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A survey of non-coding RNAs in the social and predatory myxobacterium Myxococcus xanthus DK1622.
Molecular Omics ( IF 3.0 ) Pub Date : 2020-08-06 , DOI: 10.1039/d0mo00068j David E Whitworth 1 , Martin T Swain 1
Molecular Omics ( IF 3.0 ) Pub Date : 2020-08-06 , DOI: 10.1039/d0mo00068j David E Whitworth 1 , Martin T Swain 1
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Prokaryotic ncRNAs are important regulators of gene expression, and can be involved in complex signalling networks. The myxobacteria are model organisms for studies into multicellular development and microbial predation, being particularly renowned for their large genomes and exceptionally sophisticated signalling networks. However, apart from two specific examples, little is known about their regulatory ncRNAs. Here, we integrate bioinformatic predictions and transcriptome sequence data to provide a comprehensive survey of the ncRNAs made by the exemplar myxobacterium M. xanthus DK1622. M. xanthus RNA-seq data from four experimental conditions was interrogated to identify transcripts mapping outside coding sequences and to known ncRNAs. The resulting 37 ncRNAs were clustered on the genome and most (30/37) were conserved across the myxobacteria. A majority of ncRNAs (22/37) were intergenic, while 13 were at least partially antisense to protein-coding genes. Predicted promoter and terminator sequences explained the start/stop sites of 18 ncRNAs. mRNA targets for the ncRNAs were predicted, including plausible candidates for a known regulatory ncRNA. 22 ncRNAs were differentially expressed by nutrient availability and expression of 25 predicted targets was found to correlate strongly with that of their regulatory ncRNAs. Sharing of predicted mRNA targets by multiple ncRNAs suggests that some ncRNAs might regulate each other within signalling networks. This genomic survey of M. xanthus ncRNA biology provides a starting point for further studies of myxobacterial ncRNAs, which are likely to have important functions in these industrially important and sophisticated organisms.
中文翻译：
社交和掠食性粘杆菌Myxococcus xanthus DK1622中非编码RNA的调查。
原核ncRNA是基因表达的重要调控因子，可参与复杂的信号网络。粘细菌是用于研究多细胞发育和微生物捕食的模型生物，因其庞大的基因组和异常复杂的信号网络而闻名。但是，除了两个具体的例子，对其调节性ncRNA知之甚少。在这里，我们整合了生物信息学预测和转录组序列数据，以提供对示例性粘杆菌M. xanthus DK1622制作的ncRNA的全面调查。黄花木兰询问来自四个实验条件的RNA-seq数据，以鉴定映射到编码序列外部和已知ncRNA的转录本。所得的37个ncRNA聚集在基因组上，并且大多数（30/37）在整个粘细菌中均保守。大多数ncRNA（22/37）是基因间的，而13个至少部分地反义于蛋白质编码基因。预测的启动子和终止子序列解释了18个ncRNA的起始/终止位点。预测了ncRNA的mRNA靶标，包括已知调控ncRNA的合理候选物。营养素可利用性差异表达22种ncRNA，发现25个预测靶标的表达与其调控性ncRNA强烈相关。多个ncRNA共享预测的mRNA靶标表明某些ncRNA可能在信号网络内相互调节。这项基因组调查X.anthus ncRNA生物学为进一步研究粘细菌ncRNA提供了起点，这些细菌在这些工业上重要且复杂的生物中可能具有重要功能。
更新日期：2020-10-12
中文翻译：
社交和掠食性粘杆菌Myxococcus xanthus DK1622中非编码RNA的调查。
原核ncRNA是基因表达的重要调控因子，可参与复杂的信号网络。粘细菌是用于研究多细胞发育和微生物捕食的模型生物，因其庞大的基因组和异常复杂的信号网络而闻名。但是，除了两个具体的例子，对其调节性ncRNA知之甚少。在这里，我们整合了生物信息学预测和转录组序列数据，以提供对示例性粘杆菌M. xanthus DK1622制作的ncRNA的全面调查。黄花木兰询问来自四个实验条件的RNA-seq数据，以鉴定映射到编码序列外部和已知ncRNA的转录本。所得的37个ncRNA聚集在基因组上，并且大多数（30/37）在整个粘细菌中均保守。大多数ncRNA（22/37）是基因间的，而13个至少部分地反义于蛋白质编码基因。预测的启动子和终止子序列解释了18个ncRNA的起始/终止位点。预测了ncRNA的mRNA靶标，包括已知调控ncRNA的合理候选物。营养素可利用性差异表达22种ncRNA，发现25个预测靶标的表达与其调控性ncRNA强烈相关。多个ncRNA共享预测的mRNA靶标表明某些ncRNA可能在信号网络内相互调节。这项基因组调查X.anthus ncRNA生物学为进一步研究粘细菌ncRNA提供了起点，这些细菌在这些工业上重要且复杂的生物中可能具有重要功能。
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