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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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Leishmania Donovani

TISSUE(S): Diploid Cell

DISEASE(S): Visceral Leishmaniasis

SUBMITTER: Akhilesh Pandey

LAB HEAD: Akhilesh Pandey

PROVIDER: PXD004338 | Pride | 2016-12-14

REPOSITORIES: Pride

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

Nirujogi Raja Sekhar RS Pawar Harsh H Renuse Santosh S Kumar Praveen P Chavan Sandip S Sathe Gajanan G Sharma Jyoti J Khobragade Sweta S Pande Janhavee J Modak Bhakti B Prasad T S Keshava TS Harsha H C HC Patole Milind S MS Pandey Akhilesh A

Journal of proteomics 20130509

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 a ...[more]

PMID: 23665000

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Project description:Protozoa of the genus Leishmania are the causative agents of leishmaniasis in humans. These parasites cycle between promastigotes in the sand fly mid-gut and amastigotes in phagolysosome of mammalian macrophages. During infection, host up-regulate nitric oxide synthase and parasite induce host arginase expression, both of which use arginine as a substrate. These elevated activities deplete macrophage arginine pools, a situation that invading Leishmania must overcome since it is an essential amino acid. Leishmania donovani imports exogenous arginine via a mono-specific amino acid transporter (AAP3) and utilizes it primarily through the polyamine pathway to provide precursors for trypanothione biosynthesis. Here we report the discovery of a pathway whereby promastigote and amastigote forms of the Leishmania sense the lack of environmental arginine and respond with rapid up-regulation in AAP3 expression and activity, as well as several other transporters. Significantly, this arginine deprivation response is also activated in parasites during macrophage infection. Phosphoproteomic analyses of L. donovani promastigotes have implicated a Mitogen-Activated Protein Kinase 2 (MPK2)-mediated signaling cascade in this response and L. mexicana mutants lacking MPK2 are unable to respond to arginine deprivation. In this study, we established that Leishmania cells sense the absence of arginine in their environment; both in culture (axenic promastigotes and amastigotes) and in macrophages during infection (amastigotes). This study describes the first amino acid deprivation sensing mechanism and the pathway that transduce this response, and reveals a novel host-pathogen metabolic interplay. Total RNA from Ten Leishmania donovani samples were analyzed using RNA-Seq. Cells from two life stages (promastigotes and amastigotes) were grown in axenic culture in the presence and absense of arginine. For each condition two biological replicates were grown and analyzed. In addition two macrophage grown amastigotes were analyzed.

Project description:Post Kala Azar Dermal Leishmaniasis (PKDL) is a non-fatal dermal sequel of Visceral Leishmaniasis (VL), caused by protozoan parasite Leishmania donovani. On the global scenario, PKDL in mainly restricted to distinct zones of South Asia (India, Nepal and Bangladesh) and East Africa, mainly Sudan. In India, the most prominent fatal form of leishmaniasis present is VL, affecting entirely the eastern region of the country. The clinical presentation of VL and PKDL differ substantially; where VL patients suffer from sustained fever, hepatospleenomegaly, weight loss and anemia, PKDL patients manifest dermal lesions in the form of macular, nodular and polymorphic. Although, compared to VL, the mortality rate of PKDL is significantly lower, yet it is observed as a stigmatizing disease that brings a substantial socioeconomic burden, further intensified by a hesitancy of patients, to obtain treatment, or due to noncompliance. Lesions, especially the polymorphic forms, are parasite-rich, concluding that PKDL plays a crucial role in the anthroponotic transmission of VL. PKDL patients with Macular lesions, having comparatively lower parasitic load, and thus lacks detection sensitivity with standard techniques like rK39 (73% sensitivity), Leishmanin skin test (54% sensitivity) and Histopathological studies with patients’ skin biopsy sample (7-33% sensitivity) and is often misdiagnosed as Vitiligo cases. In order to completely eliminate Kala-azar in Southeast Asia, proper identification of various routes of the disease is essential, which could efficiently distinguish between cured PKDL and active PKDL as well as active PKDL from other cross disease like Leprosy and Vitiligo. Till now very less work has been done towards biomarker identification for PKDL from patients’ plasma. Most of the methods for disease identification are based on highly invasive tissue biopsy followed by PCR/qPCR. Recently investigations from our group have demonstrated the presence of novel glycoproteins in the circulating immune complexes (CICs) from serum, as biomarkers for early identification of PKDL patients. An Immune complex (IC), sometimes called an antigen-antibody complex, is a molecule formed from the integral binding of an antibody to a soluble antigen. After an antigen-antibody reaction, the immune complexes can be subject to any number of responses, including complement deposition, opsonisation, phagocytosis, or processing by proteases. Accumulation of ICs leads to a broad spectrum of pro-inflammatory effects, including activation of the complement cascade and induction of cytokine secretion. These complexes may also be deposited in tissues and vessel walls, leading to inflammation, tissue damage and, ultimately, disease manifestations. Immune complexes also affect disease progression and outcome in various disorders through the induction of pro-inflammatory or anti-inflammatory cytokines. In the present study we hypothesize that the CICs’ proteome is altered among PKDL patients with different dermal manifestations (Macular and Polymorphic) as compared to Cured individuals (CR) and Healthy controls (HI). The aim of this current study is to identify differentially expressed CIC proteomic profile among different forms PKDL patients as compared to HI. The differential protein expression of specific unique peptide fragments, representing specific proteins, could be used as diagnostic biomarkers in early detection of both Macular and Polymorphic PKDL cases. In this prospective study, we included PKDL patients with Macular and/or Polymorphic lesion, Cured individuals and HI. Among the enrolled patients, blood samples were collected from 20 primarily confirmed PKDL patients with Macular lesions, 20 primarily confirmed PKDL patients with Polymorphic lesions, 12 Cured individuals previously suffering from PKDL and 12 Healthy individuals; collected during the period of 2015-2016, stored at -80°C. Next the CICs were purified from PKDL patients’ plasma and LC MS/MS analysis was performed using Q-ExactivePlusOrbitrap mass spectrometer. This work for the first time revealed the differential CICs proteome profile among different forms of PKDL patients as compared to their Cured and Healthy counterparts.

Project description:Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis or kala-azar, the most severe form of leishmaniasis in humans. To date, our understanding of the molecular mechanisms associated with the pathogenicity of Leishmania infection is still limited. RNA interference—collectively RNA silencing pathways—participates in the regulation of various biological processes in most eukaryotic cells. Complexes of Argonaute proteins with small RNAs are core components of the RNA interference system and play a key role in silencing gene expression. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference pathways to promote their survival. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Western blot analysis showed that protein abundance of infected macrophage Argonaute 1 (Ago1) was selectively and significantly higher than that of non-infected control at 24 h post-infection, suggesting that Ago1 plays a role in pathogenicity. In fact, siRNA-mediated downregulation of Ago1 enhanced Leishmania clearance from infected host cells, linking macrophage Ago1 to Leishmania virulence. To investigate the mechanisms of host Ago1 in Leishmania pathogenesis, a stable isotope labeling by amino acids in cell culture (SILAC)-based whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins were dependent on the level of macrophage Ago1. Moreover, the proteomic-based detailed biochemical analysis showed that Leishmania modulated host RNA-induced silencing complex (RISC) composition during infection, strongly suggesting macrophage RISC targeting. Strikingly, Leishmania proteins were detected as part of host RISC in infected cells. Together, our results demonstrate that Leishmania targets host RNA interference machinery to promote its survival inside the host macrophage.

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	Ama_SCX_10.msf	Msf