Guimarães A C R, Otto T D, Alves-Ferreira M, Miranda A B, Degrave W M
Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brasil.
Genet Mol Res. 2008 Sep 23;7(3):872-82. doi: 10.4238/vol7-3x-meeting05.
Trypanosoma cruzi is the epidemiological agent of Chagas' disease, affecting most of Central and South America, constituting a significant health and socio-economic problem. The parasite has a metabolism largely based on the consumption of amino acids, which participate in a diversity of metabolic pathways, leading to many crucial compounds for the survival of this parasite. Study of its enzymes has the potential to disclose new therapeutic targets and foster the development of new drugs. In this study, we employed computational approaches to reconstruct in silico the amino acid metabolic pathways of T. cruzi, aiming to link genomic information with functional information. For that, protein sequences from 570 EC classes belonging to 25 different pathways in general amino acid metabolism were downloaded from KEGG. A subset of 471 EC classes had at least one sequence deposited. Clustering of the proteins belonging to each EC class was performed using a similarity-based approach implemented in the tool AnEnPi. Reconstruction of the metabolic pathways comprising the amino acid metabolism of T. cruzi was performed by analyzing the output of BLASTP, using as query the dataset of predicted proteins of T. cruzi against all sequences of each individual cluster. This approach allowed us to identify 764 T. cruzi proteins probably involved in the metabolism of amino acids as well as the identification of several putative cases of analogy. Furthermore, we were able to identify several enzymatic activities of T. cruzi that were not previously included in KEGG.
克氏锥虫是恰加斯病的病原体，影响中美洲和南美洲的大部分地区，构成了一个重大的健康和社会经济问题。该寄生虫的新陈代谢很大程度上基于氨基酸的消耗，氨基酸参与多种代谢途径，产生许多对该寄生虫生存至关重要的化合物。对其酶的研究有可能揭示新的治疗靶点并促进新药的开发。在本研究中，我们采用计算方法在计算机上重建克氏锥虫的氨基酸代谢途径，旨在将基因组信息与功能信息联系起来。为此，从KEGG下载了属于一般氨基酸代谢中25条不同途径的570个酶委员会（EC）类别的蛋白质序列。其中471个EC类别至少有一个序列被存档。使用工具AnEnPi中实现的基于相似性的方法对属于每个EC类别的蛋白质进行聚类。通过分析BLASTP的输出结果，以克氏锥虫预测蛋白质数据集作为查询，针对每个单独聚类的所有序列，重建了包含克氏锥虫氨基酸代谢的代谢途径。这种方法使我们能够鉴定出764种可能参与氨基酸代谢的克氏锥虫蛋白质，以及识别出几个推定的类比案例。此外，我们还能够鉴定出克氏锥虫的几种以前未包含在KEGG中的酶活性。
