Li Fei, Zhang Qinye, Lu Yuntong, Chen Xiaoyan, Liu Xing, Qiu Xiangting, Gu Yunying, Wang Puchang, Liu Jie
School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China.
Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China.
Front Plant Sci. 2025 Sep 1;16:1623360. doi: 10.3389/fpls.2025.1623360. eCollection 2025.
Codon usage bias (CUB) can influence host-microbe interactions and stress adaptation. In this study, we aimed to investigate how codon usage bias (CUB) similarity between and influences their interaction and contributes to the adaptation of to high calcium stress.
The CUB indices of both species were computed, and genes with high correlations were identified. The transcriptome sequencing data of gene expression in cultured under normal and high calcium conditions, with and without treatment was used to analyze the expression of genes with CUB similar to that of B. amyloliquefaciens in relation with the adaptation of to high calcium stress and the interaction between both organisms.
We identified 19210 genes with CUB similar to and 95 -responsive and calcium-responsive genes in , which were involved in transport, carbohydrate metabolism, and response to chemical, and cellular homeostasis. Differential expression analysis showed a total of 733 A. thaliana genes with CUB similar to to be dysregulated, among which 47 changed when was cultivated in the presence of the LZ04 strain, 643 under high calcium condition and 43 with calcium treatment and the presence of the LZO4 strain. The gene ontology (GO) biological processes termed among others of response to endogenous stimulus, response to oxygen containing compound, response to organic substance, response to abiotic and biotic stimuli, response to stress, and response to light stimulus, regulation of hormone levels, response to nutrient levels, post-embryonic plant morphogenesis, metabolic process, cell growth.
These findings highlight the importance of CUB in the interaction between and as well as in the adaptation of to high calcium stress. They also show the underlying regulatory role of , which could help develop new tactics for improving growth and yield in karst regions. A more elaborate analysis of the value of CUB in the interaction of these two organisms could assist in engineering host- sensitive micro-organism strains and enhance the microbial-based approaches for the improvement of growth and yield in such areas and for managing abiotic stress in crops.
密码子使用偏好（CUB）会影响宿主与微生物的相互作用以及应激适应。在本研究中，我们旨在探究[具体物种1]和[具体物种2]之间的密码子使用偏好（CUB）相似性如何影响它们的相互作用，并有助于[具体物种1]适应高钙胁迫。
计算了两个物种的CUB指数，并鉴定了具有高相关性的基因。利用在正常和高钙条件下，有无[具体物种2]处理时培养的[具体物种1]中基因表达的转录组测序数据，分析了与解淀粉芽孢杆菌CUB相似的[具体物种1]基因的表达与[具体物种1]对高钙胁迫的适应以及两种生物之间相互作用的关系。
我们鉴定出19210个与[具体物种2]CUB相似的[具体物种1]基因，以及[具体物种1]中95个对[具体物种2]有响应和对钙有响应的基因，这些基因参与运输、碳水化合物代谢、对化学物质的响应以及细胞内稳态。差异表达分析表明，共有733个与[具体物种2]CUB相似的拟南芥基因表达失调，其中47个在存在[具体物种2]LZ04菌株时培养的拟南芥中发生变化，643个在高钙条件下发生变化，43个在钙处理且存在[具体物种2]LZO4菌株时发生变化。基因本体（GO）生物学过程包括对内源刺激的响应、对含氧化合物的响应、对有机物质的响应、对非生物和生物刺激的响应、对应激的响应、对光刺激的响应、激素水平的调节、对营养水平的响应、胚后植物形态发生、代谢过程、细胞生长等。
这些发现突出了CUB在[具体物种1]和[具体物种2]相互作用以及[具体物种1]适应高钙胁迫中的重要性。它们还显示了[具体物种2]的潜在调节作用，这有助于开发新策略来提高喀斯特地区[具体物种1]的生长和产量。对CUB在这两种生物相互作用中的价值进行更详尽的分析，有助于构建对宿主敏感的微生物菌株，并加强基于微生物的方法，以提高此类地区[具体物种1]的生长和产量，以及应对作物中的非生物胁迫。
