Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 977-152, Berkeley, California 94720, USA.
J Bacteriol. 2011 Oct;193(20):5716-27. doi: 10.1128/JB.05563-11. Epub 2011 Aug 12.
We used high-resolution tiling microarrays and 5' RNA sequencing to identify transcripts in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. We identified the first nucleotide position for 1,124 transcripts, including 54 proteins with leaderless transcripts and another 72 genes for which a major transcript initiates within the upstream protein-coding gene, which confounds measurements of the upstream gene's expression. Sequence analysis of these promoters showed that D. vulgaris prefers -10 and -35 boxes different from those preferred by Escherichia coli. A total of 549 transcripts ended at intrinsic (rho-independent) terminators, but most of the other transcripts seemed to have variable ends. We found low-level antisense expression of most genes, and the 5' ends of these transcripts mapped to promoter-like sequences. Because antisense expression was reduced for highly expressed genes, we suspect that elongation of nonspecific antisense transcripts is suppressed by transcription of the sense strand. Finally, we combined the transcript results with comparative analysis and proteomics data to make 505 revisions to the original annotation of 3,531 proteins: we removed 255 (7.5%) proteins, changed 123 (3.6%) start codons, and added 127 (3.7%) proteins that had been missed. Tiling data had higher coverage than shotgun proteomics and hence led to most of the corrections, but many errors probably remain. Our data are available at http://genomics.lbl.gov/supplemental/DvHtranscripts2011/.
我们使用高分辨率平铺微阵列和 5' RNA 测序来鉴定脱硫弧菌 Hildenborough 的转录本，这是一种模型硫酸盐还原菌。我们确定了 1124 个转录本的第一个核苷酸位置，包括 54 个无启动子转录本的蛋白质和另外 72 个基因，这些基因的主要转录本起始于上游蛋白质编码基因内，这使得上游基因表达的测量变得复杂。这些启动子的序列分析表明，脱硫弧菌更喜欢与大肠杆菌不同的 -10 和 -35 框。共有 549 个转录本在内在（rho 独立）终止子处终止，但大多数其他转录本似乎具有可变末端。我们发现大多数基因都有低水平的反义表达，这些转录本的 5' 端映射到启动子样序列。由于高度表达的基因的反义表达减少，我们怀疑非特异性反义转录本的延伸被正义链的转录所抑制。最后，我们将转录本结果与比较分析和蛋白质组学数据相结合，对 3531 个蛋白质的原始注释进行了 505 次修订：我们删除了 255 个（7.5%）蛋白质，改变了 123 个（3.6%）起始密码子，并添加了 127 个（3.7%）之前未被发现的蛋白质。平铺数据的覆盖度高于鸟枪法蛋白质组学，因此导致了大部分的修正，但可能仍有许多错误。我们的数据可在 http://genomics.lbl.gov/supplemental/DvHtranscripts2011/ 获得。
