IS4 family goes genomic.
IS4 family goes genomic.
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DOI：
10.1186/1471-2148-8-18
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发表时间：
2008-01-23
影响因子：
3.4
通讯作者：
Mahillon, Jacques
中科院分区：
文献类型：
--
作者：
De Palmenaer, Daniel;Siguier, Patricia;Mahillon, Jacques
插入序列 (IS) 是小型、可移动的 DNA 实体，能够在原核基因组中扩展并触发重要的重排。要了解它们在进化中的作用，准确的信息系统分类至关重要。 IS4 家族由约 70 个元素组成，与其他一些家族一样，其内部分歧水平极高，阻碍了其分类。完整基因组序列的不断增加为发现其他 IS4 元件提供了宝贵的来源。在本研究中，该基因组数据库用于更新 IS4 家族的结构和功能定义。在 500 多个已测序的细菌和古菌基因组中总共收集了 227 个 IS4 相关序列，比初始库存增加了三倍多。发现了清晰的划分为七个连贯的亚群以及三个新兴的家族，它们表现出独特的结构和功能特性。 IS4 家族零星地存在于 17% 的分析基因组中，其中大多数显示单个或少量 IS4 元件。仅在某些病原体以及某些极端微生物中检测到显着的扩增，这表明某些元素可能参与细菌和古菌的适应和/或进化。最后，应该指出的是，一些 IS4 亚群和两个新兴科优先出现在特定门或仅出现在特定属内。 IS4 和新兴家族目前的分类学更新将有助于对来自正在进行的基因组测序的未来元素进行分类。它们的基因组影响范围很窄，以及 IS 贫乏和 IS 丰富的繁荣原核生物的存在表明，这些家族，可能还有一般的 IS，偶尔被用作基因组灵活性和进化的工具，而不仅仅是代表自我维持的 DNA 实体。
Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of ~70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family. A total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS4 subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus. The present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.
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影响因子：
56.9
作者：
FRASER, CM;GOCAYNE, JD;VENTER, JC
通讯作者：
VENTER, JC
DOI：
10.1073/pnas.95.18.10716
发表时间：
1998-09-01
影响因子：
11.1
作者：
Goryshin, IY;Miller, JA;Reznikoff, WS
通讯作者：
Reznikoff, WS
影响因子：
7
作者：
Jaffe, JD;Stange-Thomann, N;Church, GM
通讯作者：
Church, GM
影响因子：
3.6
作者：
De Palmenaer, D;Vermeiren, C;Mahillon, J
通讯作者：
Mahillon, J
影响因子：
64.8
作者：
Heidelberg JF;Eisen JA;Nelson WC;Clayton RA;Gwinn ML;Dodson RJ;Haft DH;Hickey EK;Peterson JD;Umayam L;Gill SR;Nelson KE;Read TD;Tettelin H;Richardson D;Ermolaeva MD;Vamathevan J;Bass S;Qin H;Dragoi I;Sellers P;McDonald L;Utterback T;Fleishmann RD;Nierman WC;White O;Salzberg SL;Smith HO;Colwell RR;Mekalanos JJ;Venter JC;Fraser CM
通讯作者：
Fraser CM