Table_1_Changes in Vibrio natriegens Growth Under Simulated Microgravity.XLSX

The growth rate of bacteria increases under simulated microgravity (SMG) with low-shear force. The next-generation microbial chassis Vibrio natriegens (V. natriegens) is a fast-growing Gram-negative, non-pathogenic bacterium with a generation time of less than 10 min. Screening of a V. natriegens strain with faster growth rate was attempted by 2-week continuous long-term culturing under SMG. However, the rapid growth rate of this strain made it difficult to obtain the desired mutant strain with even more rapid growth. Thus, a mutant with slower growth rate emerged. Multi-omics integration analysis was conducted to explore why this mutant grew more slowly, which might inform us about the molecular mechanisms of rapid growth of V. natriegens instead. The transcriptome data revealed that whereas genes related to mechanical signal transduction and flagellin biogenesis were up-regulated, those involved in adaptive responses, anaerobic and nitrogen metabolism, chromosome segregation and cell vitality were down-regulated. Moreover, genome-wide chromosome conformation capture (Hi-C) results of the slower growth mutant and wide type indicated that SMG-induced great changes of genome 3D organization were highly correlated with differentially expressed genes (DEGs). Meanwhile, whole genome re-sequencing found a significant number of structure variations (SVs) were enriched in regions with lower interaction frequency and down-regulated genes in the slower growth mutant compared with wild type (WT), which might represent a prophage region. Additionally, there was also a decreased interaction frequency in regions associated with well-orchestrated chromosomes replication. These results suggested that SMG might regulate local gene expression by sensing stress changes through conformation changes in the genome region of genes involved in flagellin, adaptability and chromosome segregation, thus followed by alteration of some physiological characteristics and affecting the growth rate and metabolic capacity.

在模拟微重力（SMG）条件下，细菌的生长速率因低剪切力而增加。下一代微生物底盘菌种大肠杆菌纳提根（Vibrio natriegens，简称V. natriegens）是一种生长迅速的革兰氏阴性、非致病菌，其代时短于10分钟。尝试通过在SMG下进行为期两周的持续长期培养，筛选出具有更快生长速率的V. natriegens菌株。然而，该菌株的快速生长特性使得获得生长速率更为迅速的突变菌株变得异常困难，从而产生了一种生长速率较慢的突变体。为了探究该突变体生长缓慢的原因，并可能揭示V. natriegens快速生长的分子机制，进行了多组学整合分析。转录组数据显示，与机械信号转导和鞭毛素生物合成相关的基因上调，而参与适应性反应、厌氧和氮代谢、染色体分离和细胞活力的基因下调。此外，较慢生长突变体和野生型（WT）的全基因组染色体构象捕获（Hi-C）结果表明，SMG引起的基因组三维组织巨大变化与差异表达基因（DEGs）高度相关。同时，全基因组重测序发现，在较慢生长突变体中，与野生型相比，结构变异（SVs）在相互作用频率较低的区域富集，并且下调的基因也出现在这些区域，这可能与前噬菌体区域有关。此外，与有序染色体复制相关的区域也出现了相互作用频率的降低。这些结果表明，SMG可能通过感知基因参与鞭毛素、适应性和染色体分离的基因组区域构象变化带来的应激变化，从而调节局部基因表达，进而改变某些生理特性，影响生长速率和代谢能力。