Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
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DOI：
10.1128/mbio.03530-23
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发表时间：
2024-02-15
期刊：
影响因子：
6.4
通讯作者：
Pakrasi，Himadri B.
中科院分区：
文献类型：
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作者：
Sengupta，Annesha;Bandyopadhyay，Anindita;Pakrasi，Himadri B.
蓝藻是光合生物，作为可持续生物生产的潜在宿主已获得广泛认可。然而，它们复杂的调控网络对主要的代谢工程工作提出了重大挑战，从而限制了它们作为生产宿主的可行性。基因组精简已被证明是提高异养生物生产力和适应性的成功方法，但尚未充分探索其在光养生物中的潜力。在这里，我们展示了对表现出最快指数增长的蓝藻基因组的系统减少，即细长聚球藻UTEX 2973。这项工作是光合自养生物中的第一项工作，涉及在实验分析和计算工具指导下使用最先进的基因组编辑技术的迭代过程。 CRISPR-Cas3 能够对预测的可有可无的区域进行大规模、渐进性的删除，并有助于识别必需基因。将大的缺失组合起来以获得基因组减少了 55 kb 的菌株。与野生型 (WT) 相比，具有精简基因组的菌株显示出生长（高达 23%）和生产力（22.7%）的改善。这种精简策略不仅有可能开发出具有改善的生长和生产力特征的蓝藻菌株，而且还可以促进更好地理解其基因组与表型组的关系。重要性基因组精简是自然生命系统使用的一种进化策略，用于从基因组中分配不必要的基因，作为适应和进化的机制。虽然这种策略已被成功借用来开发具有所需表型的合成异养微生物系统，但它尚未在光合自养生物中得到广泛探索。基因组精简策略结合了计算预测来识别可有可无的区域和使用基因组编辑工具进行的实验验证，在本研究中，我们采用了一种修改后的策略，其目标是将基因组大小最小化到在特定条件下实现最佳细胞适应性的程度。我们的策略在光合自养生物中探索了一种新型基因组编辑工具，与其他现有工具不同，它能够从基因组中进行大量、自发的最佳删除。我们的研究结果证明了这种修改策略在获得具有精简基因组的菌株方面的有效性，表现出改善的适应性和生产力。
Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here, we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth,Synechococcus elongatusUTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR-Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55-kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the wild type (WT). This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome-to-phenome relationships.IMPORTANCEGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome-editing tool, and in this study, we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs, which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.