Multiple mutations in RNA polymerase β-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory
Multiple mutations in RNA polymerase β-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory
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Streptomyces incarnatus NRRL8089 中 RNA 聚合酶 β 亚基基因 (rpoB) 的多个突变增强了抗病毒抗生素 Sinefungin 的产量：通过密度泛函理论对 rif 簇区域进行建模
DOI：
10.1093/bbb/zbab011
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发表时间：
2021
期刊：
影响因子：
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通讯作者：
Tamura Takashi
中科院分区：
文献类型：
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作者：
Ogawa Saori;Shimidzu Hitomi;Fukuda Koji;Tsunekawa Naoki;Hirano Toshiyuki;Sato Fumitoshi;Yura Kei;Hasunuma Tomohisa;Ochi Kozo;Yamamoto Michio;Sakamoto Wataru;Hashimoto Kentaro;Ogata Hiroyuki;Kanao Tadayoshi;Nemoto Michiko;Inagaki Kenji;Tamura Takashi
Streptomyces incarnatusNRRL 8089产生抗病毒、抗真菌、抗原生动物核苷抗生素sinefungin。为了提高sinefungin的产量，在编码RNA聚合酶（RNAP）β-亚基的therpoB基因的靶残基D447、S453、H457和R460处引入多个突变。稀疏回归分析，使用弹性网络套索脊处罚先前报告的H457 X突变确定了一个数字参数集，这表明H457 R/Y/F可能会导致生产增强。H457 R/R460 C突变成功地使sinefungin的产量增加了3倍，而其他组突变，如D447 G/R460 C或D447 G/H457 Y，则产生中度甚至负面影响。为了确定rif簇残基对sinefungin产生不同影响的原因，通过同源建模和分子动力学模拟构建了RNAP/DNA/mRNA复合物模型。这4个残基位于mRNA链附近。基于密度泛函理论的计算表明，D447，H457和R460与核苷酸直接接触，部分正电荷被带负电荷的mRNA链诱导。
Streptomyces incarnatusNRRL8089 produces the antiviral, antifungal, antiprotozoal nucleoside antibiotic sinefungin. To enhance sinefungin production, multiple mutations were introduced to therpoBgene encoding RNA polymerase (RNAP) β-subunit at the target residues, D447, S453, H457, and R460. Sparse regression analysis using elastic-net lasso-ridge penalties on previously reported H457X mutations identified a numeric parameter set, which suggested that H457R/Y/F may cause production enhancement. H457R/R460C mutation successfully enhanced the sinefungin production by 3-fold, while other groups of mutations, such as D447G/R460C or D447G/H457Y, made moderate or even negative effects. To identify why the rif cluster residues have diverse effects on sinefungin production, an RNAP/DNA/mRNA complex model was constructed by homology modeling and molecular dynamics simulation. The 4 residues were located near the mRNA strand. Density functional theory–based calculation suggested that D447, H457, and R460 are in direct contact with ribonucleotide, and partially positive charges are induced by negatively charged chain of mRNA.