Mora Marcelo, Mell Joshua Chang, Ehrlich Garth D, Ehrlich Rachel L, Redfield Rosemary J
Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
Department of Microbiology & Immunology, Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 12 Philadelphia, PA 19102, USA.
iScience. 2020 Dec 30;24(1):102007. doi: 10.1016/j.isci.2020.102007. eCollection 2021 Jan 22.
The genomes of naturally competent Pasteurellaceae and Neisseriaceae have many short uptake sequences (USS), which allow them to distinguish self-DNA from foreign DNA. To fully characterize this preference we developed genome-wide maps of DNA uptake using both a sequence-based computational model and genomic DNA that had been sequenced after uptake by and recovery from competent cells. When DNA fragments were shorter than the average USS spacing of ∼1,000 bp, sharp peaks of uptake were centered at USS and separated by valleys with 1000-fold lower uptake. Long DNA fragments (1.5-17 kb) gave much less variation, with 90% of positions having uptake within 2-fold of the mean. All detectable uptake biases arose from sequences that fit the USS uptake motif. Simulated competition predicted that, in its respiratory tract environment, will efficiently take up its own DNA even when human DNA is present in 100-fold excess.
天然感受态巴斯德氏菌科和奈瑟氏菌科的基因组中有许多短摄取序列（USS），这使它们能够区分自身DNA和外源DNA。为了全面表征这种偏好，我们使用基于序列的计算模型和经感受态细胞摄取并回收后测序的基因组DNA，绘制了全基因组DNA摄取图谱。当DNA片段短于平均USS间距（约1000 bp）时，摄取的尖峰以USS为中心，被摄取量低1000倍的低谷隔开。长DNA片段（1.5 - 17 kb）的变化要小得多，90%的位置摄取量在平均值的2倍以内。所有可检测到的摄取偏差都源于符合USS摄取基序的序列。模拟竞争预测，在其呼吸道环境中，即使人类DNA以100倍的过量存在，[具体物种名称缺失]也会有效地摄取自身DNA。
