Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, United Kingdom.
J Struct Biol. 2010 May;170(2):202-15. doi: 10.1016/j.jsb.2010.02.008. Epub 2010 Feb 21.
In recent years, a number of bacterial coiled-coil proteins have been characterised which have roles in cell growth and morphology. Several have been shown to have a cytoskeletal function and some have been proposed to have an IF-like character in particular. We recently demonstrated in Streptomyces coelicolor a cytoskeletal role of Scy, a large protein implicated in filamentous growth, whose sequence is dominated by an unusual coiled-coil repeat. We present a detailed analysis of this 51-residue repeat and conclude that it is likely to form a parallel dimeric non-canonical coiled coil based on hendecads but with regions of local underwinding reflecting highly periodic modifications in the sequence. We also demonstrate that traditional sequence similarity searching is insufficient to identify all but the close orthologues of such repeat-dominated proteins, but that by an analysis of repeat periodicity and composition, remote homologues can be found. One clear candidate, despite a great size discrepancy and unremarkable sequence identity, is the known filament-former FilP in the same species. Both proteins appear distinct from the archetypal bacterial IF-like protein; they therefore may constitute a new class of bacterial filamentous protein. The similar sequence characteristics of both suggest their likely oligomer state and a possible mechanism for higher-order assembly into filaments. Another remote homologue in Actinomyces was highlighted by this method. Further, a known coiled-coil protein, DivIVA, appears to share some of these sequence characteristics.
近年来，已经鉴定出许多细菌卷曲螺旋蛋白，它们在细胞生长和形态中发挥作用。一些已经被证明具有细胞骨架功能，一些被认为具有 IF 样特征。我们最近在链霉菌中证明了 Scy 的细胞骨架作用，Scy 是一种与丝状生长有关的大型蛋白，其序列主要由一种不寻常的卷曲螺旋重复组成。我们对这个 51 个残基的重复序列进行了详细分析，并得出结论，它可能形成一种基于 hendecads 的平行二聚体非典型卷曲螺旋，但具有局部扭曲的区域，反映了序列中高度周期性的修饰。我们还证明，传统的序列相似性搜索不足以识别除密切同源物以外的此类重复主导蛋白，但通过对重复周期性和组成的分析，可以找到远程同源物。尽管大小差异很大且序列同一性不明显，但一个明显的候选者是同一物种中已知的丝状形成蛋白 FilP。这两种蛋白质都与典型的细菌 IF 样蛋白不同；因此，它们可能构成了一种新的细菌丝状蛋白类。这两种蛋白质的相似序列特征表明它们可能的寡聚状态和形成丝状的高级组装的可能机制。这种方法还突出了放线菌中的另一个远程同源物。此外，一种已知的卷曲螺旋蛋白 DivIVA 似乎也具有这些序列特征。
