Casjens Sherwood R, Gilcrease Eddie B, Vujadinovic Marija, Mongodin Emmanuel F, Luft Benjamin J, Schutzer Steven E, Fraser Claire M, Qiu Wei-Gang
Division of Microbiology and Immunology, Pathology Department and Biology Department, University of Utah School of Medicine, Room 2200 K Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT, 84112, USA.
Biology Department, University of Utah, Salt Lake City, UT, USA.
BMC Genomics. 2017 Feb 15;18(1):165. doi: 10.1186/s12864-017-3553-5.
Bacteria from the genus Borrelia are known to harbor numerous linear and circular plasmids. We report here a comparative analysis of the nucleotide sequences of 236 plasmids present in fourteen independent isolates of the Lyme disease agent B. burgdorferi.
We have sequenced the genomes of 14 B. burgdorferi sensu stricto isolates that carry a total of 236 plasmids. These individual isolates carry between seven and 23 plasmids. Their chromosomes, the cp26 and cp32 circular plasmids, as well as the lp54 linear plasmid, are quite evolutionarily stable; however, the remaining plasmids have undergone numerous non-homologous and often duplicative recombination events. We identify 32 different putative plasmid compatibility types among the 236 plasmids, of which 15 are (usually) circular and 17 are linear. Because of past rearrangements, any given gene, even though it might be universally present in these isolates, is often found on different linear plasmid compatibility types in different isolates. For example, the arp gene and the vls cassette region are present on plasmids of four and five different compatibility types, respectively, in different isolates. A majority of the plasmid types have more than one organizationally different subtype, and the number of such variants ranges from one to eight among the 18 linear plasmid types. In spite of this substantial organizational diversity, the plasmids are not so variable that every isolate has a novel version of every plasmid (i.e., there appears to be a limited number of extant plasmid subtypes).
Although there have been many past recombination events, both homologous and nonhomologous, among the plasmids, particular organizational variants of these plasmids correlate with particular chromosomal genotypes, suggesting that there has not been rapid horizontal transfer of whole linear plasmids among B. burgdorferi lineages. We argue that plasmid rearrangements are essentially non-revertable and are present at a frequency of only about 0.65% that of single nucleotide changes, making rearrangement-derived novel junctions (mosaic boundaries) ideal phylogenetic markers in the study of B. burgdorferi population structure and plasmid evolution and exchange.
已知疏螺旋体属细菌含有众多线性和环状质粒。我们在此报告对莱姆病病原体伯氏疏螺旋体14个独立分离株中存在的236个质粒的核苷酸序列进行的比较分析。
我们对14株严格意义上的伯氏疏螺旋体分离株的基因组进行了测序，这些分离株共携带236个质粒。这些单个分离株携带7至23个质粒。它们的染色体、cp26和cp32环状质粒以及lp54线性质粒在进化上相当稳定；然而，其余质粒经历了许多非同源且通常是重复的重组事件。我们在236个质粒中鉴定出32种不同的假定质粒相容性类型，其中15种是（通常）环状的，17种是线性的。由于过去的重排，任何给定的基因，即使它可能在这些分离株中普遍存在，在不同的分离株中也常常出现在不同的线性质粒相容性类型上。例如，arp基因和vls盒区域在不同的分离株中分别存在于四种和五种不同相容性类型的质粒上。大多数质粒类型有不止一种组织上不同的亚型，在18种线性质粒类型中，此类变体的数量从一种到八种不等。尽管存在这种显著的组织多样性，但质粒并非如此多变，以至于每个分离株都有每种质粒的新版本（即，现存的质粒亚型数量似乎有限）。
尽管这些质粒过去发生了许多同源和非同源重组事件，但这些质粒的特定组织变体与特定的染色体基因型相关，这表明在伯氏疏螺旋体谱系之间没有整个线性质粒的快速水平转移。我们认为质粒重排基本上是不可逆的，其发生频率仅约为单核苷酸变化频率的0.65%，这使得重排衍生的新连接（镶嵌边界）成为研究伯氏疏螺旋体种群结构以及质粒进化和交换的理想系统发育标记。
