Data_Sheet_1_Changes in Vibrio natriegens Growth Under Simulated Microgravity.ZIP

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）环境下，细菌的生长速率在低剪切力条件下呈现上升。下一代微生物底盘大肠杆菌（Vibrio natriegens，简称V. natriegens）是一种生长迅速的革兰氏阴性、非致病性细菌，其代时短于10分钟。为筛选出生长速率更快的V. natriegens菌株，研究者尝试在SMG环境下进行为期两周的持续长期培养。然而，该菌株的快速生长特性使得获得生长速率更加迅速的突变菌株变得异常困难，从而出现了一种生长速率较慢的突变体。通过对该突变体进行多组学整合分析，旨在探究其生长缓慢的原因，这或许有助于揭示V. natriegens快速生长的分子机制。转录组数据表明，与机械信号转导和鞭毛素生物合成相关的基因表达上调，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表达下调。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，由SMG诱导的基因组三维组织结构的大幅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，并且在下调基因的区域，这些可能代表噬菌体区域。此外，在关联良好协调的染色体复制的区域，也出现了相互作用频率的降低。这些结果暗示，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的构象变化来调节局部基因表达，从而引发某些生理特性的改变，进而影响生长速率和代谢能力。