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
1 Institute of Bioinformatics , International Technology Park, Bangalore, India .
OMICS. 2014 Aug;18(8):499-512. doi: 10.1089/omi.2013.0159. Epub 2014 Jun 17.
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.
在被忽视的热带疾病中，利什曼病是最具破坏性的疾病之一，会导致大量死亡，并造成近200万个伤残调整生命年。皮肤利什曼病是由动基体原生动物寄生虫硕大利什曼原虫引起的一种使人衰弱的疾病，会导致毁容和留下疤痕。硕大利什曼原虫基因组是利什曼原虫属中第一个被测序的基因组。利用蛋白质组学数据注释基因组是一种对传统基因组注释方法的补充方法，被称为蛋白质基因组学。我们采用了基于蛋白质基因组学的方法来绘制硕大利什曼原虫的蛋白质组图谱，并对其基因组进行注释。在本研究中，我们将硕大利什曼原虫前鞭毛体蛋白质组学数据与已注释的硕大利什曼原虫蛋白质数据库进行比对。此外，我们还将蛋白质组学数据与六框翻译的硕大利什曼原虫基因组进行比对。我们总共在硕大利什曼原虫前鞭毛体中鉴定出3613种蛋白质，覆盖了其蛋白质组的43%。我们还鉴定出26个基因组搜索特异性肽段，这导致鉴定出3个以前在硕大利什曼原虫中未被鉴定的新基因。我们还校正了15个基因N端的注释，这导致其蛋白质产物的延伸。我们通过逆转录聚合酶链反应和测序验证了我们的蛋白质基因组学研究结果。此外，我们的研究还鉴定出硕大利什曼原虫中266个N端乙酰化肽段，这是迄今为止利什曼原虫中最大的乙酰化肽数据集之一。该数据集对于专注于被忽视热带疾病的研究人员来说应该是一个宝贵的资源。
