Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.
Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.
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DOI：
10.1111/j.1365-2958.2007.05978.x
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发表时间：
2007-12
影响因子：
3.6
通讯作者：
Jiménez-Zurdo JI
中科院分区：
文献类型：
--
作者：
del Val C;Rivas E;Torres-Quesada O;Toro N;Jiménez-Zurdo JI
细菌小非编码RNA(SRNAs)被认为是响应环境信号的基因表达的新的广泛调控因子。在这里，我们提出了第一次在固氮内共生菌苜蓿中华根瘤菌中寻找sRNA编码基因，通过对其基因间隔区进行全基因组计算分析。获得了8个相关的α蛋白细菌的比较序列数据，并用eQRNA和RNAz程序对物种间的两两比对进行了评分，作为互补的预测工具，以确定与假定的非编码RNA相对应的保守和稳定的二级结构。Northern实验证实，从最初的32个候选基因中选出的最有可能的sRNA基因中，有8个预测的基因座表达了小转录本。这一结果支持联合使用eQRNA和RNAz作为一种强大的策略来识别细菌中的新sRNA。此外，7个转录本在自由生活和共生条件下以不同的方式积累。对检测到的转录本5‘端的实验图谱显示，它们的编码基因以自主转录单位的形式组织起来，具有可识别的启动子，在大多数情况下，还具有终止签名。这些发现提示了与α-蛋白细菌与其真核宿主相互作用相关的sRNA的新的调节功能。
Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Comparative sequence data from eight related α-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non-coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free-living and symbiotic conditions. Experimental mapping of the 5′-ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of α-proteobacteria with their eukaryotic hosts.
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影响因子：
14.9
作者：
Mandin P;Repoila F;Vergassola M;Geissmann T;Cossart P
通讯作者：
Cossart P
通过比较基因组分析鉴定蓝细菌非编码RNA。
影响因子：
12.3
作者：
Axmann, Ilka M;Kensche, Philip;Vogel, Jorg;Kohl, Stefan;Herzel, Hanspeter;Hess, Wolfgang R
通讯作者：
Hess, Wolfgang R
DOI：
10.1073/pnas.89.5.1646
发表时间：
1992-03-01
影响因子：
11.1
作者：
GOETHALS, K;VANMONTAGU, M;HOLSTERS, M
通讯作者：
HOLSTERS, M
DOI：
10.1073/pnas.0407269101
发表时间：
2004-11-23
影响因子：
11.1
作者：
Barnett, MJ;Tolman, CJ;Long, SR
通讯作者：
Long, SR
影响因子：
1.6
作者：
Chen, S;Lesnik, EA;Blyn, LB
通讯作者：
Blyn, LB