Weeks Katie E, Chuzhanova Nadia A, Donnison Iain S, Scott Ian M
Cardiff School of Computer Science, Cardiff University, Queen's Buildings, Roath, Cardiff, UK.
BMC Evol Biol. 2007 Apr 2;7:51. doi: 10.1186/1471-2148-7-51.
Evolutionary processes in gene regulatory regions are major determinants of organismal evolution, but exceptionally challenging to study. We explored the possibilities of evolutionary analysis of phylogenetic footprints in 5'-noncoding sequences (NCS) from 27 ribulose-1,5-bisphosphate carboxylase small subunit (rbcS) genes, from three dicot families (Brassicaceae, Fabaceae and Solanaceae).
Sequences of up to 400 bp encompassing proximal promoter and 5'-untranslated regions were analyzed. We conducted phylogenetic footprinting by several alternative methods: generalized Lempel-Ziv complexity (CLZ), multiple alignments with DIALIGN and ALIGN-M, and the MOTIF SAMPLER Gibbs sampling algorithm. These tools collectively defined 36 conserved blocks of mean length 12.8 bp. On average, 12.5 blocks were found in each 5'-NCS. The blocks occurred in arrays whose relative order was absolutely conserved, confirming the existence of 'conserved modular arrays' in promoters. Identities of half of the blocks confirmed past rbcS research, including versions of the I-box, G-box, and GT-1 sites such as Box II. Over 90% of blocks overlapped DNase-protected regions in tomato 5'-NCS. Regions characterized by low CLZ in sliding-window analyses were also frequently associated with DNase-protection. Blocks could be assigned to evolutionary hierarchies based on taxonomic distribution and estimated age. Lineage divergence dates implied that 13 blocks found in all three plant families were of Cretaceous antiquity, while other family-specific blocks were much younger. Blocks were also dated by formation of multigene families, using genome and coding sequence information. Dendrograms of evolutionary relations of the 5'-NCS were produced by several methods, including: cluster analysis using pairwise CLZ values; evolutionary trees of DIALIGN sequence alignments; and cladistic analysis of conserved blocks.
Dicot 5'-NCS contain conserved modular arrays of recurrent sequence blocks, which are coincident with functional elements. These blocks are amenable to evolutionary interpretation as hierarchies in which ancient, taxonomically widespread blocks can be distinguished from more recent, taxon-specific ones.
基因调控区域的进化过程是生物进化的主要决定因素，但研究极具挑战性。我们探索了对来自三个双子叶植物科（十字花科、豆科和茄科）的27个核酮糖-1,5-二磷酸羧化酶小亚基（rbcS）基因的5'非编码序列（NCS）中的系统发育足迹进行进化分析的可能性。
分析了长达400 bp的包含近端启动子和5'非翻译区的序列。我们通过几种替代方法进行系统发育足迹分析：广义莱姆尔-齐夫复杂度（CLZ）、使用DIALIGN和ALIGN-M进行多序列比对，以及MOTIF SAMPLER吉布斯采样算法。这些工具共同定义了36个平均长度为12.8 bp的保守块。每个5' NCS平均发现12.5个块。这些块以相对顺序绝对保守的阵列形式出现，证实了启动子中存在“保守模块阵列”。一半块的特征与过去的rbcS研究一致，包括I-box、G-box和GT-1位点（如Box II）的变体。超过90%的块与番茄5' NCS中的DNA酶保护区域重叠。在滑动窗口分析中以低CLZ为特征的区域也经常与DNA酶保护相关。根据分类分布和估计年龄，可将块分配到进化层次结构中。谱系分歧日期表明，在所有三个植物科中发现的13个块具有白垩纪的古老性，而其他特定科的块则年轻得多。还利用基因组和编码序列信息，通过多基因家族的形成对块进行了年代测定。通过几种方法生成了5' NCS进化关系的树状图，包括：使用成对CLZ值的聚类分析；DIALIGN序列比对的进化树；以及保守块的分支分析。
双子叶植物的5' NCS包含重复序列块的保守模块阵列，这些阵列与功能元件一致。这些块适合作为进化层次结构进行解释，其中古老的、分类学上广泛分布的块可以与较新的、特定分类群的块区分开来。
