Archaic chaos: intrinsically disordered proteins in Archaea.
Archaic chaos: intrinsically disordered proteins in Archaea.
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DOI：
10.1186/1752-0509-4-s1-s1
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发表时间：
2010-05-28
影响因子：
--
通讯作者：
Uversky VN
中科院分区：
文献类型：
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作者：
Xue B;Williams RW;Oldfield CJ;Dunker AK;Uversky VN
许多蛋白质或其区域被称为固有无序蛋白质（IDP）和固有无序区域（IDR），在生理条件下在其天然状态下缺乏独特的3D结构，但却实现关键的生物学功能。早期的生物信息学研究表明，IDPs和IDRs在不同的蛋白质组中含量很高，并且主要执行与分子识别和信号转导相关的调节功能。微生物属于一个有趣的生命领域，其成员是微生物，其特征是细菌和真核生物特性的独特马赛克式组合，包括地球上一些最极端环境的居民。随着古细菌基因组数据的扩展（现在已知来自五个不同门的五十多个古细菌物种），以及最近内在疾病预测准确性的提高，是时候重新检查古细菌领域中IDP和IDR的丰度了。分析了53种古菌中IDPs和IDRs的丰度。这些物种的氨基酸组成概况通常彼此相当不同。无序的内容是高度依赖于物种。热蛋白目蛋白质组中有14%的无序残基，而在盐细菌中，这个值增加到34%。在这两个门的蛋白质组中，含有长无序区的蛋白质分别占12%和46%，而完全无序的蛋白质分别占4%和26%。这三种无序含量指标在基因组水平上彼此线性相关。环境因子（如栖息地的盐度、pH和温度）与内禀失调的丰度之间存在弱相关性，不同的环境因子具有不同的失调促进强度。恶劣的环境条件，特别是那些结合了几个不利因素，显然有利于增加障碍内容。内在障碍是高度丰富的功能Pfam结构域的古细菌起源。基于无序度和系统发育树的分析表明，不同纲、不同种间存在着内在无序度的多样性演化。蛋白质是丰富的内在障碍。这些IDPs和IDRs中的一些可能会进化以帮助古菌适应其敌对的栖息地。其他古细菌的IDPs和IDRs具有与细菌和真核生物的IDPs/IDRs相似的重要生物学功能。
Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion of the archaea genome data (more than fifty archaea species from five different phyla are known now), and with recent improvements in the accuracy of intrinsic disorder prediction, it is time to re-examine the abundance of IDPs and IDRs in the archaea domain. The abundance of IDPs and IDRs in 53 archaea species is analyzed. The amino acid composition profiles of these species are generally quite different from each other. The disordered content is highly species-dependent. Thermoproteales proteomes have 14% of disordered residues, while in Halobacteria, this value increases to 34%. In proteomes of these two phyla, proteins containing long disordered regions account for 12% and 46%, whereas 4% and 26% their proteins are wholly disordered. These three measures of disorder content are linearly correlated with each other at the genome level. There is a weak correlation between the environmental factors (such as salinity, pH and temperature of the habitats) and the abundance of intrinsic disorder in Archaea, with various environmental factors possessing different disorder-promoting strengths. Harsh environmental conditions, especially those combining several hostile factors, clearly favor increased disorder content. Intrinsic disorder is highly abundant in functional Pfam domains of the archaea origin. The analysis based on the disordered content and phylogenetic tree indicated diverse evolution of intrinsic disorder among various classes and species of Archaea. Archaea proteins are rich in intrinsic disorder. Some of these IDPs and IDRs likely evolve to help archaea to accommodate to their hostile habitats. Other archaean IDPs and IDRs possess crucial biological functions similar to those of the bacterial and eukaryotic IDPs/IDRs.