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小非编码RNA既见于微生物细胞，也见于真核细胞。大多数已知微生物小RNA的功能是，调控核心生理过程中所涉及的基因，但我们关于小RNA的知识一直仅限于在实验室中所培养的微生物。 “环境转录组学”（Metatranscriptomics）是最近发展起来的一种技术，可让研究人员对未培养的微生物群落的集体转录组进行分析。该方法能把人们对于转录组的认识拓展到其他更为奇异的微生物。对从夏威夷以北名叫ALOHA的深水站不同深度处所取海水进行的一项新的“环境转录组学”分析，显示了来自多样化生物类群的一组数量巨大的小RNA新种类。 推荐原始出处： Nature 459, 266-269 (14 May 2009) | doi:10.1038/nature08055 Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column Yanmei Shi1, Gene W. Tyson1 & Edward F. DeLong1,2 1 Department of Civil and Environmental Engineering, and, 2 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Microbial gene expression in the environment has recently been assessed via pyrosequencing of total RNA extracted directly from natural microbial assemblages. Several such 'metatranscriptomic' studies1, 2 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 cDNA sequences detected in microbial metatranscriptomic data sets are comprised of well-known small RNAs (sRNAs)3, as well as new groups of previously unrecognized putative sRNAs (psRNAs). These psRNAs mapped specifically to intergenic regions 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 psRNAs generally reflected known depth distributions of broad taxonomic groups4, but fine-scale differences in the psRNAs within closely related populations indicated potential roles in niche adaptation. Genome-specific mapping of a subset of psRNAs derived from predominant planktonic species such as Pelagibacter revealed recently discovered as well as potentially new regulatory elements. Our analyses show that metatranscriptomic data sets can reveal new information about the diversity, taxonomic distribution and abundance of sRNAs in naturally occurring microbial communities, and indicate their involvement in environmentally relevant processes including carbon metabolism and nutrient acquisition. (责任编辑：Doctor001) |
