Identification of a novel family of sequence repeats among prokaryotes
Identification of a novel family of sequence repeats among prokaryotes
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DOI：
10.1089/15362310252780816
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发表时间：
2002-01-01
期刊：
影响因子：
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通讯作者：
Schouls, Leo M.
中科院分区：
文献类型：
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作者：
Jansen, Rund;van Embden, Jam D. A.;Schouls, Leo M.
基因组序列的快速增加为比较基因组学提供了新的机会。在这份报告中，我们描述了一个新的家庭的重复序列，是存在于细菌和细菌，但不是在真核生物。重复基因座通常由长度为25至37 bp的重复核苷酸段组成，这些核苷酸段与大小与重复序列大致相等的非重复DNA间隔区交替。核苷酸序列和重复序列的大小在一个物种内高度保守，但物种之间的序列没有显示出相似性。由于它们的特征性结构，我们将这个重复基因座家族命名为间隔区散布直接重复序列（SPIDR）。在40多种不同的原核生物中鉴定了SPIDR基因座。结核分枝杆菌等个别物种含有一个SPIDR基因座，而詹氏甲烷球菌等其他物种含有多达20个不同的基因座。一个基因座中重复序列的数量变化很大，从两个重复序列到几十个重复序列。SPIDR基因座两侧是一个共同的300-500 bp的前导序列，这似乎是保守的物种内，但不是物种之间。利用SPIDR基因座对M.结核病广泛用于菌株分型。在其他原核生物中发现SPIDR基因座，包括沙门氏菌、弯曲杆菌和巴斯德氏菌，可能会将这种监测扩展到其他物种。
The rapid increase in genomic sequences provides new opportunities for comparative genomics. In this report, we describe a novel family of repeat sequences that is present in Bacteria and Archaea but not in Eukarya. The repeat loci typically consisted of repetitive stretches of nucleotides with a length of 25 to 37 bp alternated by nonrepetitive DNA spacers of approximately equal size as the repeats. The nucleotide sequences and the size of the repeats were highly conserved within a species, but between species the sequences showed no similarity. Due to their characteristic structure, we have designated this family of repeat loci as SPacers Interspersed Direct Repeats (SPIDR). The SPIDR loci were identified in more than forty different prokaryotic species. Individual species such as Mycobacterium tuberculosis contain one SPIDR locus, while other species such as Methanococcus jannaschii contained up to 20 different loci. The number of repeats in a locus varies greatly from two repeats to several dozens of repeats. The SPIDR loci were flanked by a common 300-500-bp leader sequence, which appeared to be conserved within a species but not between species. The SPIDR locus of M. tuberculosis is extensively used for strain typing. The finding of SPIDR loci in other prokaryotes, including the pathogens Salmonella, Campylobacter, and Pasteurella may extend this surveillance to other species.