Frischkorn Kyle R, Haley Sheean T, Dyhrman Sonya T
Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
Lamont-Doherty Earth Observatory, Palisades, NY, United States.
Front Microbiol. 2019 Mar 5;10:330. doi: 10.3389/fmicb.2019.00330. eCollection 2019.
The N fixing cyanobacterium is a critically important organism in oligotrophic marine ecosystems, supplying "new" nitrogen (N) to the otherwise N-poor tropical and subtropical regions where it occurs. Low concentrations of phosphorus (P) in these regions can constrain distribution and N fixation rates. Physiological characterization of a single species in a mixed community can be challenging, and 'omic approaches are increasingly important tools for tracking nutritional physiology in a taxon-specific manner. As such, studies examining the dynamics of gene and protein markers of physiology (e.g., nutrient stress) are critical for the application and interpretation of such 'omic data . Here we leveraged combined transcriptomics, proteomics, and enzyme activity assays to track the physiological response of IMS101 to P deficiency and subsequent P re-supply over 72 h of sampling. P deficiency resulted in differential gene expression, protein abundance, and enzyme activity that highlighted a synchronous shift in P physiology with increases in the transcripts and corresponding proteins for hydrolyzing organic phosphorus, taking up phosphate with higher affinity, and modulating intracellular P demand. After P deficiency was alleviated, gene expression of these biomarkers was reduced to replete levels within 4 h of P amendment. A number of these gene biomarkers were adjacent to putative pho boxes and their expression patterns were similar to a response regulator. Protein products of the P deficiency biomarkers were slow to decline, with 84% of the original P deficient protein set still significantly differentially expressed after 72 h. Alkaline phosphatase activity tracked with proteins for this enzyme. With the rapid turnover time of transcripts, they appear to be good biomarkers of a P stress phenotype, whereas proteins, with a slower turnover time, may better reflect cellular activities. These results highlight the importance of validating and pairing transcriptome and proteome data that can be applied to physiological studies of key species .
固氮蓝细菌是贫营养海洋生态系统中的一种至关重要的生物，它为其出现的原本氮素匮乏的热带和亚热带地区提供“新的”氮。这些地区低浓度的磷会限制其分布和固氮速率。在混合群落中对单一物种进行生理特征描述可能具有挑战性，而“组学”方法是以分类群特异性方式追踪营养生理学的日益重要的工具。因此，研究生理（如营养胁迫）的基因和蛋白质标志物的动态变化对于此类“组学”数据的应用和解读至关重要。在此，我们利用转录组学、蛋白质组学和酶活性测定相结合的方法，追踪了IMS101在72小时采样期间对磷缺乏及随后磷重新供应的生理反应。磷缺乏导致基因表达、蛋白质丰度和酶活性出现差异，突出了磷生理学的同步转变，即水解有机磷、以更高亲和力吸收磷酸盐以及调节细胞内磷需求的转录本和相应蛋白质增加。磷缺乏缓解后，这些生物标志物的基因表达在添加磷后的4小时内降至充足水平。许多这些基因生物标志物与假定的pho盒相邻，其表达模式类似于一种反应调节因子。磷缺乏生物标志物的蛋白质产物下降缓慢，72小时后仍有84%的原始磷缺乏蛋白质组仍有显著差异表达。碱性磷酸酶活性与该酶的蛋白质相关。由于转录本周转时间快，它们似乎是磷胁迫表型的良好生物标志物，而周转时间较慢的蛋白质可能更能反映细胞活动。这些结果突出了验证和配对可应用于关键物种生理研究的转录组和蛋白质组数据的重要性。
