Penicillium chrysogenum UCB strain PC0814C Genome sequencing

Strain selection and strain improvement are the first, and arguably most important, steps in the industrial production of biological compounds by microorganisms. While traditional methods of mutagenesis and selection have been effective in improving production of compounds at a commercial scale, the genetic changes underpinning the altered phenotypes have remained largely unclear. We utilized high-throughput Illumina short read sequencing of a wild Penicillium chrysogenum strain in order to make whole genome comparisons to a sequenced improved strain (WIS 54-1255). We developed an assembly-free method of identifying chromosomal rearrangements and validated the in silico predictions with a PCR-based assay and Sanger sequencing. Despite many rounds of mutagen treatment and artificial selection, WIS 54-1255 differs from its wild progenitor at only one of the identified rearrangements. We suggest that the identification of natural variants predisposed to be high penicillin producers was instrumental in the success of WIS 54-1255 as an industrial producer. In addition to finding a previously published inversion in the penicillin biosynthesis cluster, we located several genes related to penicillin production associated with these rearrangements. By comparing the configuration of rearrangement events among several historically important strains known to be high penicillin producers to a collection of recently isolated wild strains, we suggest that wild strains with rearrangements similar to those in known high penicillin producers may be viable candidates for further improvement efforts.

菌株选育与菌株改良是利用微生物工业化生产生物化合物的首要步骤，也堪称最为关键的环节。传统诱变与筛选方法虽已成功实现了商业规模的化合物产量提升，但驱动表型改变的遗传基础在很大程度上仍未明确。本研究通过对野生产黄青霉（Penicillium chrysogenum）菌株进行高通量Illumina短读长测序，与已完成测序的改良菌株WIS 54-1255开展全基因组比对分析。我们开发了一种无需基因组组装的染色体重排鉴定方法，并通过基于聚合酶链式反应（PCR）的实验与桑格测序（Sanger sequencing）验证了计算机预测结果。尽管经历了多轮诱变处理与人工选育，WIS 54-1255仅在一处已鉴定的染色体重排位点上与其野生亲本菌株存在差异。我们认为，筛选出易于成为高产青霉素菌株的自然变异体，是WIS 54-1255成为工业化高产菌株的关键因素。除了在青霉素生物合成基因簇中发现此前已报道的倒位事件外，我们还定位了与这些重排相关的多个青霉素生产相关基因。通过比对多株经典高产青霉素菌株与近期分离的野生菌株的重排事件结构，我们认为携带与已知高产青霉素菌株相似重排的野生菌株，可作为后续菌株改良的潜在候选对象。