Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
PLoS One. 2011;6(11):e25570. doi: 10.1371/journal.pone.0025570. Epub 2011 Nov 1.
Vibrio cholerae, the enteropathogenic gram negative bacteria is one of the main causative agents of waterborne diseases like cholera. About 1/3(rd) of the organism's genome is uncharacterised with many protein coding genes lacking structure and functional information. These proteins form significant fraction of the genome and are crucial in understanding the organism's complete functional makeup. In this study we report the general structure and function of a family of hypothetical proteins, Domain of Unknown Function 3233 (DUF3233), which are conserved across gram negative gammaproteobacteria (especially in Vibrio sp. and similar bacteria). Profile and HMM based sequence search methods were used to screen homologues of DUF3233. The I-TASSER fold recognition method was used to build a three dimensional structural model of the domain. The structure resembles the transmembrane beta-barrel with an axial N-terminal helix and twelve antiparallel beta-strands. Using a combination of amphipathy and discrimination analysis we analysed the potential transmembrane beta-barrel forming properties of DUF3233. Sequence, structure and phylogenetic analysis of DUF3233 indicates that this gram negative bacterial hypothetical protein resembles the beta-barrel translocation unit of autotransporter Va secretory mechanism with a gene organisation that differs from the conventional Va system.
霍乱弧菌是一种革兰氏阴性肠道致病菌，是导致霍乱等水源性疾病的主要病原体之一。大约有三分之一的基因组尚未被描述，许多蛋白质编码基因缺乏结构和功能信息。这些蛋白质构成了基因组的重要部分，对于理解生物体的完整功能组成至关重要。在这项研究中，我们报告了一类假定蛋白家族的一般结构和功能，即未知功能域 3233（DUF3233），它们在革兰氏阴性γ变形菌（尤其是弧菌属和类似细菌）中保守。使用基于轮廓和 HMM 的序列搜索方法来筛选 DUF3233 的同源物。使用 I-TASSER 折叠识别方法构建该结构域的三维结构模型。该结构类似于跨膜β桶，具有轴向 N 端螺旋和十二个反平行β-链。我们结合疏水性和判别分析，分析了 DUF3233 潜在的跨膜β桶形成特性。对 DUF3233 的序列、结构和系统发育分析表明，这种革兰氏阴性细菌的假定蛋白类似于自转运子 Va 分泌机制的β桶转运单元，但其基因组织与传统的 Va 系统不同。
