State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
PLoS One. 2012;7(9):e43176. doi: 10.1371/journal.pone.0043176. Epub 2012 Sep 11.
Agrobacterium tumefaciens strain C58 is a Gram-negative soil bacterium capable of inducing tumors (crown galls) on many dicotyledonous plants. The genome of A. tumefaciens strain C58 was re-annotated based on the Z-curve method. First, all the 'hypothetical genes' were re-identified, and 29 originally annotated 'hypothetical genes' were recognized to be non-coding open reading frames (ORFs). Theoretical evidence obtained from principal component analysis, clusters of orthologous groups of proteins occupation, and average length distribution showed that these non-coding ORFs were highly unlikely to encode proteins. Results from the reverse transcription-polymerase chain reaction (RT-PCR) experiments on three different growth stages of A. tumefaciens C58 confirmed that 23 (79%) of the identified non-coding ORFs have no transcripts in these growth stages. In addition, using theoretical prediction, 19 potential protein-coding genes were predicted to be new protein-coding genes. Fifteen (79%) of these genes were verified with RT-PCR experiments. The RT-PCR experimental results confirmed the reliability of our theoretical prediction, indicating that false-positive prediction and missing genes always exist in the annotation of A. tumefaciens C58 genome. The improved annotation will serve as a valuable resource for the research of the lifestyle, metabolism, and pathogenicity of A. tumefaciens C58. The re-annotation of A. tumefaciens C58 can be obtained from http://211.69.128.148/Atum/.
根癌农杆菌 C58 菌株是一种革兰氏阴性土壤细菌，能够在许多双子叶植物上诱导肿瘤（冠瘿）。根据 Z 曲线方法，重新注释了根癌农杆菌 C58 的基因组。首先，重新鉴定了所有“假设基因”，并识别出 29 个最初注释为“假设基因”的非编码开放阅读框（ORF）。主成分分析、同源簇蛋白占据和平均长度分布的理论证据表明，这些非编码 ORF 极不可能编码蛋白质。对根癌农杆菌 C58 三个不同生长阶段的反转录-聚合酶链反应（RT-PCR）实验结果证实，在这些生长阶段，23 个（79%）鉴定出的非编码 ORF 没有转录物。此外，通过理论预测，预测了 19 个潜在的蛋白编码基因是新的蛋白编码基因。其中 15 个（79%）通过 RT-PCR 实验得到验证。RT-PCR 实验结果证实了我们理论预测的可靠性，表明在根癌农杆菌 C58 基因组的注释中总是存在假阳性预测和缺失基因。改进的注释将成为研究根癌农杆菌 C58 生活方式、代谢和致病性的有价值的资源。根癌农杆菌 C58 的重新注释可以从 http://211.69.128.148/Atum/ 获得。
