The Experimental Proteome of Leishmania infantum Promastigote and Its Usefulness for Improving Gene Annotations

Abstract

Leishmania infantum causes visceral leishmaniasis (kala-azar), the most severe form of leishmaniasis, which is lethal if untreated. A few years ago, the re-sequencing and de novo assembling of the L. infantum (JPCM5 strain) genome was accomplished, and now we aimed to describe and characterize the experimental proteome of this species. In this work, we performed a proteomic analysis from axenic cultured promastigotes and carried out a detailed comparison with other Leishmania experimental proteomes published to date. We identified 2352 proteins based on a search of mass spectrometry data against a database built from the six-frame translated genome sequence of L. infantum. We detected many proteins belonging to organelles such as glycosomes, mitochondria, or flagellum, as well as many metabolic enzymes and many putative RNA binding proteins and molecular chaperones. Moreover, we listed some proteins presenting post-translational modifications, such as phosphorylations, acetylations, and methylations. On the other hand, the identification of peptides mapping to genomic regions previously annotated as non-coding allowed for the correction of annotations, leading to the N-terminal extension of protein sequences and the uncovering of eight novel protein-coding genes. The alliance of proteomics, genomics, and transcriptomics has resulted in a powerful combination for improving the annotation of the L. infantum reference genome.

Leishmania infantum (JPCM5) Transcriptome, Gene Models and Resources for an Active Curation of Gene Annotations

“…Additionally, it may not be adequate for general repositories (ENA, NCBI) to update a genome sequence every time the annotation of a sole gene is changed. However, genomic annotations are being continuously improved on the basis of new experimental data, such as proteomics, for instance [ 50 ]. In addition, many groups working on particular genes/proteins are contributing to greatly increasing our knowledge about them, and, in consequence, functional annotations of genes/proteins are continuously improved, and these should be registered in the databases as soon as possible and the contributors recognized.…”

Expanded Proteomic Survey of the Human Parasite Leishmania major Focusing on Changes in Null Mutants of the Golgi GDP-Mannose/Fucose/Arabinopyranose Transporter LPG2 and of the Mitochondrial Fucosyltransferase FUT1

“…No predicted mitochondrion-encoded proteins were identified, despite the inclusion of many of them in our predicted proteome database (described in Materials and Methods). Often these are omitted from proteomic computational analysis completely, and due to their hydrophobicity, they are often not detected by standard or general approaches similar to those used here ( 38 – 40 ).…”

The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast

“…The equivalent proteins in L. donovani , LdBPK_080080 (LINF08), LdBPK_320410 (LINF32), and LdBPK_353150 (LINF35) were recovered in both promastigotes and amastigotes, but LdBPK_080080 showed a weak signal [ 108 ]. This might explain why only LINF32 and LINF35 were found in L. infantum promastigotes [ 109 ].…”