Annotation and evolutionary relationships of a small regulatory RNA gene micF and its target ompF in Yersinia species.
Annotation and evolutionary relationships of a small regulatory RNA gene micF and its target ompF in Yersinia species.
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DOI：
10.1186/1471-2180-3-13
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发表时间：
2003-06-30
期刊：
影响因子：
4.2
通讯作者：
Delihas N
中科院分区：
文献类型：
--
作者：
Delihas N
MICF RNA是细菌中发现的一种小分子调节性RNA，通过与OmpF mRNA5‘UTR相互作用，在转录后调节外膜蛋白F(OmpF)的表达。系统发育学数据可用于RNA/RNA双链结构分析，并有助于阐明调控机制。然而，由于核苷酸序列的相似性或差异性，MICF及其相关基因OmpF和OMPC很难解释。我们通过使用代表“基因特征”的序列作为探针，例如mRNA5‘非编码区序列，可以在基因组序列中准确地定位密切相关的基因。使用NCBI BLAST程序的比对和搜索方法已被用于鉴定鼠疫耶尔森菌和小肠结肠炎耶尔森菌中的MICF、OmpF和OMPC。通过与其他细菌的DNA序列比对，预测了基因的5‘起始点和启动子区域的上游转录调控位点。来自耶尔森氏菌物种的注释基因提供了关于MICF调控系统的系统发育信息。在MICF基因上游的启动子区域，转录调控因子结合位点的序列高度保守，在MICF RNA基因的片段中，序列片段具有高度的保守性和明显的序列变异。在相互作用的RNA转录本、MICF RNA和OmpF mRNA的5‘UTR之间发现了意想不到的巨大进化速度。用MFold程序模拟MICF RNA/OmpF mRNA5‘非编码区双链结构。除了小肠结肠炎耶尔森菌MICF RNA的显著变化外，RNA/RNA相互作用位点等功能结构域似乎在序列上表现出最小的进化漂移。新注释的耶尔森氏菌MICF和OmpF基因以及由此产生的RNA/RNA双链结构为广义双链模型提供了强有力的系统发育支持。当注释基因在明确定义的参考生物体中可用时，使用5‘非编码区签名的比对和搜索方法可能是帮助确定其他基因及其起始点的模型。
micF RNA, a small regulatory RNA found in bacteria, post-transcriptionally regulates expression of outer membrane protein F (OmpF) by interaction with the ompF mRNA 5'UTR. Phylogenetic data can be useful for RNA/RNA duplex structure analyses and aid in elucidation of mechanism of regulation. However micF and associated genes, ompF and ompC are difficult to annotate because of either similarities or divergences in nucleotide sequence. We report by using sequences that represent "gene signatures" as probes, e.g., mRNA 5'UTR sequences, closely related genes can be accurately located in genomic sequences. Alignment and search methods using NCBI BLAST programs have been used to identify micF, ompF and ompC in Yersinia pestis and Yersinia enterocolitica. By alignment with DNA sequences from other bacterial species, 5' start sites of genes and upstream transcriptional regulatory sites in promoter regions were predicted. Annotated genes from Yersinia species provide phylogenetic information on the micF regulatory system. High sequence conservation in binding sites of transcriptional regulatory factors are found in the promoter region upstream of micF and conservation in blocks of sequences as well as marked sequence variation is seen in segments of the micF RNA gene. Unexpected large differences in rates of evolution were found between the interacting RNA transcripts, micF RNA and the 5' UTR of the ompF mRNA. micF RNA/ompF mRNA 5' UTR duplex structures were modeled by the mfold program. Functional domains such as RNA/RNA interacting sites appear to display a minimum of evolutionary drift in sequence with the exception of a significant change in Y. enterocolitica micF RNA. Newly annotated Yersinia micF and ompF genes and the resultant RNA/RNA duplex structures add strong phylogenetic support for a generalized duplex model. The alignment and search approach using 5' UTR signatures may be a model to help define other genes and their start sites when annotated genes are available in well-defined reference organisms.
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影响因子：
3.2
作者：
FERRARIO, M;ERNSTING, BR;MATTHEWS, RG
通讯作者：
MATTHEWS, RG
DOI：
10.1006/bbrc.2002.6559
发表时间：
2002-03-08
影响因子：
3.1
作者：
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通讯作者：
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影响因子：
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作者：
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影响因子：
64.5
作者：
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通讯作者：
Cossart, P
影响因子：
3.6
作者：
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通讯作者：
Foster, JW