Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle.
Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle.
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DOI：
10.1371/journal.pone.0043432
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Chisholm SW
中科院分区：
文献类型：
--
作者：
Waldbauer JR;Rodrigue S;Coleman ML;Chisholm SW
海洋中最丰富的初级生产者，蓝藻原绿球藻的生长与自然的24小时光暗周期紧密同步。我们试图量化转录组和蛋白质组动态之间的关系，这种专性光合自养生物的高度编排的响应，每天的能量供应的振荡的基础。使用RNA测序转录组学和基于质谱的定量蛋白质组学，我们测量了312个基因在光暗循环中每2小时配对的mRNA-蛋白质丰度的时间过程。这些时间表达模式揭示了转录本丰度的强烈振荡，其在蛋白质水平上被广泛抑制，mRNA水平的变化平均比相应的蛋白质高2.3倍。观察到的蛋白质水平振荡最强的是核糖核苷酸还原酶，这可能反映了对噬菌体感染的防御策略。大多数蛋白质的丰度峰值也比它们的转录物的丰度峰值滞后2-8小时，并且对于某些基因来说，这两者是完全反相的。虽然检测到大量的反义RNA，但显然不能解释观察到的表达水平之间的差异。从白天的碳固定到夜间呼吸，通过中央碳代谢的通量的重新定向与相对酶丰度的相当小的变化有关。我们的研究结果表明，在自然生态系统中常见的周期性刺激（如昼夜循环）的表达反应可以在mRNA和蛋白质水平之间显着分歧。与同源mRNA不同的蛋白质表达模式对转录组和元转录组数据在细胞代谢及其生物化学影响方面的解释有影响。
Growth of the ocean's most abundant primary producer, the cyanobacterium Prochlorococcus, is tightly synchronized to the natural 24-hour light-dark cycle. We sought to quantify the relationship between transcriptome and proteome dynamics that underlie this obligate photoautotroph's highly choreographed response to the daily oscillation in energy supply. Using RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics, we measured timecourses of paired mRNA-protein abundances for 312 genes every 2 hours over a light-dark cycle. These temporal expression patterns reveal strong oscillations in transcript abundance that are broadly damped at the protein level, with mRNA levels varying on average 2.3 times more than the corresponding protein. The single strongest observed protein-level oscillation is in a ribonucleotide reductase, which may reflect a defense strategy against phage infection. The peak in abundance of most proteins also lags that of their transcript by 2–8 hours, and the two are completely antiphase for some genes. While abundant antisense RNA was detected, it apparently does not account for the observed divergences between expression levels. The redirection of flux through central carbon metabolism from daytime carbon fixation to nighttime respiration is associated with quite small changes in relative enzyme abundances. Our results indicate that expression responses to periodic stimuli that are common in natural ecosystems (such as the diel cycle) can diverge significantly between the mRNA and protein levels. Protein expression patterns that are distinct from those of cognate mRNA have implications for the interpretation of transcriptome and metatranscriptome data in terms of cellular metabolism and its biogeochemical impact.
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影响因子：
64.8
作者：
CRICK, F
通讯作者：
CRICK, F
氰基属的新型代谢属性，包括一组单细胞氮固定氰基。
影响因子：
6.4
作者：
Bandyopadhyay A;Elvitigala T;Welsh E;Stöckel J;Liberton M;Min H;Sherman LA;Pakrasi HB
通讯作者：
Pakrasi HB
影响因子：
5.8
作者：
Craig, R;Beavis, RC
通讯作者：
Beavis, RC
DOI：
10.1073/pnas.071538098
发表时间：
2001-04-10
影响因子：
11.1
作者：
Grünenfelder, B;Rummel, G;Jenal, U
通讯作者：
Jenal, U
影响因子：
3.7
作者：
Britos L;Abeliuk E;Taverner T;Lipton M;McAdams H;Shapiro L
通讯作者：
Shapiro L