COMPILATION, ALIGNMENT, AND PHYLOGENETIC-RELATIONSHIPS OF DNA-POLYMERASES
COMPILATION, ALIGNMENT, AND PHYLOGENETIC-RELATIONSHIPS OF DNA-POLYMERASES
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DOI：
10.1093/nar/21.4.787
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发表时间：
1993-02-25
影响因子：
14.9
通讯作者：
ITO, J
中科院分区：
文献类型：
--
作者：
BRAITHWAITE, DK;ITO, J
在大多数情况下，本更新的氨基酸序列的多重比对只是在可能的情况下添加到我们的原始比对(1)中。由于B族的比对中增加了大量的序列，我们在明显的保守序列块之间的一些区域改变了原有的比对。新的序列是通过将每个序列与已经对齐的最接近的相关序列对齐来添加的，或者在许多情况下与已经对齐的最接近的相关序列组对齐。最近加入UWGCG（威斯康星大学遗传计算机组）程序包的PILEUP是一个多重比对程序，广泛用于尝试和定位密切相关序列组中的重要同源性。然后将这些新形成的高度相关序列组重新划分，使其符合基于原始比对的新组中这些序列的先前比对的整个比对。在之前的论文中，所有的最终调整都必须由眼睛来完成，正如上面所述，在B族中，添加的序列导致了对原始对齐的一些改进，当它们与整个手工对齐组合时，这一点对眼睛来说是显而易见的。使用Felsenstein的philips程序包（71），特别是下面大纲中提到的程序，我们为9个A家族DNA聚合酶（图2A和2B）和47个B家族DNA聚合酶（图3A和3B）生成了系统发生树。A族的树是根据图1A中的比对创建的，使用了在以下位置发现的最保守的区域：798至814、877至998、1047至1090、1104至1123、1131至1158、1175至1206、1236至1251、1284至1305、1322至1340和1365至1379。利用SEQBOOT程序对这些保守区域进行重组，生成100个bootstrap样本。利用DNADIST程序，利用Kimura-2参数法将样本转化为距离矩阵。然后使用UPGMA方法将得到的矩阵输入到NEIGHBOR程序中，生成大约100棵树。最后，使用CONSENSE程序将这些树简化为单个树。然后使用两种不同的方法绘制最后的树以供发表。图2A和3A中的树是由DRAWGRAM程序设置创建的，以产生一个表型类型树，图2B和3B中的树是由DRAWTREE程序创建的。B族的树是根据图1B中的排列，按照相同的步骤，使用在以下位置发现的最保守区域创建的：1407至1760、1885至1901、1956至1990、2081至2100、2181至2210和2280至2320。B族DNA聚合酶可细分为两个亚家族，即蛋白质引物DNA聚合酶亚家族和rna引物DNA聚合酶亚家族。
SEQUENCE ALIGNMENT The multiple alignments ofthe amino acid sequences for this update were performed in most cases by merely adding on to our original alignments (1) where possible. Due to the large number of sequences added to the alignment for Family B we have changed the original alignment in some areas between obvious blocks of conserved sequences. Thenewer sequences were added by aligning each to the closest related sequence already aligned, or in many cases to the closest related group of sequences already aligned. A more recent addition to the UWGCG (University of Wisconsin Genetic Computer Group) program package, PILEUP, a multiple alignment program, was used extensively to try and locate significant homology in groups of closely related sequences. These newly formed groups of highly related sequences were then regapped to conform with the entire alignment based upon the previous alignment of those sequences in the new group from the original alignment. As in the previous paper, all the final adjustments had to be made by eye and, as stated above, in Family B the added sequences led to some improvements to the original alignment that became evident to the eye when they were being combined with the entire alignment by hand.GENERATION OF PHYLOGENETIC TREES FOR THE DNA POLYMERASE DOMAINS Using Felsenstein's PHYLIP program package (71), specifically the programs named in the outline below, we generated phylogenetic trees for the 9 Family A DNA polymerases (Figures 2A and 2B) and for the 47 Family B DNA polymerases (Figures 3A and 3B). The trees for Family A were created from the alignment in Figure 1A using the most conserved regions found at the following positions: 798 to 814, 877 to 998, 1047 to 1090, 1104 to 1123, 1131 to 1158, 1175 to 1206, 1236 to 1251, 1284 to 1305, 1322 to 1340, and 1365 to 1379. These conserved regions were recombined and 100 bootstrap samples were generated using SEQBOOT program. Using the DNADIST program, we turned the samples into distance matrices using the Kimura-2 parameter method. The resulting matrices were then input to the NEIGHBOR program using the UPGMA method to produce approximately 100 trees. Finally those trees were reduced to a single tree using the CONSENSE program. This final tree was then plotted for publication using two different methods. The trees in Figures 2A and 3A were created by the DRAWGRAM program setup to produce a phenogram type tree and the trees in Figures 2B and 3B were created by the DRAWTREE program. The trees for Family B were created from the alignment in Figure 1B, according to the same procedure, using the most conserved regions found at the following positions: 1407 to 1760, 1885 to 1901, 1956 to 1990, 2081 to 2100, 2181 to 2210, and 2280 to 2320. The Family B DNA polymerases can be subdivided into two subfamilies, the protein-primed DNA polymerase subfamily and the RNA-primed DNA polymerase subfamily.