The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.
The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.
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DOI：
10.1021/acs.biochem.2c00488
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发表时间：
2022-11-15
期刊：
影响因子：
2.9
通讯作者：
Bevilacqua, Philip C.
中科院分区：
文献类型：
--
作者：
Sieg, Jacob P.;McKinley, Lauren N.;Huot, Melanie J.;Yennawar, Neela H.;Bevilacqua, Philip C.
我们在模拟大肠杆菌的条件下研究了RNA、代谢组和二价Mg 2+之间相互作用的复杂网络。coli细胞质。我们确定了前15个E的Mg 2+结合常数。大肠杆菌代谢物，包括80%的总代谢物的浓度，在生理pH值和单价离子浓度。这些数据被用于开发一种模拟体内大肠杆菌的人工细胞质。大肠杆菌条件下，我们称之为“Eco 80”。我们经验地确定，E. Eco 80中的大肠杆菌代谢物在生物学相关的游离Mg 2+范围内（约0.5至3 mM Mg 2+）对Mg 2+的单位点结合行为接近，使用Mg 2+敏感的荧光染料。研究了Eco 80条件对RNA的热力学稳定性、化学稳定性、结构和催化作用的影响。我们发现Eco 80条件导致对RNA的热力学和化学稳定性的相反影响。特别是，RNA螺旋的热力学稳定性减弱了0.69±0.12 kcal/mol，而化学稳定性增强了约2倍，这可以使用Eco 80中弱和强Mg 2 +-代谢物复合物之间的Mg 2+形态来理解。总的来说，Eco 80的使用反映了RNA在体内的功能，并增强了RNA机制研究的生物相关性。
We examined the complex network of interactions amongst RNA, the metabolome, and divalent Mg2+ under conditions that mimic the E. coli cytoplasm. We determined Mg2+ binding constants for the top 15 E. coli metabolites, comprising 80% of the total metabolome by concentration, at physiological pH and monovalent ion concentrations. These data were used to inform the development of an artificial cytoplasm that mimics in vivo E. coli conditions, which we term “Eco80”. We empirically determined that the mixture of E. coli metabolites in Eco80 approximated single-site binding behavior towards Mg2+ in the biologically relevant free Mg2+ range of ~0.5 to 3 mM Mg2+, using a Mg2+-sensitive fluorescent dye. Effects of Eco80 conditions on the thermodynamic stability, chemical stability, structure, and catalysis of RNA were examined. We found that Eco80 conditions lead to opposing effects on the thermodynamic and chemical stability of RNA. In particular, the thermodynamic stability of RNA helices was weakened by 0.69±0.12 kcal/mol while the chemical stability was enhanced ~2-fold, which can be understood using the speciation of Mg2+ between weak and strong Mg2+-metabolite complexes in Eco80. Overall, the use of Eco80 reflects RNA function in vivo and enhances the biological relevance of mechanistic studies of RNA.
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影响因子：
16.6
作者：
Lan TCT;Allan MF;Malsick LE;Woo JZ;Zhu C;Zhang F;Khandwala S;Nyeo SSY;Sun Y;Guo JU;Bathe M;Näär A;Griffiths A;Rouskin S
通讯作者：
Rouskin S
影响因子：
2.9
作者：
Cheng, Xian;Shkel, Irina A.;Record, M. Thomas, Jr.
通讯作者：
Record, M. Thomas, Jr.
DOI：
10.1073/pnas.1913418116
发表时间：
2019-11-12
影响因子：
11.1
作者：
Leamy, Kathleen A.;Yamagami, Ryota;Bevilacqua, Philip C.
通讯作者：
Bevilacqua, Philip C.
弥合体外和体内RNA折叠之间的间隙。
影响因子：
6.1
作者：
Leamy KA;Assmann SM;Mathews DH;Bevilacqua PC
通讯作者：
Bevilacqua PC
影响因子：
64.8
作者：
Batey, RT;Gilbert, SD;Montange, RK
通讯作者：
Montange, RK