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。具体地说，我们详细研究了真核RNA干扰机制中涉及的蛋白质结构域，表明真核RNAi的蛋白质机制是由参与DNA修复和RNA加工的祖先古生菌、细菌和噬菌体蛋白拼凑而成的。我们还使用计算方法确定了一种新的毒素-抗毒素系统，预计这些系统通过RNA结合或裂解和其他不同的机制发挥作用。我们探索了真核生物蛋白质创新的一般机制，特别是各种类型的多结构域蛋白质的进化模式，并表明有限的混杂结构域对真核蛋白质组和信号网络的多样性和进化性做出了重要贡献。我们研究了几个独立结构域的分布和进化，这些结构域可能对真核细胞的起源具有重要意义。特别是，研究表明，细菌和古菌中存在的4-乙烯基还原酶(V4R)蛋白结构域与TRAPP1囊泡拴系复合体的Bet3亚基同源，后者在所有真核生物中都是保守的。这表明，这是第一次，一个关键的真核运输蛋白的原核起源。

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. Specifically, we studied in detail the protein domains that are involved in eukaryotic RNA interference mechanisms and showed that the protein machinery of eukaryotic RNAi was pieced together from ancestral archaeal, bacterial and phage proteins that are involved in DNA repair and RNA processing. We also used computational methods to identify a novel toxin-antitoxin systems that are predicted to function via RNA binding or cleavage and other, diverse mechanisms. We explored the general mechanisms of protein innovation in eukaryotes, in particular, the patterns of evolution of vairous classes of multidomain proteins and showed that a limited repertoire of promiscuous domains makes a major contribution to the diversity and evolvability of eukaryotic proteomes and signaling networks. We investigated the distribution and evolution of several individual domains that might have been important for the origin of eukaryotic cells. In particular, it has been shown that the 4-vinyl reductase (V4R) protein domain present in bacteria and archaea is homologous to the Bet3 subunit of the TRAPP1 vesicle-tethering complex that is conserved in all eukaryotes. This suggests, for the first time, a prokaryotic origin for one of the key eukaryotic trafficking proteins.