Gopal Shubha, Srinivas Vanishree, Zameer Farhan, Kreft Jürgen
Department of Studies in Microbiology, University of Mysore, Manasagangothri, Mysore, India.
In Silico Biol. 2009;9(5-6):407-14. doi: 10.3233/ISB-2009-0409.
Thiol:disulfide redox metabolism (TDRM) is a central metabolic network in all living cells. However, numerous proteins with different biochemical functions and several structural domains are involved, making it not trivial to identify and annotate its constituents in sequenced genomes. We developed an uncomplicated approach to solve the problem using existing web-based tools and public databases with the gram-positive bacterium Listeria monocytogenes EGD-e as a model organism. A pattern search for the Cys-Xaa-Xaa-Cys (CXXC) motif--a hallmark of TDRM proteins--in the genome sequence of the bacterium yielded 156 proteins. After initial refinement by protein and domain analysis, 14 candidate proteins remained. Subsequent detailed analyses, supported by modeling of 3D structures and data integration yielded 6 thioredoxin-like proteins plus thioredoxin reductase, glutaredoxin, one redox-sensitive regulator, one peptide methionine reductase - all typical TDRM constituents - and three putative novel components of the TDRM. For all 14 proteins orthologues were found in other Listeria species. Homology searches and phylogenetic analyses showed that related proteins are present mainly in other Firmicutes. This fast approach required minimal resources. It is immediately applicable to any genome with appropriate modifications and should be practicable also for other conserved, functionally important amino acid motifs.
二硫键氧化还原代谢（TDRM）是所有活细胞中的核心代谢网络。然而，涉及众多具有不同生化功能的蛋白质和多个结构域，这使得在已测序基因组中识别和注释其组成成分并非易事。我们以革兰氏阳性细菌单核细胞增生李斯特菌EGD-e作为模式生物，利用现有的基于网络的工具和公共数据库，开发了一种简单的方法来解决这个问题。在该细菌的基因组序列中对Cys-Xaa-Xaa-Cys（CXXC）基序（TDRM蛋白的一个标志）进行模式搜索，得到了156种蛋白质。经过蛋白质和结构域分析的初步筛选，剩下14种候选蛋白质。随后在三维结构建模和数据整合的支持下进行详细分析，得到了6种硫氧还蛋白样蛋白以及硫氧还蛋白还原酶、谷氧还蛋白、一种氧化还原敏感调节因子、一种肽甲硫氨酸还原酶（均为典型的TDRM组成成分）以及三种TDRM的假定新成分。在其他李斯特菌物种中发现了所有14种蛋白质的直系同源物。同源性搜索和系统发育分析表明，相关蛋白质主要存在于其他厚壁菌门细菌中。这种快速方法所需资源最少。经过适当修改后可立即应用于任何基因组，对于其他保守的、功能重要的氨基酸基序也应该是可行的。
