Davis-Richardson Austin G, Russell Jordan T, Dias Raquel, McKinlay Andrew J, Canepa Ronald, Fagen Jennie R, Rusoff Kristin T, Drew Jennifer C, Kolaczkowski Bryan, Emerich David W, Triplett Eric W
Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA.
Biochemistry Department, University of Missouri Columbia, MO, USA.
Front Microbiol. 2016 Apr 22;7:518. doi: 10.3389/fmicb.2016.00518. eCollection 2016.
Very little is known about the role of epigenetics in the differentiation of a bacterium from the free-living to the symbiotic state. Here genome-wide analysis of DNA methylation changes between these states is described using the model of symbiosis between soybean and its root nodule-forming, nitrogen-fixing symbiont, Bradyrhizobium diazoefficiens. PacBio resequencing of the B. diazoefficiens genome from both states revealed 43,061 sites recognized by five motifs with the potential to be methylated genome-wide. Of those sites, 3276 changed methylation states in 2921 genes or 35.5% of all genes in the genome. Over 10% of the methylation changes occurred within the symbiosis island that comprises 7.4% of the genome. The CCTTGAG motif was methylated only during symbiosis with 1361 adenosines methylated among the 1700 possible sites. Another 89 genes within the symbiotic island and 768 genes throughout the genome were found to have methylation and significant expression changes during symbiotic development. Of those, nine known symbiosis genes involved in all phases of symbiotic development including early infection events, nodule development, and nitrogenase production. These associations between methylation and expression changes in many B. diazoefficiens genes suggest an important role of the epigenome in bacterial differentiation to the symbiotic state.
关于表观遗传学在细菌从自由生活状态向共生状态转变过程中所起的作用，人们了解甚少。本文利用大豆与其根瘤形成、固氮共生菌慢生根瘤菌之间的共生模型，描述了这两种状态之间DNA甲基化变化的全基因组分析。对处于这两种状态的慢生根瘤菌基因组进行PacBio重测序，发现有43,061个位点可被5种基序识别，这些位点有可能在全基因组范围内被甲基化。在这些位点中，3276个位点在2921个基因中发生了甲基化状态变化，占基因组中所有基因的35.5%。超过10%的甲基化变化发生在占基因组7.4%的共生岛内。CCTTGAG基序仅在共生期间被甲基化，在1700个可能的位点中有1361个腺苷被甲基化。在共生岛内还发现另外89个基因以及全基因组中的768个基因在共生发育过程中发生了甲基化和显著的表达变化。其中，9个已知的共生基因参与了共生发育的各个阶段，包括早期感染事件、根瘤发育和固氮酶的产生。慢生根瘤菌许多基因中甲基化与表达变化之间的这些关联表明，表观基因组在细菌向共生状态的分化过程中起着重要作用。
