Neglected tropical diseases and omics science: Proteogenomics analysis of the promastigote stage of leishmania major parasite

Harsh Pawar, Santosh Renuse, Sweta N. Khobragade, Sandip Chavan, Gajanan Sathe, Praveen Kumar, Kiran N. Mahale, Kalpita Gore, Aditi Kulkarni, Tanwi Dixit, Rajesh Raju, T. S.Keshava Prasad, H. C. Harsha, Milind S. Patole, Akhilesh Pandey

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Among the neglected tropical diseases, leishmaniasis is one of the most devastating, resulting in significant mortality and contributing to nearly 2 million disability-adjusted life years. Cutaneous leishmaniasis is a debilitating disorder caused by the kinetoplastid protozoan parasite Leishmania major, which results in disfiguration and scars. L. major genome was the first to be sequenced within the genus Leishmania. Use of proteomic data for annotating genomes is a complementary approach to conventional genome annotation approaches and is referred to as proteogenomics. We have used a proteogenomics-based approach to map the proteome of L. major and also annotate its genome. In this study, we searched L. major promastigote proteomic data against the annotated L. major protein database. Additionally, we searched the proteomic data against six-frame translated L. major genome. In all, we identified 3613 proteins in L. major promastigotes, which covered 43% of its proteome. We also identified 26 genome search-specific peptides, which led to the identification of three novel genes previously not identified in L. major. We also corrected the annotation of N-termini of 15 genes, which resulted in extension of their protein products. We have validated our proteogenomics findings by RT-PCR and sequencing. In addition, our study resulted in identification of 266 N-terminally acetylated peptides in L. major, one of the largest acetylated peptide datasets thus far in Leishmania. This dataset should be a valuable resource to researchers focusing on neglected tropical diseases.

Original languageEnglish (US)
Pages (from-to)499-512
Number of pages14
JournalOMICS A Journal of Integrative Biology
Volume18
Issue number8
DOIs
StatePublished - Aug 1 2014
Externally publishedYes

Fingerprint

Neglected Diseases
Leishmania major
Parasites
Genes
Genome
Proteomics
Leishmania
Proteome
Peptides
Protein Databases
Cutaneous Leishmaniasis
Proteins
Leishmaniasis
Quality-Adjusted Life Years
Proteogenomics
Cicatrix
Research Personnel
Polymerase Chain Reaction
Mortality

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Genetics

Cite this

Neglected tropical diseases and omics science : Proteogenomics analysis of the promastigote stage of leishmania major parasite. / Pawar, Harsh; Renuse, Santosh; Khobragade, Sweta N.; Chavan, Sandip; Sathe, Gajanan; Kumar, Praveen; Mahale, Kiran N.; Gore, Kalpita; Kulkarni, Aditi; Dixit, Tanwi; Raju, Rajesh; Prasad, T. S.Keshava; Harsha, H. C.; Patole, Milind S.; Pandey, Akhilesh.

In: OMICS A Journal of Integrative Biology, Vol. 18, No. 8, 01.08.2014, p. 499-512.

Research output: Contribution to journalArticle

Pawar, H, Renuse, S, Khobragade, SN, Chavan, S, Sathe, G, Kumar, P, Mahale, KN, Gore, K, Kulkarni, A, Dixit, T, Raju, R, Prasad, TSK, Harsha, HC, Patole, MS & Pandey, A 2014, 'Neglected tropical diseases and omics science: Proteogenomics analysis of the promastigote stage of leishmania major parasite', OMICS A Journal of Integrative Biology, vol. 18, no. 8, pp. 499-512. https://doi.org/10.1089/omi.2013.0159
Pawar, Harsh ; Renuse, Santosh ; Khobragade, Sweta N. ; Chavan, Sandip ; Sathe, Gajanan ; Kumar, Praveen ; Mahale, Kiran N. ; Gore, Kalpita ; Kulkarni, Aditi ; Dixit, Tanwi ; Raju, Rajesh ; Prasad, T. S.Keshava ; Harsha, H. C. ; Patole, Milind S. ; Pandey, Akhilesh. / Neglected tropical diseases and omics science : Proteogenomics analysis of the promastigote stage of leishmania major parasite. In: OMICS A Journal of Integrative Biology. 2014 ; Vol. 18, No. 8. pp. 499-512.
@article{569f572104e949599586964d9b0df0cd,
title = "Neglected tropical diseases and omics science: Proteogenomics analysis of the promastigote stage of leishmania major parasite",
abstract = "Among the neglected tropical diseases, leishmaniasis is one of the most devastating, resulting in significant mortality and contributing to nearly 2 million disability-adjusted life years. Cutaneous leishmaniasis is a debilitating disorder caused by the kinetoplastid protozoan parasite Leishmania major, which results in disfiguration and scars. L. major genome was the first to be sequenced within the genus Leishmania. Use of proteomic data for annotating genomes is a complementary approach to conventional genome annotation approaches and is referred to as proteogenomics. We have used a proteogenomics-based approach to map the proteome of L. major and also annotate its genome. In this study, we searched L. major promastigote proteomic data against the annotated L. major protein database. Additionally, we searched the proteomic data against six-frame translated L. major genome. In all, we identified 3613 proteins in L. major promastigotes, which covered 43{\%} of its proteome. We also identified 26 genome search-specific peptides, which led to the identification of three novel genes previously not identified in L. major. We also corrected the annotation of N-termini of 15 genes, which resulted in extension of their protein products. We have validated our proteogenomics findings by RT-PCR and sequencing. In addition, our study resulted in identification of 266 N-terminally acetylated peptides in L. major, one of the largest acetylated peptide datasets thus far in Leishmania. This dataset should be a valuable resource to researchers focusing on neglected tropical diseases.",
author = "Harsh Pawar and Santosh Renuse and Khobragade, {Sweta N.} and Sandip Chavan and Gajanan Sathe and Praveen Kumar and Mahale, {Kiran N.} and Kalpita Gore and Aditi Kulkarni and Tanwi Dixit and Rajesh Raju and Prasad, {T. S.Keshava} and Harsha, {H. C.} and Patole, {Milind S.} and Akhilesh Pandey",
year = "2014",
month = "8",
day = "1",
doi = "10.1089/omi.2013.0159",
language = "English (US)",
volume = "18",
pages = "499--512",
journal = "OMICS A Journal of Integrative Biology",
issn = "1536-2310",
publisher = "Mary Ann Liebert Inc.",
number = "8",

