Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli.
Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli.
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DOI：
10.1093/nar/gkw273
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发表时间：
2016-08-19
影响因子：
14.9
通讯作者：
Stavans J
中科院分区：
文献类型：
--
作者：
Arbel-Goren R;Tal A;Parasar B;Dym A;Costantino N;Muñoz-García J;Court DL;Stavans J
转录后调节过程可能改变转录水平并影响细胞间变异性或噪音。我们研究了小RNA下调，以阐明其对大肠杆菌铁稳态网络噪声的影响。在这个网络中，小RNA RyhB与靶基因的转录本在铁胁迫下发生化学计量降解。使用单分子荧光原位杂交，我们测量的RyhB调节基因sodB和fumA在个别细胞的铁剥夺的功能的转录本数量。我们观察到的噪音与铁应力单调增加，但没有证据表明理论预测，增强化学计量的转录本数量的波动，也没有转录本分布的波动行为。在单个细胞中直接检测RyhB表明，当RyhB产生显著时，其噪声远小于这两个靶标的噪声。一个广义的两态模型的突发性转录，忽略RyhB的波动定量描述了依赖的噪音和转录分布铁剥夺，使提取体内RyhB介导的转录降解率。转录本的阈值线性行为表明RyhB与其两种靶转录本之间的有效体内相互作用强度相当。引人注目的是，细菌细胞的反应表现出毛皮依赖性，开关样激活，而不是一个梯度响应铁剥夺。
Post-transcriptional regulatory processes may change transcript levels and affect cell-to-cell variability or noise. We study small-RNA downregulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli. In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of target genes in response to iron stress. Using single-molecule fluorescence in situ hybridization, we measured transcript numbers of the RyhB-regulated genes sodB and fumA in individual cells as a function of iron deprivation. We observed a monotonic increase of noise with iron stress but no evidence of theoretically predicted, enhanced stoichiometric fluctuations in transcript numbers, nor of bistable behavior in transcript distributions. Direct detection of RyhB in individual cells shows that its noise is much smaller than that of these two targets, when RyhB production is significant. A generalized two-state model of bursty transcription that neglects RyhB fluctuations describes quantitatively the dependence of noise and transcript distributions on iron deprivation, enabling extraction of in vivo RyhB-mediated transcript degradation rates. The transcripts’ threshold-linear behavior indicates that the effective in vivo interaction strength between RyhB and its two target transcripts is comparable. Strikingly, the bacterial cell response exhibits Fur-dependent, switch-like activation instead of a graded response to iron deprivation.
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影响因子：
11.3
作者：
Beisel CL;Storz G
通讯作者：
Storz G
影响因子：
64.5
作者：
Feng L;Rutherford ST;Papenfort K;Bagert JD;van Kessel JC;Tirrell DA;Wingreen NS;Bassler BL
通讯作者：
Bassler BL
影响因子：
14.9
作者：
Arbel-Goren, Rinat;Tal, Asaf;Stavans, Joel
通讯作者：
Stavans, Joel
DOI：
10.1073/pnas.1100432108
发表时间：
2011-07-26
影响因子：
11.1
作者：
Hao, Yue;Zhang, Zhongge J.;Shi, Hualin
通讯作者：
Shi, Hualin
DOI：
10.1007/4735_86
发表时间：
2005-01-01
期刊：
SYSTEMS BIOLOGY: DEFINITIONS AND PERSPECTIVES
影响因子：
--
作者：
Elf, Johan;Paulsson, Johan;Ehrenberg, Mans
通讯作者：
Ehrenberg, Mans