Stem-loop structures in prokaryotic genomes.
Stem-loop structures in prokaryotic genomes.
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DOI：
10.1186/1471-2164-7-170
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发表时间：
2006-07-04
期刊：
影响因子：
4.4
通讯作者：
Paolella G
中科院分区：
文献类型：
--
作者：
Petrillo M;Silvestro G;Di Nocera PP;Boccia A;Paolella G
预测细菌基因组表达序列中的二级结构可以研究相应RNA的自发折叠。这在未翻译的mRNA区域中尤其相关，其中碱基配对较少受到与翻译机器的相互作用的影响。相对较大的茎环显著有助于形成更复杂的二级结构，这对于控制基因表达的序列元件的活性通常是重要的。系统分析了40个细菌全基因组中茎环结构（SLS）的分布。SLS被搜索为测量至少12 bp的茎，长度为5至100 nt的邻接环。允许股骨柄中的G-U配对。在自然基因组中发现的SLS总是比那些预期随机形成的具有可比大小和组成的序列中的SLS更多和更稳定。绝大多数的SLS落在蛋白质编码区，但富集特定的，非随机的，SLS亚群的更高的稳定性观察到几个物种的染色体的基因间区域内。在低GC厚壁菌门中，大多数更高稳定性的基因间SLS类似于典型的rho非依赖性转录终止子，但非常频繁地在5 '端具有与3'尿苷互补的额外的富含A的延伸。在所有物种中，在基因间空间内观察到明显偏向的SLS分布，其中大部分集中在侧翼CDS的3 '端侧。一些基因间SLS区域是新的重复序列家族的成员。对40种不同细菌基因组中SLS特征和分布的深入分析表明，所有物种中都存在这种结构的非随机群体。这些结构中的许多是可转录的，并且可能参与转录终止的控制，或者可能作为RNA元件，其可以增强共转录的mRNA的稳定性或周转。在耶尔森氏菌、博德特氏菌和肠球菌中发现了三个以前未描述的重复序列家族。
Prediction of secondary structures in the expressed sequences of bacterial genomes allows to investigate spontaneous folding of the corresponding RNA. This is particularly relevant in untranslated mRNA regions, where base pairing is less affected by interactions with the translation machinery. Relatively large stem-loops significantly contribute to the formation of more complex secondary structures, often important for the activity of sequence elements controlling gene expression. Systematic analysis of the distribution of stem-loop structures (SLSs) in 40 wholly-sequenced bacterial genomes is presented. SLSs were searched as stems measuring at least 12 bp, bordering loops 5 to 100 nt in length. G-U pairing in the stems was allowed. SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and composition. The large majority of SLSs fall within protein-coding regions but enrichment of specific, non random, SLS sub-populations of higher stability was observed within the intergenic regions of the chromosomes of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs. Some intergenic SLS regions are members of novel repeated sequence families. In depth analysis of SLS features and distribution in 40 different bacterial genomes showed the presence of non random populations of such structures in all species. Many of these structures are plausibly transcribed, and might be involved in the control of transcription termination, or might serve as RNA elements which can enhance either the stability or the turnover of cotranscribed mRNAs. Three previously undescribed families of repeated sequences were found in Yersiniae, Bordetellae and Enterococci.
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影响因子：
3.2
作者：
CARLOMAGNO, MS;RICCIO, A;BRUNI, CB
通讯作者：
BRUNI, CB
影响因子：
5.8
作者：
Coward, E
通讯作者：
Coward, E
影响因子：
7
作者：
Katz, L;Burge, CB
通讯作者：
Burge, CB
影响因子：
14.9
作者：
Davidsen, T;Rodland, EA;Tonjum, T
通讯作者：
Tonjum, T
影响因子：
2.6
作者：
Jin, RZ;Novick, RP
通讯作者：
Novick, RP