Natural Genetic Transformation Generates a Population of Merodiploids in Streptococcus pneumoniae

Partial duplication of genetic material is prevalent in eukaryotes and provides potential for evolution of new traits. Prokaryotes, which are generally haploid in nature, can evolve new genes by partial chromosome duplication, known as merodiploidy. Little is known about merodiploid formation during genetic exchange processes, although merodiploids have been serendipitously observed in early studies of bacterial transformation. Natural bacterial transformation involves internalization of exogenous donor DNA and its subsequent integration into the recipient genome by homology. It contributes to the remarkable plasticity of the human pathogen Streptococcus pneumoniae through intra and interspecies genetic exchange. We report that lethal cassette transformation produced merodiploids possessing both intact and cassette-inactivated copies of the essential target gene, bordered by repeats (R) corresponding to incomplete copies of IS861. We show that merodiploidy is transiently stimulated by transformation, and only requires uptake of a ∼3-kb DNA fragment partly repeated in the chromosome. We propose and validate a model for merodiploid formation, providing evidence that tandem-duplication (TD) formation involves unequal crossing-over resulting from alternative pairing and interchromatid integration of R. This unequal crossing-over produces a chromosome dimer, resolution of which generates a chromosome with the TD and an abortive chromosome lacking the duplicated region. We document occurrence of TDs ranging from ∼100 to ∼900 kb in size at various chromosomal locations, including by self-transformation (transformation with recipient chromosomal DNA). We show that self-transformation produces a population containing many different merodiploid cells. Merodiploidy provides opportunities for evolution of new genetic traits via alteration of duplicated genes, unrestricted by functional selective pressure. Transient stimulation of a varied population of merodiploids by transformation, which can be triggered by stresses such as antibiotic treatment in S. pneumoniae, reinforces the plasticity potential of this bacterium and transformable species generally.

遗传物质的部分重复在真核生物中广泛存在，为新性状的演化提供了潜在可能。原核生物本质上通常为单倍体，可通过染色体部分重复演化出新基因，该过程被称为部分二倍性（merodiploidy）。尽管在早期细菌转化研究中曾偶然观察到部分二倍体，但对于遗传交换过程中部分二倍体的形成机制，目前仍知之甚少。天然细菌转化指外源供体DNA的内化，以及其随后通过同源序列整合至受体基因组的过程。该过程通过种内及种间遗传交换，赋予人类病原菌肺炎链球菌（Streptococcus pneumoniae）极强的遗传可塑性。本研究发现，致死盒转化可产生部分二倍体，该二倍体同时携带必需靶基因的完整拷贝与致死盒失活拷贝，两者侧翼的重复序列（R）对应IS861的不完全拷贝。研究表明，转化可瞬时诱导部分二倍性的产生，且该过程仅需摄取一段在染色体中存在部分重复的约3kb DNA片段。本研究提出并验证了部分二倍体形成的模型，证据表明串联重复（tandem-duplication, TD）的形成涉及由重复序列（R）的交替配对与染色单体间整合所导致的不等交换。此种不等交换会产生染色体二聚体，其解离后可生成携带串联重复的染色体与缺失重复区域的无活性染色体。本研究证实，在包括自体转化（即使用受体自身染色体DNA进行的转化）在内的多种条件下，染色体不同位置均可产生长度约100kb至900kb的串联重复。研究表明，自体转化可产生包含多种不同部分二倍体细胞的种群。部分二倍性为通过重复基因的变异演化出新遗传性状提供了契机，且不受功能选择压力的限制。在肺炎链球菌中，转化可由抗生素处理等胁迫因素触发，其对多样化部分二倍体种群的瞬时诱导，进一步强化了该细菌以及其他可转化物种的遗传可塑性潜力。