Department of Biology and the Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
PLoS One. 2011;6(12):e28919. doi: 10.1371/journal.pone.0028919. Epub 2011 Dec 21.
In Gram-negative bacteria, type IV pili (TFP) have long been known to play important roles in such diverse biological phenomena as surface adhesion, motility, and DNA transfer, with significant consequences for pathogenicity. More recently it became apparent that Gram-positive bacteria also express type IV pili; however, little is known about the diversity and abundance of these structures in Gram-positives. Computational tools for automated identification of type IV pilins are not currently available.
To assess TFP diversity in Gram-positive bacteria and facilitate pilin identification, we compiled a comprehensive list of putative Gram-positive pilins encoded by operons containing highly conserved pilus biosynthetic genes (pilB, pilC). A surprisingly large number of species were found to contain multiple TFP operons (pil, com and/or tad). The N-terminal sequences of predicted pilins were exploited to develop PilFind, a rule-based algorithm for genome-wide identification of otherwise poorly conserved type IV pilins in any species, regardless of their association with TFP biosynthetic operons (http://signalfind.org). Using PilFind to scan 53 Gram-positive genomes (encoding >187,000 proteins), we identified 286 candidate pilins, including 214 in operons containing TFP biosynthetic genes (TBG+ operons). Although trained on Gram-positive pilins, PilFind identified 55 of 58 manually curated Gram-negative pilins in TBG+ operons, as well as 53 additional pilin candidates in operons lacking biosynthetic genes in ten species (>38,000 proteins), including 27 of 29 experimentally verified pilins. False positive rates appear to be low, as PilFind predicted only four pilin candidates in eleven bacterial species (>13,000 proteins) lacking TFP biosynthetic genes.
We have shown that Gram-positive bacteria contain a highly diverse set of type IV pili. PilFind can be an invaluable tool to study bacterial cellular processes known to involve type IV pilus-like structures. Its use in combination with other currently available computational tools should improve the accuracy of predicting the subcellular localization of bacterial proteins.
在革兰氏阴性菌中，已经长期以来人们知道，四型菌毛（TFP）在表面黏附、运动和 DNA 转移等多种生物现象中发挥着重要作用，对致病性有重要影响。最近，人们逐渐意识到革兰氏阳性菌也表达四型菌毛；然而，人们对这些结构在革兰氏阳性菌中的多样性和丰度知之甚少。目前还没有用于自动识别四型菌毛菌毛蛋白的计算工具。
为了评估革兰氏阳性菌中的 TFP 多样性并促进菌毛蛋白的鉴定，我们编制了一个由含有高度保守菌毛生物合成基因（pilB、pilC）的操纵子编码的推定革兰氏阳性菌菌毛蛋白的综合列表。令人惊讶的是，发现许多物种都含有多个 TFP 操纵子（pil、com 和/或 tad）。预测菌毛蛋白的 N 端序列被用于开发 PilFind，这是一种基于规则的算法，用于在任何物种中识别其他保守性较差的四型菌毛蛋白，而无需考虑它们与 TFP 生物合成操纵子的关联（http://signalfind.org）。使用 PilFind 扫描 53 个革兰氏阳性基因组（编码 >187,000 个蛋白质），我们鉴定了 286 个候选菌毛蛋白，其中 214 个在含有 TFP 生物合成基因的操纵子中（TBG+ 操纵子）。尽管 PilFind 是在革兰氏阳性菌菌毛蛋白上进行训练的，但它在 TBG+ 操纵子中识别了 55 个经过人工精心挑选的革兰氏阴性菌毛蛋白，以及在十个物种（>38,000 个蛋白质）中缺少生物合成基因的操纵子中鉴定了 53 个额外的菌毛蛋白候选物，其中包括 29 个经过实验验证的菌毛蛋白中的 27 个。假阳性率似乎很低，因为 PilFind 在十一个缺乏 TFP 生物合成基因的细菌物种（>13,000 个蛋白质）中仅预测了四个菌毛蛋白候选物。
我们已经表明，革兰氏阳性菌含有一套高度多样化的四型菌毛。PilFind 可以成为研究已知涉及四型菌毛样结构的细菌细胞过程的宝贵工具。将其与其他当前可用的计算工具结合使用，应该可以提高预测细菌蛋白亚细胞定位的准确性。
