The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters
The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters
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DOI：
10.1093/nar/gkq106
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发表时间：
2010-06-01
影响因子：
14.9
通讯作者：
de la Campa, Adela G.
中科院分区：
文献类型：
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作者：
Ferrandiz, Maria-Jose;Martin-Galiano, Antonio J.;de la Campa, Adela G.
在暴露于GyrB抑制剂新生霉素后检查肺炎链球菌的转录应答。内部质粒的拓扑异构体分布证实了在低新生霉素浓度下超螺旋的天然水平的DNA松弛和恢复。这是由于DNA促旋酶的上调和拓扑异构酶I和IV的下调。此外，>13%的基因组表现出弛豫依赖性转录。大多数响应基因（>68%）落入15个物理簇（14.6-85.6 kb），这些簇独立于操纵子组织进行协调调节。这些基因组簇与AT含量和密码子组成相关，显示染色体被组织成响应DNA超螺旋的拓扑反应基因簇。特别是，下调的簇两侧的11-40 kb AT丰富的区域，可能有一个推定的结构功能。这是第一次发现以协调方式响应超螺旋水平变化的基因被组织为功能簇。这样的组织揭示了DNA超螺旋作为控制基因表达的一般特征叠加在其他种类的更具体的调控机制上。
The transcriptional response of Streptococcus pneumoniae was examined after exposure to the GyrB-inhibitor novobiocin. Topoisomer distributions of an internal plasmid confirmed DNA relaxation and recovery of the native level of supercoiling at low novobiocin concentrations. This was due to the up-regulation of DNA gyrase and the down-regulation of topoisomerases I and IV. In addition, >13% of the genome exhibited relaxation-dependent transcription. The majority of the responsive genes (>68%) fell into 15 physical clusters (14.6-85.6 kb) that underwent coordinated regulation, independently of operon organization. These genomic clusters correlated with AT content and codon composition, showing the chromosome to be organized into topology-reacting gene clusters that respond to DNA supercoiling. In particular, down-regulated clusters were flanked by 11-40 kb AT-rich zones that might have a putative structural function. This is the first case where genes responding to changes in the level of supercoiling in a coordinated manner were found organized as functional clusters. Such an organization revealed DNA supercoiling as a general feature that controls gene expression superimposed on other kinds of more specific regulatory mechanisms.