Simple sequence repeats in prokaryotic genomes
Simple sequence repeats in prokaryotic genomes
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DOI：
10.1073/pnas.0702412104
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发表时间：
2007-05-15
影响因子：
11.1
通讯作者：
Shah, Apurva
中科院分区：
文献类型：
--
作者：
Mrazek, Jan;Guo, Xiangxue;Shah, Apurva
DNA序列中的简单序列重复序列(SSR)由短寡核苷酸的串联迭代组成，可能具有区别于一般DNA序列的功能和/或结构特性。由于滑链突变，它们的长度是可变的，也可能影响DNA分子或编码蛋白质的局部结构。长SSR在真核生物中很常见，但在大多数原核生物中很少见。在病原体中，SSR可以通过一种抵消宿主免疫反应的策略来增强病原体群体的抗原变异。我们分析了SSR在>；300原核生物基因组中的表达，并报告了不同原核生物以及不同类型SSR之间的显著差异。LSSRs由短的寡核苷酸组成(长度为1-4bp，命名为LSSR1-4)，通常存在于基因组减少的宿主适应病原体中，而这些基因组在宿主外的自然环境中并不容易存活。相反，由较长的寡核苷酸组成的LSSRs(长度为5-11bp，命名为LSSR5-11)主要存在于非病原体和具有大基因组的条件病原体中。不同长度的SSR之间的比较表明，LSSR1-4可能是通过选择保持的。这与一些LSSR1-4在增强抗原变异方面的既定作用是一致的。相比之下，LSSR5-11在某些基因组中的丰度可能反映了SSR的总体扩张趋势，而不是它们在生物体生理中的具体作用。讨论了基因组在SSR表示及其可能的解释方面的差异。
Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in > 300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1-4 bp length, designated LSSR1-4) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5-11 bp length, designated LSSR5-11) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR1-4 are likely maintained by selection. This is consistent with the established role of some LSSR1-4 in enhancing antigenic variance. By contrast, abundance of LSSR5-11 in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed.