Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.
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Rho独立转录终结剂的快速，准确，计算发现阐明了它们与DNA摄取的关系。
DOI：
10.1186/gb-2007-8-2-r22
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Salzberg, Steven L.
中科院分区：
文献类型：
--
作者：
Kingsford, Carleton L.;Ayanbule, Kunmi;Salzberg, Steven L.
利用一种新的计算方法，从343种原核生物中获得了大量预测的不依赖Rho因子的转录终止子，这为了解它们与DNA摄取的关系提供了见解。
在许多原核生物中，DNA到RNA的转录在一个发夹环之后由一段富含胸腺嘧啶的DNA片段终止。检测这种不依赖Rho因子的转录终止子可以阐明细菌基因组的组织情况，并能改进基因组注释。以前用于预测不依赖Rho因子的终止子的计算方法要么速度慢，要么在所考虑的生物种类上有限。
我们描述了TransTermHP，这是一种快速且准确地检测不依赖Rho因子的转录终止子的新计算方法。我们预测了343个原核生物基因组中终止子的位置，这是现有的最大规模的预测集合。在枯草芽孢杆菌中，我们能够检测到93%的已知终止子，假阳性率仅为6%，与最知名的方法相当。在厚壁菌门之外，我们发现不依赖Rho因子的终止作用在奈瑟氏菌属和弧菌属、巴斯德氏菌科（包括嗜血杆菌属）以及其他几个物种中起着重要作用。在奈瑟氏菌属和巴斯德氏菌科中，终止子发夹结构经常由紧密间隔的、互补的外源DNA摄取信号序列形成。我们量化了终止子包含这些序列的倾向。在此过程中，我们首次讨论了杜克雷嗜血杆菌和产琥珀酸曼氏杆菌中潜在的摄取信号，并讨论了终止子内摄取信号序列的特定配置偏好。
我们用于检测转录终止子的这种新的快速且准确的方法使我们能够识别和分析许多新基因组中的终止子，并在几个以前未报道过的物种中识别DNA摄取信号序列。我们的软件和预测结果是免费提供的。
Using a novel computational method, an extensive collection of predicted Rho-independent transcription terminators is derived from 343 prokaryotes, offering insight into their relationship to DNA uptake In many prokaryotes, transcription of DNA to RNA is terminated by a thymine-rich stretch of DNA following a hairpin loop. Detecting such Rho-independent transcription terminators can shed light on the organization of bacterial genomes and can improve genome annotation. Previous computational methods to predict Rho-independent terminators have been slow or limited in the organisms they consider. We describe TransTermHP, a new computational method to rapidly and accurately detect Rho-independent transcription terminators. We predict the locations of terminators in 343 prokaryotic genomes, representing the largest collection of predictions available. In Bacillus subtilis, we can detect 93% of known terminators with a false positive rate of just 6%, comparable to the best-known methods. Outside the Firmicutes division, we find that Rho-independent termination plays a large role in the Neisseria and Vibrio genera, the Pasteurellaceae (including the Haemophilus genus) and several other species. In Neisseria and Pasteurellaceae, terminator hairpins are frequently formed by closely spaced, complementary instances of exogenous DNA uptake signal sequences. We quantify the propensity for terminators to include these sequences. In the process, we provide the first discussion of potential uptake signals in Haemophilus ducreyi and Mannheimia succiniciproducens, and we discuss the preference for a particular configuration of uptake signal sequences within terminators. Our new fast and accurate method for detecting transcription terminators has allowed us to identify and analyze terminators in many new genomes and to identify DNA uptake signal sequences in several species where they have not been previously reported. Our software and predictions are freely available.
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巴斯德菌科 DNA 摄取信号序列的进化稳定性
DOI：
10.1073/pnas.0306366101
发表时间：
2004-03-30
影响因子：
11.1
作者：
Bakkali, M;Chen, TY;Redfield, RJ
通讯作者：
Redfield, RJ
11 个碱基对序列决定了嗜血杆菌转化过程中 DNA 吸收的特异性
影响因子：
3.5
作者：
DANNER, DB;DEICH, RA;SMITH, HO
通讯作者：
SMITH, HO
预测单链 RNA 二级结构的快速算法
DOI：
10.1073/pnas.77.11.6309
发表时间：
1980-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
NUSSINOV, R;JACOBSON, AB
通讯作者：
JACOBSON, AB
影响因子：
14.9
作者：
Unniraman, S;Prakash, R;Nagaraja, V
通讯作者：
Nagaraja, V
DOI：
10.1073/pnas.92.19.8793
发表时间：
1995-09-12
影响因子：
11.1
作者：
WILSON, KS;VONHIPPEL, PH
通讯作者：
VONHIPPEL, PH