Hyperaerated metalation calculator for E. coli strain JM109 (DE3) grown in LB media
Hyperaerated metalation calculator for E. coli strain JM109 (DE3) grown in LB media
复制标题
用于在 LB 培养基中生长的大肠杆菌菌株 JM109 (DE3) 的过度通气金属化计算器
DOI：
10.1101/2022.09.02.506343
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Clough S
中科院分区：
文献类型：
--
作者：
Clough S
我们最近制作了三个基于网络的计算器，根据感兴趣的蛋白质的金属亲和力以及细胞内不稳定缓冲金属池的可用性估计，预测蛋白质的体内金属占位。根据dna结合、金属感应和转录调节因子的校准反应计算金属可利用性。估计细胞内Fe（II）的可用性与inE相似。与在LB培养基中好氧生长的细胞相比，厌氧条件下的细胞颜色变大。本文的目的是将背景数据存档，以支持在带有挡板的烧瓶中生长的过度充气细胞的新计算器的发布，该计算器具有相对低的培养体积和高震动速度，以提高氧合。根据细胞内铁（II）传感器Fur的响应计算出的细胞内铁（II）的可用性估计在这些过度充气的细胞中明显低于之前在厌氧或好氧培养中确定的任何一个值。尽管从Mn（II）传感器MntR的响应估计细胞内Mn（II）可用性只有适度变化，但在过度充气的细胞中，每个细胞的Mn（II）原子总数增加。细胞内Ni（II）可用性的准确测定将需要进一步校准Ni（II）传感器NikR在过度充气细胞中的响应幅度，以考虑Fnr的状态。过度充气的金属化计算器可以在网上获得，也可以作为电子表格，供其他人使用。
We recently produced three web-based calculators that predictin vivometal occupancies of proteins, based on the metal affinities of a protein of interest along with estimates of the availabilities of the labile buffered pools of metals inside a cell. Metal availabilities were calculated from the calibrated responses of DNA-binding, metal-sensing, transcriptional regulators. The availability of intracellular Fe(II) was estimated to be similar inE. coligrown under anaerobic conditions compared to cells grown aerobically in LB medium. The purpose of this article is to archive the background data that underpins the release of a new calculator for hyperaerated cells grown in flasks with baffles, with relatively low culture volumes plus high shaking speeds to give elevated oxygenation. The intracellular availability of Fe(II) calculated from the responses of the intracellular Fe(II) sensor Fur was estimated to be significantly lower in these hyperaerated cells than either of the previous values determined for anaerobic or aerobic cultures. The total number of atoms of Mn(II) per cell increased in hyperaerated cells albeit with only modest change in intracellular Mn(II) availability as estimated from the responses of the Mn(II) sensor MntR. Accurate determination of intracellular Ni(II) availability will require further calibration of the magnitude of the responses of the Ni(II) sensor NikR in hyperaerated cells to take account of the state of Fnr. The hyperaerated metalation calculator is made available online and as a spreadsheet, for use by others.