Re-annotating the Mycoplasma pneumoniae genome sequence:: adding value, function and reading frames
Re-annotating the Mycoplasma pneumoniae genome sequence:: adding value, function and reading frames
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DOI：
10.1093/nar/28.17.3278
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发表时间：
2000-09-01
影响因子：
14.9
通讯作者：
Bork, P
中科院分区：
文献类型：
--
作者：
Dandekar, T;Huynen, M;Bork, P
在原始序列提交四年后，我们重新注释了肺炎支原体的基因组以纳入新的数据，ORFs的总数从677增加到688（在基因间区域预测了10个新蛋白，另外两个通过质谱新鉴定，一个蛋白ORF被排除）和来自39至42个基因的RNA的数量，对于现在35种tRNA中的19种和其他6种功能性RNA，重新注释了确切的基因组位置，并鉴定了两种新的tRNA（Leu）和一种小的200 nt RNA。16个蛋白质阅读框延长，8个缩短。对于每个ORF，引入了一致的注释词汇表。注释推理，注释类别和与其他已发表的数据M。pneumoniae的功能分配。实验证据包括二维凝胶电泳结合质谱分析以及本研究的基因表达数据。与原始注释相比，我们将具有预测功能特征的蛋白质数量从349增加到458，其中包括36个新的预测和73个已发表文献证实的蛋白质分配。此外，相对于先前的注释，有23个减少和30个增加。mRNA表达数据支持184个功能上未分配的阅读框的转录。
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data, The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes, For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M. pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458, The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.