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【分享】宏基因组揭示在海洋的水柱中有独特的微生物小RNA
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Metatranscriptomicsreveals unique microbial small RNAs in the ocean's water column 宏基因组揭示在海洋的水柱中有独特的微生物小RNA YanmeiShi, Gene W. Tyson & Edward F. DeLong NATURE 14 May 2009 摘要：Microbial gene expression in the environment has recently been assessed via pyrosequencingof total RNA extracted directly from natural microbial assemblages. Several such 'metatranscriptomic' studies have reported that many complementary DNA sequences shared no significant homology with known peptide sequences, and so might represent transcripts from uncharacterized proteins. Here we report that a large fraction of cDNAsequences detected in microbial metatranscriptomicdata sets are comprised of well-known small RNAs (sRNAs), as well as new groups of previously unrecognized putative sRNAs(psRNAs). These psRNAsmapped specifically to intergenicregions of microbial genomes recovered from similar habitats, displayed characteristic conserved secondary structures and were frequently flanked by genes that indicated potential regulatory functions. Depth-dependent variation of psRNAsgenerally reflected known depth distributions of broad taxonomic groups, but fine-scale differences in the psRNAswithin closely related populations indicated potential roles in niche adaptation. Genome-specific mapping of a subset of psRNAsderived from predominant planktonicspecies such as Pelagibacterrevealed recently discovered as well as potentially new regulatory elements. Our analyses show that metatranscriptomicdata sets can reveal new information about the diversity, taxonomic distribution and abundance of sRNAsin naturally occurring microbial communities, and indicate their involvement in environmentally relevant processes including carbon metabolism and nutrient acquisition. 环境中微生物基因表达可通过提取自然界微生物群中的总RNA进行测序而得到。这些宏基因组的研究发现许多新的cDNA，可能表达新的的蛋白。 我们发现了一些包含小RNA（sRNA）和以前未发现的sRNA（psRNA）。这些psRNA定位在有相同栖息地的微生物基因组的基因间区，二级结构具有保守性，有潜在的调控功能。 不同深度的psRNA反映了已知生物分类群的分布，但一些精细的差别与相近物种的利基适应。 宏基因组数据能揭示新的信息，包括多样性，分类学分布和自然界微生物群的sRNA丰度，并说明它们参与和环境相关的过程，如碳代谢和营养获得。 更多资料请登录www.bioknow.cn |
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