Improving N-terminal protein annotation of <it>Plasmodium</it> species based on signal peptide prediction of orthologous proteins

• Main Authors: Neto Armando, Alvarenga Denise A, Rezende Antônio M, Resende Sarah S, Ribeiro Ricardo, Fontes Cor JF, Carvalho Luzia H, de Brito Cristiana F
• Format: Article
• Language: English
• Published: BMC 2012-11-01
• Series: Malaria Journal
• Subjects: Signal peptide; Orthologous; Gene annotation; Malaria; Plasmodium
• Online Access: http://www.malariajournal.com/content/11/1/375

<p>Abstract</p> <p>Background</p> <p>Signal peptide is one of the most important motifs involved in protein trafficking and it ultimately influences protein function. Considering the expected functional conservation among orthologs it was hypothesized that divergence in signal peptides within orthologous groups is mainly due to N-terminal protein sequence misannotation. Thus, discrepancies in signal peptide prediction of orthologous proteins were used to identify misannotated proteins in five <it>Plasmodium</it> species.</p> <p>Methods</p> <p>Signal peptide (SignalP) and orthology (OrthoMCL) were combined in an innovative strategy to identify orthologous groups showing discrepancies in signal peptide prediction among their protein members (Mixed groups). In a comparative analysis, multiple alignments for each of these groups and gene models were visually inspected in search of misannotated proteins and, whenever possible, alternative gene models were proposed. Thresholds for signal peptide prediction parameters were also modified to reduce their impact as a possible source of discrepancy among orthologs. Validation of new gene models was based on RT-PCR (few examples) or on experimental evidence already published (ApiLoc).</p> <p>Results</p> <p>The rate of misannotated proteins was significantly higher in <it>Mixed</it> groups than in <it>Positive</it> or <it>Negative</it> groups, corroborating the proposed hypothesis. A total of 478 proteins were reannotated and change of signal peptide prediction from negative to positive was the most common. Reannotations triggered the conversion of almost 50% of all <it>Mixed</it> groups, which were further reduced by optimization of signal peptide prediction parameters.</p> <p>Conclusions</p> <p>The methodological novelty proposed here combining orthology and signal peptide prediction proved to be an effective strategy for the identification of proteins showing wrongly N-terminal annotated sequences, and it might have an important impact in the available data for genome-wide searching of potential vaccine and drug targets and proteins involved in host/parasite interactions, as demonstrated for five <it>Plasmodium</it> species.</p>