A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation.
A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation.
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DOI：
10.1073/pnas.2010087117
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发表时间：
2020-11-24
影响因子：
11.1
通讯作者：
Gourse RL
中科院分区：
文献类型：
--
作者：
Henry KK;Ross W;Myers KS;Lemmer KC;Vera JM;Landick R;Donohue TJ;Gourse RL
细菌启动子通常通过与大肠杆菌-10和-35共有元件的相似性来预测。尽管这些元件在不同的细菌门中高度保守，但我们分析的球形红杆菌和另外两种α-变形菌的启动子中只有30%至43%含有-7T，-10元件中的碱基存在于90%至99%的非α-变形菌启动子中。体外测试的 16 个球形 R. sphaeroides 启动子中的 15 个缺乏 -7T，其表达非常弱，但我们鉴定了一个重要的转录因子 CarD，它激活了所有 15 个启动子。我们认为，在共有元件中缺乏关键碱基的启动子可以通过单个转录因子协调大量基因的表达来塑造转录组。使用带有纯化 RNA 聚合酶 (RNAP) 的体外转录系统来研究光异养 α-变形杆菌球形红细菌中的 rRNA 合成，我们发现了主要全酶识别的启动子的一个令人惊讶的特征。 R. sphaeroides rRNA启动子的转录出乎意料地弱，这与-7T的缺失有关，-7T是在大多数细菌物种启动子的-10个元件的最后一个位置发现的高度保守的胸腺嘧啶。三个 rRNA 启动子中 -7 位的胸腺嘧啶取代大大增加了内在启动子活性，表明 R. sphaeroides RNAP 在存在时可以利用 -7T。 rRNA 启动子由纯化的球形 R. sphaeroides CarD 激活，这是一种在许多细菌物种中发现的转录因子，但在 β-和 γ-变形菌中不存在。总体而言，CarD 增加了体外测试的 16 个缺乏 -7T 的天然球形 R. sphaeroides 启动子中的 15 个的活性，而它对含有 -7T 的 4 个天然启动子中的 3 个没有影响。对球形 R. sphaeroides 和其他两种 α-变形菌物种的启动子进行全基因组生物信息分析表明，30% 至 43% 含有 -7T，而来自非 α-变形菌的启动子中 90% 至 99% 含有 -7T。因此，缺乏−7T的启动子似乎在α-变形菌中广泛存在，并且可能已经进化出远离共识的启动子，以使其能够通过CarD等转录因子进行协调调节。我们观察到，当细胞进入静止期时，球形 R. sphaeroides CarD 水平大幅降低，这表明当细胞进入静止期（细菌核糖体合成下降的生长阶段）时，CarD 激活的减少可能有助于抑制 rRNA 转录。
Bacterial promoters are often predicted by similarity to the Escherichia coli −10 and −35 consensus elements. Although these elements are highly conserved in diverse bacterial phyla, only 30 to 43% of promoters we analyzed from Rhodobacter sphaeroides and two other α-proteobacteria contained −7T, a base in the −10 element present in 90 to 99% of promoters from non–α-proteobacteria. Expression from 15 of 16 R. sphaeroides promoters tested in vitro that lacked −7T was very weak, but we identified an essential transcription factor, CarD, that activated all 15 of these promoters. We suggest that promoters lacking a critical base in a consensus element can shape the transcriptome by coordinating expression of large numbers of genes by a single transcription factor. Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacterium Rhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription from R. sphaeroides rRNA promoters was unexpectedly weak, correlating with absence of −7T, the very highly conserved thymine found at the last position in −10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position −7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating that R. sphaeroides RNAP can utilize −7T when present. rRNA promoters were activated by purified R. sphaeroides CarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 native R. sphaeroides promoters tested in vitro that lacked −7T, whereas it had no effect on three of the four native promoters that contained −7T. Genome-wide bioinformatic analysis of promoters from R. sphaeroides and two other α-proteobacterial species indicated that 30 to 43% contained −7T, whereas 90 to 99% of promoters from non–α-proteobacteria contained −7T. Thus, promoters lacking −7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction in R. sphaeroides CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.
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影响因子：
14.9
作者：
Davis E;Chen J;Leon K;Darst SA;Campbell EA
通讯作者：
Campbell EA
影响因子：
16.6
作者：
Jeong Y;Kim JN;Kim MW;Bucca G;Cho S;Yoon YJ;Kim BG;Roe JH;Kim SC;Smith CP;Cho BK
通讯作者：
Cho BK
影响因子：
64.5
作者：
Feklistov A;Darst SA
通讯作者：
Darst SA
对RNA聚合酶识别的结构洞察力和粘膜CDNL的基本功能。
影响因子：
3.7
作者：
Gallego-García A;Mirassou Y;García-Moreno D;Elías-Arnanz M;Jiménez MA;Padmanabhan S
通讯作者：
Padmanabhan S
影响因子：
6.4
作者：
Lennon CW;Lemmer KC;Irons JL;Sellman MI;Donohue TJ;Gourse RL;Ross W
通讯作者：
Ross W