Finding Protein Sequence Motifs--methods And Applications

在过去的十年中，基因组序列和蛋白质结构的快速积累伴随着序列数据库搜索方法的重大进步。NCBI开发的强大的位置特定迭代BLAST(PSI-BLAST)方法形成了我们在蛋白质基序分析方面的工作基础。此外，还应用了隐马尔可夫模型(HMM)和蛋白质结构比较方法。在过去的一年里，我们在对几类蛋白质的分类、进化和功能的详细分析方面取得了进一步的进展。特别是，我们详细研究了原核生物毒素-抗毒素盒和防御自私成分的系统中涉及的蛋白质结构域。我们先前提出，所谓的Cas蛋白组成了一个新的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片段，从而修正了这一假说。CASS似乎最有可能是一个通过RNAi机制发挥作用的针对噬菌体和质粒的原核防御系统。这一系统的功能似乎涉及到将外来基因片段整合到古生菌和细菌的染色体中，从而产生对各自病原体的遗传免疫力。然而，这种遗传在进化规模上似乎是极其不稳定的，以至于即使在密切相关的原核生物中，独特的psiRNAs的谱系也被完全替换，推测是为了响应优势噬菌体和质粒的快速变化的谱系。我们在CAS系统上的工作促进了实验研究，所提出的机制已经得到了部分实验验证。我们还使用计算方法确定了一种新的毒素-抗毒素系统，该系统被预测通过RNA结合或切割发挥作用。此外，我们还探索了真核生物中蛋白质创新的机制，特别是不同类别的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.