Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.
Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.
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DOI：
10.1371/journal.pone.0144275
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发表时间：
2015-12-22
期刊：
影响因子：
3.7
通讯作者：
Hartig, Joerg S.
中科院分区：
文献类型：
--
作者：
Rehm, Charlotte;Wurmthaler, Lena A.;Hartig, Joerg S.
在原核生物中，单位大小为1-5个核苷酸（nt）的简单序列重复（SSR）是引起相位和抗原变异的原因。尽管在细菌中注意到七聚体重复的丰度增加，但关于6-9 nt的SSR的报道很少。特别是具有折叠成G-四链体（G4）结构的倾向的富含G的重复序列很少受到关注。原核基因组的计算机分析显示推定的G4形成序列是丰富的。这份报告的重点是一个令人惊讶的丰富的G-丰富的重复类型GGGNATC在黄单胞菌和蓝藻，如念珠藻。我们详细研究了野油菜黄单胞菌致病变种的基因组。campestris ATCC 33913（Xcc）、轴足黄单胞菌致病变种（Xanthomonas axonopodis pv.）citri str.306（Xac）和念珠藻属菌株PCC 7120（Ana）。在这三种生物中，重复序列遍布整个基因组，在非编码区过度表达。观察到重复单元数的广泛变化，重复数范围从2到26个单元。然而，检测到对四个单位的明显偏好。四个单元的强偏差与G4形成的四个连续G-段的要求一致。在利用CD光谱的生物物理研究中发现了G4形成的一致重复序列的证据。富G重复序列优选位于对齐的开放阅读框（ORF）之间，并且在编码区中或在不同的ORF之间代表不足。富含G的重复序列优先位于反义链上ORF上游50 bp的距离内或有义链上终止密码子50 bp内。全转录组序列数据的分析表明，大多数重复序列被转录。重复区域附近的遗传位点显示出增加的基因组稳定性。总之，我们介绍和表征一类特殊的高度丰富和广泛传播的四链体形成重复序列的细菌。
In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.