Transcriptomic differences between E. coli B REL606 and K-12 MG1655

Transcriptome profiles were analyzed using the samples taken at the exponential and stationary phases during the cultivation of REL606 and MG1655 in LB medium. At the exponential growth phase, most highly expressed genes of B were those for replication, translation, or nucleotide transport and metabolism, while many of the K-12 genes were involved in cell motility, transcription, carbohydrate transport, or energy production. At the stationary phase, many of the genes highly expressed in B were for transport and metabolism of various amino acids and carbohydrates, whereas those in K-12 had functions related to cell motility, ribosomal subunit protein production, or energy generation. Many genes in REL606 and MG1655 showed highly distinct expression levels irrespective of growth conditions. Highly expressed genes in REL606 included those encoding enzymes for biosynthesis of L-arginine (argAGDECBHI) and branched-chain amino acid (ilvGMEDA), and those encoding a subunit of the L-arginine transporter (artJ), cytochrome b562 (cybC), subunits of the histidine ABC transporter (hisPJ), cytotoxins (hokED), outer membrane porin (ompF), L-arginine decarboxylase (speA), and cell division inhibitor (sulA). Highly expressed genes in MG1655 included those for chemotaxis (cheZYRWA, tap, trg, tsr), Lon protease (lon), C4-dicarboxylate-sensing histidine kinase (dcuS), chaperones (clpB, dnaK, groES, htpG, ibpA), the major subunit of type 1 fimbriae (fimA), a regulator of flagellar biosynthesis (flhC), glycerol-3-phosphate-dehydrogenase (glpABCD), glycerophosphoryl diester phosphodiesterase (glpQ), glycerol-3-phosphate transporter (glpT), hydrogenase 2 (hybCBO), outer membrane porins (nmpC, ompA, ompC), and galactitol transport and metabolism (gatYZC). All microarray experiments were performed in duplicate with dye-swapping. The probes were spotted in duplicate onto the microarray. Thus, the log2 of the intensity ratio with the two dyes for each spot was calculated from up to four values from the duplicated spot on the microarray and the dye-swap experiment.

本研究以LB培养基中培养的REL606与MG1655菌株在指数生长期与稳定期采集的样本为材料，对其转录组表达谱（transcriptome profile）进行分析。在指数生长阶段，REL606的高表达基因多参与复制、翻译或核苷酸转运与代谢过程；而MG1655（K-12菌株）的多数高表达基因则涉及细胞运动、转录、碳水化合物转运或能量生成。进入稳定期后，REL606的高表达基因多负责各类氨基酸与碳水化合物的转运及代谢；而MG1655的高表达基因则多与细胞运动、核糖体亚基蛋白合成或能量产生相关。无论生长条件如何，REL606与MG1655中的大量基因均呈现出显著差异的表达水平。REL606的高表达基因包括：编码L-精氨酸（L-arginine，argAGDECBHI）与支链氨基酸（branched-chain amino acid，ilvGMEDA）生物合成酶的基因、编码L-精氨酸转运蛋白亚基（artJ）的基因、细胞色素b562（cybC）编码基因、组氨酸ABC转运蛋白亚基（hisPJ）编码基因、细胞毒素（hokED）编码基因、外膜孔蛋白（ompF）编码基因、L-精氨酸脱羧酶（speA）编码基因以及细胞分裂抑制剂（sulA）编码基因。MG1655的高表达基因则涵盖：参与趋化作用的基因（cheZYRWA、tap、trg、tsr）、Lon蛋白酶（lon）编码基因、C4-二羧酸感应组氨酸激酶（dcuS）编码基因、分子伴侣（clpB、dnaK、groES、htpG、ibpA）编码基因、1型菌毛主要亚基（fimA）编码基因、鞭毛生物合成调控因子（flhC）编码基因、甘油-3-磷酸脱氢酶（glpABCD）编码基因、甘油磷酸二酯磷酸二酯酶（glpQ）编码基因、甘油-3-磷酸转运蛋白（glpT）编码基因、氢化酶2（hybCBO）编码基因、外膜孔蛋白（nmpC、ompA、ompC）编码基因以及半乳糖醇转运与代谢（gatYZC）相关基因。所有微阵列（microarray）实验均采用重复实验并辅以染料交换（dye-swapping）设计。探针在微阵列上以重复点样方式排布。因此，针对每个点样位点，可基于微阵列重复点样与染料交换实验得到的至多四组数据，计算两种荧光染料对应的信号强度比的以2为底的对数值。