Microcystis-containing pond water in Viet Nam Epigenomics. Microcystis-containing pond water in Viet Nam

We sought to expand the complement of characterized DrdV family Type IIL restriction enzymes by exploring the distribution and diversity of these systems within natural populations. Through bioinformatic analysis, we identified putative DrdV family Type IIL restriction enzymes within sequenced Microcystis strains that had the unusual property of high sequence conservation everywhere excepted within the DNA recognition domain, indicating similar function but diverse DNA binding specificities. As Microcystis are locally abundant in ponds during summer months, we sampled visibly-green waters in Vietnam containing populations of Microcystis from which metagenomic DNA were extracted. From these eDNA samples entire RM genes were amplified by PCR, expressed in Escherichia coli and their DNA binding specificities were characterized. We determined the DNA recognition motif for 29 enzymes, including 17 different novel DNA motifs not previously known.

本研究旨在通过探究天然种群中这类系统的分布与多样性，扩充已表征的DrdV家族IIL型限制性内切酶（Type IIL restriction enzymes）的储备。通过生物信息学分析，我们在已测序的微囊藻（Microcystis）菌株中鉴定出推定的DrdV家族IIL型限制性内切酶；这类酶具备一项罕见特性：除DNA识别结构域外，其余区域序列均高度保守，提示其功能相似但DNA结合特异性存在差异。鉴于夏季池塘中微囊藻局部大量繁殖，我们对越南境内可见绿色的含微囊藻种群的水体开展采样，并从中提取宏基因组DNA（metagenomic DNA）。我们通过聚合酶链式反应（PCR，Polymerase Chain Reaction）从这些环境DNA（eDNA，environmental DNA）样本中扩增得到完整的限制性修饰（RM，Restriction-Modification）基因，并在大肠杆菌（Escherichia coli）中进行表达，随后对其DNA结合特异性进行表征。我们共确定了29种酶的DNA识别基序（DNA recognition motif），其中包含17种此前未被报道的全新DNA识别基序。