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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Deep sequencing analysis of the Methanosarcina mazei Goe1 transcriptome in response to nitrogen availability
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Deep sequencing analysis of the Methanosarcina mazei Goe1 transcriptome in response to nitrogen availability

机译：响应甲烷可用性的甲烷甲烷八叠球菌Goe1转录组的深度测序分析

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Methanosarcina mazei and related mesophilic archaea are the only organisms fermenting acetate, methylamines, and methanol to methane and carbon dioxide, contributing significantly to greenhouse gas production. The biochemistry of these metabolic processes is well studied, and genome sequences are available, yet little is known about the overall transcriptional organization and the noncoding regions representing 25% of the 4.01-Mb genome of M. mazei. We present a genome-wide analysis of transcription start sites (TSS) in M. mazei grown under different nitrogen availabilities. Pyrosequencing-based differential analysis of primary vs. processed 5' ends of transcripts discovered 876 TSS across the M. mazei genome. Unlike in other archaea, in which leaderless mRNAs are prevalent, the majority of the detected mRNAs in M. mazei carry long untranslated 5' regions. Our experimental data predict a total of 208 small RNA (sRNA) candidates, mostly from intergenic regions but also antisense to 5' and 3' regions of mRNAs. In addition, 40 new small mRNAs with ORFs of ≤30 aa were identified, some of which might have dual functions as mRNA and regulatory sRNA. We confirmed differential expression of several sRNA genes in response to nitrogen availability. Inspection of their promoter regions revealed a unique conserved sequence motif associated with nitrogen-responsive regulation, which might serve as a regulator binding site upstream of the common MB recognition element. Strikingly, several sRNAs antisense to mRNAs encoding transposases indicate nitrogen-dependent transposition events. This global TSS map in archaea will facilitate a better understanding of transcriptional and posttranscriptional control in the third domain of life.
机译：马氏甲烷八叠球菌和相关的嗜温古生菌是唯一将乙酸盐，甲胺和甲醇发酵为甲烷和二氧化碳的生物，对温室气体的产生做出了重要贡献。这些代谢过程的生物化学已得到很好的研究，并且可获得基因组序列，但对整体转录组织和非编码区知之甚少，该非编码区占马氏甲烷八叠球菌4.01-Mb基因组的25％。我们目前在不同氮素利用率下生长的马氏甲烷八叠球转录起始位点（TSS）的全基因组分析。基于焦磷酸测序的转录本的原始序列和经过处理的5'末端的差异分析在马氏甲烷八叠球菌基因组中发现876个TSS。与在其他古细菌中普遍存在无前导mRNA的情况不同，在马氏甲烷八叠球菌中检测到的大多数mRNA都带有长的未翻译的5'区。我们的实验数据预测总共有208个小RNA（sRNA）候选物，主要来自基因间区域，但也反义于mRNA的5'和3'区域。此外，还鉴定出40个新的ORF≤30 aa的小mRNA，其中一些可能具有mRNA和调控sRNA的双重功能。我们证实了几个sRNA基因在氮素利用率方面的差异表达。对它们的启动子区域的检查揭示了与氮响应性调节相关的独特的保守序列基序，其可能充当常见MB识别元件上游的调节子结合位点。令人惊讶的是，与编码转座酶的mRNA反义的几种sRNA表示氮依赖性转座事件。该古细菌中的全球TSS图谱将有助于更好地理解生活第三域中的转录和转录后控制。

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