Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 196608 Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
Department of Genetics and Biotechnology, St. Petersburg State University, 199034 Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
Int J Mol Sci. 2017 Oct 16;18(10):2155. doi: 10.3390/ijms18102155.
Amyloids are protein fibrils with characteristic spatial structure. Though amyloids were long perceived to be pathogens that cause dozens of incurable pathologies in humans and mammals, it is currently clear that amyloids also represent a functionally important form of protein structure implicated in a variety of biological processes in organisms ranging from archaea and bacteria to fungi and animals. Despite their social significance, plants remain the most poorly studied group of organisms in the field of amyloid biology. To date, amyloid properties have only been demonstrated in vitro or in heterologous systems for a small number of plant proteins. Here, for the first time, we performed a comprehensive analysis of the distribution of potentially amyloidogenic proteins in the proteomes of approximately 70 species of land plants using the Waltz and SARP (Sequence Analysis based on the Ranking of Probabilities) bioinformatic algorithms. We analyzed more than 2.9 million protein sequences and found that potentially amyloidogenic proteins are abundant in plant proteomes. We found that such proteins are overrepresented among membrane as well as DNA- and RNA-binding proteins of plants. Moreover, seed storage and defense proteins of most plant species are rich in amyloidogenic regions. Taken together, our data demonstrate the diversity of potentially amyloidogenic proteins in plant proteomes and suggest biological processes where formation of amyloids might be functionally important.
淀粉样蛋白是具有特征空间结构的蛋白质纤维。尽管淀粉样蛋白长期以来一直被认为是病原体，会导致人类和哺乳动物数十种无法治愈的病理学，但目前清楚的是，淀粉样蛋白也代表了一种功能重要的蛋白质结构形式，涉及从古菌和细菌到真菌和动物等生物体的各种生物学过程。尽管淀粉样蛋白具有重要的社会意义，但在淀粉样蛋白生物学领域，植物仍然是研究最少的生物群体。迄今为止，淀粉样蛋白特性仅在体外或少数植物蛋白的异源系统中得到证明。在这里，我们首次使用 Waltz 和 SARP（基于概率排序的序列分析）生物信息学算法，对大约 70 种陆地植物的蛋白质组中的潜在淀粉样蛋白形成蛋白进行了全面分析。我们分析了超过 290 万个蛋白质序列，发现潜在的淀粉样蛋白在植物蛋白质组中非常丰富。我们发现，这类蛋白质在植物的膜蛋白以及 DNA 和 RNA 结合蛋白中大量存在。此外，大多数植物物种的种子储存和防御蛋白富含淀粉样蛋白区域。总之，我们的数据表明植物蛋白质组中存在多种潜在的淀粉样蛋白形成蛋白，并提示了可能具有功能重要性的淀粉样蛋白形成的生物学过程。
