Nirujogi Raja Sekhar, Pawar Harsh, Renuse Santosh, Kumar Praveen, Chavan Sandip, Sathe Gajanan, Sharma Jyoti, Khobragade Sweta, Pande Janhavee, Modak Bhakti, Prasad T S Keshava, Harsha H C, Patole Milind S, Pandey Akhilesh
Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Rajiv Gandhi University of Health Sciences, Bangalore 560041, India.
J Proteomics. 2014 Jan 31;97:48-61. doi: 10.1016/j.jprot.2013.04.021. Epub 2013 May 9.
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.
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. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
动质体原生动物寄生虫杜氏利什曼原虫是黑热病或内脏利什曼病的病原体。黑热病是利什曼病的一种严重形式，在大多数未经治疗的病例中是致命的。迄今为止，对杜氏利什曼原虫的蛋白质组分析研究是基于已测序基因组的相关利什曼原虫物种（婴儿利什曼原虫、硕大利什曼原虫和巴西利什曼原虫）进行基于同源性的鉴定。最近，杜氏利什曼原虫的基因组已被完全测序，数据已公开可用。我们利用其基因组序列的可用性，使用我们之前生成的数据集对杜氏利什曼原虫蛋白质组进行了更准确的蛋白质基因组分析。在对杜氏利什曼原虫注释蛋白进行基于数据库的搜索后，这导致鉴定出17504个独特肽段。这些肽段被分配到杜氏利什曼原虫的3999个独特蛋白质中。在杜氏利什曼原虫的两个生命阶段都鉴定出2296种蛋白质，而分别仅从无鞭毛体和前鞭毛体阶段鉴定出613种和1090种蛋白质。蛋白质组数据还与六框架翻译的杜氏利什曼原虫基因组进行了比对，这产生了255个基因组搜索特异性肽段（GSSPs），从而鉴定出20个新基因并纠正了杜氏利什曼原虫中40个现有基因模型。
杜氏利什曼原虫基因组测序最近完成，这使我们能够使用蛋白质基因组学方法来绘制其蛋白质组图谱并对其基因组进行注释。这导致绘制出杜氏利什曼原虫蛋白质组的50%（3999种蛋白质）。我们的研究除了纠正40个现有基因模型的注释外，还鉴定出20个以前未从杜氏利什曼原虫基因组预测到的新基因。所鉴定的蛋白质可能有助于更好地理解杜氏利什曼原虫中阶段特异性蛋白质表达谱，并鉴定杜氏利什曼原虫中可用于治疗利什曼病的新的阶段特异性药物靶点。本文是名为《微生物蛋白质组学趋势》的特刊的一部分。
