAST-annotated proteins (4.8%) showed statistically significant quantitative differences in the proteome signals among different TPA strains. Despite the previously found differences in the growth rates of several TPA strains, proteome analysis revealed only a limited number of detectable quantitative differences in the proteomes.
Katerina Hanakova 
