Finding Protein Sequence Motifs--methods And Applications

基因组序列和蛋白质结构在过去十年中的快速积累已经被序列数据库搜索方法的重大进展所证实。NCBI开发的强大的位置特异性迭代BLAST（PSI-BLAST）方法构成了我们蛋白质基序分析工作的基础。此外，隐马尔可夫模型（HMM）和蛋白质结构的比较方法。在过去的一年中，我们在详细分析几类蛋白质的分类，进化和功能方面取得了进一步的进展。特别是，我们详细研究了参与原核毒素-抗毒素盒和防御自私元素系统的蛋白质结构域。我们以前提出，所谓的Cas蛋白质组包含一种新的DNA修复系统。cas基因与CRISPR的关联，特别是在CRISPR单元中存在与噬菌体和质粒基因同源的独特插入物，以修改这一假设。卡斯似乎最有可能是一种通过RNAi机制发挥功能的原核防御系统。这个系统的功能似乎涉及到整合到古细菌和细菌的染色体产生遗传免疫力，以各自的代理人的外源基因片段。然而，似乎这种遗传在进化尺度上是极其不稳定的，使得即使在密切相关的原核生物中，独特的psiRNAs的库也被完全替换，推测是响应于快速变化的显性质粒和质粒的库。我们对cas系统的工作已经激发了实验研究，所提出的机理已经得到了部分实验验证。我们还使用计算方法来确定一种新的毒素-抗毒素系统，该系统预计通过RNA结合或切割发挥作用。此外，我们还探讨了真核生物中蛋白质创新的机制，特别是各种多结构域蛋白质的进化模式。

The rapid accumulation of genome sequences and protein structures during the last decade has been paralleled by major advances in sequence database search methods. The powerful Position-Specific Iterating BLAST (PSI-BLAST) method developed at the NCBI formed the basis of our work on protein motif analysis. In addition, Hidden Markov Models (HMM) and protein structure comparison methods were applied. During the last year, we made further progress in detailed analysis of the classification, evolution, and functions of several classes of proteins. In particular, we studied in detail the protein domains that are involved in prokaryotic toxin-antitoxin cassettes and in systems of defense against selfish elements. We proposed previously that the group of so-called Cas proteins comprise a novel DNA repair system. The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes made to modify this hypothesis. It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism. The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. However, it appears that this inheritance is extremely unstable on the evolutionary scale such that the repertoires of unique psiRNAs are completely replaced even in closely related prokaryotes, presumably, in response to rapidly changing repertoires of dominant phages and plasmids. Our work on the cas system has stimulated exprimental research, and the proposed mechanism has already received partial experimental validation. We also used computational methods to identify a novel toxin-antitoxin system that is predicted to function via RNA binding or cleavage. In addition, we explored mechanisms of protein innovation in eukaryotes, in particular, the patterns of evolution of vairous classes of multidomain proteins.