Genomic loci of the Porphyromonas gingivalis insertion element IS1126
Genomic loci of the Porphyromonas gingivalis insertion element IS1126
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DOI：
10.1128/iai.67.7.3416-3423.1999
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发表时间：
1999-07-01
影响因子：
3.1
通讯作者：
Duncan, MJ
中科院分区：
文献类型：
--
作者：
Dong, H;Chen, TT;Duncan, MJ
牙龈卟啉单胞菌基因组包含插入元件 IS1126 的多个拷贝。当用 IS1126 探测不同菌株的染色体 DNA 消化物时，每个基因组检测到 25 到 35 个杂交片段，具体取决于菌株，不相关的菌株具有非常不同的限制性片段长度多态性 (RFLP) 模式。当检查特定菌株的不同实验室副本时，IS1126 RFLP 模式非常相似，但观察到微小差异，表明在实验室传代期间发生了与元素相关的变化。年内，牙龈卟啉单胞菌W83的基因组测序、组装和注释将完成。由于重复元件使随机测序的 DNA 片段的组装变得复杂，我们分离并测序了菌株 W83 中 IS1126 拷贝的侧翼区域，我们还分离并测序了菌株 ATCC 33277 中 IS1126 拷贝的侧翼区域，以便比较系统发育差异菌株中的插入位点。我们从菌株 ATCC 33277 中鉴定出 37 个 IS1126 侧翼序列，从菌株中鉴定出 30 个新序列。 W83，在基因之间发现了插入元件，但它转置为另一个插入元件的地方除外。对可识别的侧翼基因或开放阅读框的检查表明，两个菌株中的插入位点不同，除了两个菌株都具有与 Lys-gingipain 基因相邻的插入（J.P.Lewis 和 F.L.Macrina，Infect，Immun，66：3035-3042，1998）。 ATCC 33277 中 IS1126 侧翼的大多数基因或序列存在于 W83 中，但是连续的且不与插入元件相关。因此，在两个菌株中鉴定出基因的地方，它们的顺序保持不变，表明两个基因组的组织相似，但 IS1126 的基因座不同。在两个菌株中，插入元件相关的重复靶位点从 IS1126 的几个拷贝中丢失，提供了元件之间同源重组的证据。基因组之间较大的组织差异，例如缺失和倒位，可能是由插入元件介导的重组事件造成的。
The Porphyromonas gingivalis genome contains multiple copies of insertion element IS1126. When chromosomal DNA digests of different strains were probed with IS1126, between 25 and 35 hybridizing fragments per genome were detected, depending on the strain, Unrelated strains had very different restriction fragment length polymorphism (RFLP) patterns. When different laboratory copies of a specific strain were examined, the IS1126 RFLP patterns were very similar but small differences were observed, indicating that element associated changes had occurred during laboratory passage. Within the nest year, genome sequencing, assembly, and annotation for P. gingivalis W83 will be completed. Because repetitive elements complicate the assembly of randomly sequenced DNA fragments, we isolated and sequenced the flanking regions of IS1126 copies in strain W83, We also isolated and sequenced the flanking regions of IS1126 copies in strain ATCC 33277 in order to compare insertion sites in phylogenetically divergent strains, We identified 37 new sequences flanking IS1126 from strain ATCC 33277 and 30 from strain W83, The insertion element was found between genes except where it transposed into another insertion element. Examination of identifiable flanking genes or open reading frames indicated that the insertion sites were different in the two strains, except that both strains possess an insertion adjacent to the Lys-gingipain gene (J. P. Lewis and F. L. Macrina, Infect, Immun, 66:3035-3042, 1998). Most of the genes or sequences flanking IS1126 in ATCC 33277 were present in W83 but were contiguous and not insertion element associated. Thus, where genes were identified in both strains, their order was maintained, indicating that the two genomes are organized similarly, but the loci of IS1126 are different, In both strains, insertion element-associated duplicated target sites were lost from several copies of IS1126, providing evidence of homologous recombination between elements. Larger organizational differences between the genomes, such as deletions and inversions, may result from insertion element-mediated recombination events.