Email updates

Keep up to date with the latest news and content from Malaria Journal and BioMed Central.

Open Access Highly Accessed Methodology

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

Armando de Menezes Neto1, Denise A Alvarenga1, Antônio M Rezende2, Sarah S Resende1, Ricardo de Souza Ribeiro1, Cor JF Fontes3, Luzia H Carvalho1 and Cristiana F Alves de Brito1*

Author Affiliations

1 Laboratory of Malaria, Rene Rachou Research Institute, Fiocruz Minas, Belo Horizonte, Brazil

2 Laboratory of Cellular and Molecular Parasitology, Rene Rachou Research Institute, Fiocruz Minas, Belo Horizonte, Brazil

3 Universitary Hospital Julio Muller, Cuiabá, Mato Grosso, Brazil

For all author emails, please log on.

Malaria Journal 2012, 11:375  doi:10.1186/1475-2875-11-375

Published: 15 November 2012

Abstract

Background

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 Plasmodium species.

Methods

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).

Results

The rate of misannotated proteins was significantly higher in Mixed groups than in Positive or Negative 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 Mixed groups, which were further reduced by optimization of signal peptide prediction parameters.

Conclusions

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 Plasmodium species.

Keywords:
Signal peptide; Orthologous; Gene annotation; Malaria; Plasmodium