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

Abstract

Leishmania infantum is causative of visceral leishmaniasis (kala-azar), the most severe form of leishmaniasis, lethal if untreated. Few years ago, re-sequencing and de novo assembling of the L. infantum (strain JPCM5) genome was accomplished, and now we aimed to describe and characterize the experimental proteome of this species. In this work, we have performed a proteomic analysis from axenic cultured promastigotes and carried out a detailed comparison with other Leishmania experimental proteomes published to date. We identified 2,352 proteins based on the search of mass spectrometry data against a database built from the six-frame translated genome sequence of L. infantum. We have detected many proteins belonging to organelles such as glycosomes, mitochondria or flagellum, as well as many metabolic enzymes, and a large number of putative RNA binding proteins and molecular chaperones. Moreover, we listed the proteins presenting post-translational modifications, such as phosphorylations, acetylations and methylations, among others. On the other hand, the identification of peptides mapping to genomic regions previously annotated as non-coding has allowed to correct annotations, leading to 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 L. infantum reference genome annotation.

An expanded proteomic survey of the human parasiteLeishmania majorfocusing on changes in null mutants of the Golgi GDP-Mannose/Fucose/ArabinopyranosetransporterLPG2or the mitochondrial fucosyltransferaseFUT1

“…No predicted mitochondrion-encoded proteins were identified, despite the inclusion of many of them in our predicted proteome database (described in the 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)(39)(40).…”

How Common is Gain of Function

“…Multiple and drastic environmental changes are dealt with in such a way as to maintain proteostasis, by degradation of aggregated, misfolded or unfolded proteins. A number of heat shock proteins of various classes has been identified in the proteome of Leishmania infantum [7]. Further demonstrating the importance of protein stability is the tradeoff between protein stability and activity, a marking feature and general mechanism of all cold-adapted enzymes, where the flexible active site becomes tolerant of mutations.…”