Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp PCC7120
Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp PCC7120
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DOI：
10.1073/pnas.1112724108
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发表时间：
2011-12-13
影响因子：
11.1
通讯作者：
Muro-Pastor, Alicia M.
中科院分区：
文献类型：
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作者：
Mitschke, Jan;Vioque, Agustn;Muro-Pastor, Alicia M.
蓝藻对大气中N2的固定是生物圈中氮的主要来源。在褐藻中，这一过程在空间上与含氧光合作用分离，发生在异囊中。当氮减少时，这些特化细胞在两个主要调节因子：NtcA和HetR控制的过程中从营养细胞分化。然而，由这两个因素控制的规律只是部分定义，分化过程的几个方面仍然是谜。利用差分RNA-seq技术，我们实验确定了Anabaena sp. PCC7120（一种用于研究原核细胞分化和N-2固定的模式生物）的bb1010000个转录起始位点（TSS）的全基因组图谱。通过分析对氮胁迫的适应，我们的全球TSS图谱提供了在分化过程的关键步骤中改变转录组织的动态变化的见解。我们鉴定出bbb900 TSS在8个缺氮条件下变化最小。在这些TSS中，至少有209例受HetR控制，而至少有158例其他TSS可能由NtcA直接控制。我们对在N2固定转换过程中激活的启动子的分析增加了数百个蛋白质编码基因和非编码转录物到潜在的相关因素列表中。这些数据通过实验确定了NtcA调控和DIF+基序，DIF+基序位于或接近-35位，似乎对某些基因的异囊特异性表达至关重要。
The fixation of atmospheric N2 by cyanobacteria is a major source of nitrogen in the biosphere. In Nostocales, such as Anabaena, this process is spatially separated from oxygenic photosynthesis and occurs in heterocysts. Upon nitrogen step-down, these specialized cells differentiate from vegetative cells in a process controlled by two major regulators: NtcA and HetR. However, the regulon controlled by these two factors is only partially defined, and several aspects of the differentiation process have remained enigmatic. Using differential RNA-seq, we experimentally define a genome-wide map of >10,000 transcriptional start sites (TSS) of Anabaena sp. PCC7120, a model organism for the study of prokaryotic cell differentiation and N-2 fixation. By analyzing the adaptation to nitrogen stress, our global TSS map provides insight into the dynamic changes that modify the transcriptional organization at a critical step of the differentiation process. We identify >900 TSS with minimum fold change in response to nitrogen deficiency of eight. From these TSS, at least 209 were under control of HetR, whereas at least 158 other TSS were potentially directly controlled by NtcA. Our analysis of the promoters activated during the switch to N2 fixation adds hundreds of protein-coding genes and noncoding transcripts to the list of potentially involved factors. These data experimentally define the NtcA regulon and the DIF+ motif, a palindrome at or close to position -35 that seems essential for heterocyst-specific expression of certain genes.