}

TY - JOUR

T1 - Neglected tropical diseases and omics science

T2 - Proteogenomics analysis of the promastigote stage of leishmania major parasite

AU - Pawar, Harsh

AU - Renuse, Santosh

AU - Khobragade, Sweta N.

AU - Chavan, Sandip

AU - Sathe, Gajanan

AU - Kumar, Praveen

AU - Mahale, Kiran N.

AU - Gore, Kalpita

AU - Kulkarni, Aditi

AU - Dixit, Tanwi

AU - Raju, Rajesh

AU - Prasad, T. S.Keshava

AU - Harsha, H. C.

AU - Patole, Milind S.

AU - Pandey, Akhilesh

PY - 2014/8/1

Y1 - 2014/8/1

N2 - Among the neglected tropical diseases, leishmaniasis is one of the most devastating, resulting in significant mortality and contributing to nearly 2 million disability-adjusted life years. Cutaneous leishmaniasis is a debilitating disorder caused by the kinetoplastid protozoan parasite Leishmania major, which results in disfiguration and scars. L. major genome was the first to be sequenced within the genus Leishmania. Use of proteomic data for annotating genomes is a complementary approach to conventional genome annotation approaches and is referred to as proteogenomics. We have used a proteogenomics-based approach to map the proteome of L. major and also annotate its genome. In this study, we searched L. major promastigote proteomic data against the annotated L. major protein database. Additionally, we searched the proteomic data against six-frame translated L. major genome. In all, we identified 3613 proteins in L. major promastigotes, which covered 43% of its proteome. We also identified 26 genome search-specific peptides, which led to the identification of three novel genes previously not identified in L. major. We also corrected the annotation of N-termini of 15 genes, which resulted in extension of their protein products. We have validated our proteogenomics findings by RT-PCR and sequencing. In addition, our study resulted in identification of 266 N-terminally acetylated peptides in L. major, one of the largest acetylated peptide datasets thus far in Leishmania. This dataset should be a valuable resource to researchers focusing on neglected tropical diseases.

AB - Among the neglected tropical diseases, leishmaniasis is one of the most devastating, resulting in significant mortality and contributing to nearly 2 million disability-adjusted life years. Cutaneous leishmaniasis is a debilitating disorder caused by the kinetoplastid protozoan parasite Leishmania major, which results in disfiguration and scars. L. major genome was the first to be sequenced within the genus Leishmania. Use of proteomic data for annotating genomes is a complementary approach to conventional genome annotation approaches and is referred to as proteogenomics. We have used a proteogenomics-based approach to map the proteome of L. major and also annotate its genome. In this study, we searched L. major promastigote proteomic data against the annotated L. major protein database. Additionally, we searched the proteomic data against six-frame translated L. major genome. In all, we identified 3613 proteins in L. major promastigotes, which covered 43% of its proteome. We also identified 26 genome search-specific peptides, which led to the identification of three novel genes previously not identified in L. major. We also corrected the annotation of N-termini of 15 genes, which resulted in extension of their protein products. We have validated our proteogenomics findings by RT-PCR and sequencing. In addition, our study resulted in identification of 266 N-terminally acetylated peptides in L. major, one of the largest acetylated peptide datasets thus far in Leishmania. This dataset should be a valuable resource to researchers focusing on neglected tropical diseases.

UR - http://www.scopus.com/inward/record.url?scp=84904999159&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84904999159&partnerID=8YFLogxK

U2 - 10.1089/omi.2013.0159

DO - 10.1089/omi.2013.0159

M3 - Article

C2 - 24937402

AN - SCOPUS:84904999159

VL - 18

SP - 499

EP - 512

JO - OMICS A Journal of Integrative Biology

JF - OMICS A Journal of Integrative Biology

SN - 1536-2310

IS - 8

ER -