Salgado H, Moreno-Hagelsieb G, Smith T F, Collado-Vides J
Centro de Investigacion sobre Fijacion de Nitrogeno, Universidad Nacional Autónoma de México, A.P. 565-A Cuernavaca, Morelos 62100, Mexico.
Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6652-7. doi: 10.1073/pnas.110147297.
The rich knowledge of operon organization in Escherichia coli, together with the completed chromosomal sequence of this bacterium, enabled us to perform an analysis of distances between genes and of functional relationships of adjacent genes in the same operon, as opposed to adjacent genes in different transcription units. We measured and demonstrated the expected tendencies of genes within operons to have much shorter intergenic distances than genes at the borders of transcription units. A clear peak at short distances between genes in the same operon contrasts with a flat frequency distribution of genes at the borders of transcription units. Also, genes in the same operon tend to have the same physiological functional class. The results of these analyses were used to implement a method to predict the genomic organization of genes into transcription units. The method has a maximum accuracy of 88% correct identification of pairs of adjacent genes to be in an operon, or at the borders of transcription units, and correctly identifies around 75% of the known transcription units when used to predict the transcription unit organization of the E. coli genome. Based on the frequency distance distributions, we estimated a total of 630 to 700 operons in E. coli. This step opens the possibility of predicting operon organization in other bacteria whose genome sequences have been finished.
大肠杆菌中丰富的操纵子组织知识，以及该细菌完整的染色体序列，使我们能够分析同一操纵子中基因之间的距离以及相邻基因的功能关系，这与不同转录单元中的相邻基因形成对比。我们测量并证明了操纵子内基因的基因间距离比转录单元边界处的基因短得多的预期趋势。同一操纵子中基因间短距离处的明显峰值与转录单元边界处基因的平坦频率分布形成对比。此外，同一操纵子中的基因往往具有相同的生理功能类别。这些分析结果被用于实施一种预测基因基因组组织成转录单元的方法。该方法在正确识别相邻基因对是否在操纵子中或转录单元边界处的准确率最高可达88%，当用于预测大肠杆菌基因组的转录单元组织时，能正确识别约75%的已知转录单元。基于频率距离分布，我们估计大肠杆菌中共有630至700个操纵子。这一步为预测其他已完成基因组序列的细菌中的操纵子组织开辟了可能性。
