Moving from unsequenced to sequenced genome: Reanalysis of the proteome of Leishmania donovani

Abstract

The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-based identification based on related Leishmania species (L. infantum, L. major and L. braziliensis) whose genomes have been sequenced. Recently, the genome of L. donovani was fully sequenced and the data became publicly available. We took advantage of the availability of its genomic sequence to carry out a more accurate proteogenomic analysis of L. donovani proteome using our previously generated dataset. This resulted in identification of 17,504 unique peptides upon database-dependent search against the annotated proteins in L. donovani. These peptides were assigned to 3999 unique proteins in L. donovani. 2296 proteins were identified in both the life stages of L. donovani, while 613 and 1090 proteins were identified only from amastigote and promastigote stages, respectively. The proteomic data was also searched against six-frame translated L. donovani genome, which led to 255 genome search-specific peptides (GSSPs) resulting in identification of 20 novel genes and correction of 40 existing gene models in L. donovani. Biological significance Leishmania donovani genome sequencing was recently completed, which permitted us to use a proteogenomic approach to map its proteome and to carry out annotation of it genome. This resulted in mapping of 50% (3999 proteins) of L. donovani proteome. Our study identified 20 novel genes previously not predicted from the L. donovani genome in addition to correcting annotations of 40 existing gene models. The identified proteins may help in better understanding of stage-specific protein expression profiles in L. donovani and to identify novel stage-specific drug targets in L. donovani which could be used in the treatment of leishmaniasis.

Comprehensive Proteomics Analysis of Glycosomes fromLeishmania donovani

“…Such contaminating proteins have been previously reported in different proteomic studies but it was neatly overcome by using SILAC labeling technique while profiling T. brucei glycosomes (Guther et al, 2014). In our previously published proteogenomic study of L. donovani promastigotes and axenic amastigotes, we identified 3999 proteins (Nirujogi et al, 2014). In glycosomal fractions, we could identify 85 proteins that were not detected in the total proteome of the parasite.…”

Secretome analysis of diarrhea‐inducing strains of Escherichia coli

“…Hypothetical proteins are significant fraction of protein class found in many MS‐based proteomic studies whose existence is predicted based on the computational algorithms . MS‐based protein identification of these uncharacterized proteins provides a direct translational evidence, which can be further studied to ascertain their functional role.…”

An Insight into the Constitutive Proteome Throughout Leishmania donovani Promastigote Growth and Differentiation

“…This protein is a mammalian cytokine ortholog released by basophils in inflammatory processes (MacDonald et al 1991) and its function in the parasite is unknown. Expression of the encoding gene has been demonstrated in promastigotes and amastigotes (Nirujogi et al 2014;Pawar et al 2012), but no hypothetical roles at the first infection stages have been tested. Regarding surface molecule biosynthesis, the glucose-regulated protein 94 (GRP94, LPG3) is involved in lypophosphoglycan (LPG) biosynthesis.…”