Tomas Christopher A, Alsaker Keith V, Bonarius Hendrik P J, Hendriksen Wouter T, Yang He, Beamish Jeffrey A, Paredes Carlos J, Papoutsakis Eleftherios T
Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60208, USA.
J Bacteriol. 2003 Aug;185(15):4539-47. doi: 10.1128/JB.185.15.4539-4547.2003.
The large-scale transcriptional program of two Clostridium acetobutylicum strains (SKO1 and M5) relative to that of the parent strain (wild type [WT]) was examined by using DNA microarrays. Glass DNA arrays containing a selected set of 1,019 genes (including all 178 pSOL1 genes) covering more than 25% of the whole genome were designed, constructed, and validated for data reliability. Strain SKO1, with an inactivated spo0A gene, displays an asporogenous, filamentous, and largely deficient solventogenic phenotype. SKO1 displays downregulation of all solvent formation genes, sigF, and carbohydrate metabolism genes (similar to genes expressed as part of the stationary-phase response in Bacillus subtilis) but also several electron transport genes. A major cluster of genes upregulated in SKO1 includes abrB, the genes from the major chemotaxis and motility operons, and glycosylation genes. Strain M5 displays an asporogenous and nonsolventogenic phenotype due to loss of the megaplasmid pSOL1, which contains all genes necessary for solvent formation. Therefore, M5 displays downregulation of all pSOL1 genes expressed in the WT. Notable among other genes expressed more highly in WT than in M5 were sigF, several two-component histidine kinases, spo0A, cheA, cheC, many stress response genes, fts family genes, DNA topoisomerase genes, and central-carbon metabolism genes. Genes expressed more highly in M5 include electron transport genes (but different from those downregulated in SKO1) and several motility and chemotaxis genes. Most of these expression patterns were consistent with phenotypic characteristics. Several of these expression patterns are new or different from what is known in B. subtilis and can be used to test a number of functional-genomic hypotheses.
利用DNA微阵列技术，研究了两株丙酮丁醇梭菌（SKO1和M5）相对于亲本菌株（野生型[WT]）的大规模转录程序。设计、构建并验证了包含一组选定的1019个基因（包括所有178个pSOL1基因）的玻璃DNA阵列，这些基因覆盖了整个基因组的25%以上，以确保数据可靠性。菌株SKO1的spo0A基因失活，表现出无芽孢、丝状且在很大程度上缺乏溶剂生成表型。SKO1表现出所有溶剂形成基因、sigF以及碳水化合物代谢基因（类似于枯草芽孢杆菌中作为稳定期反应一部分表达的基因）的下调，但也有几个电子传递基因下调。在SKO1中上调的主要基因簇包括abrB、主要趋化性和运动性操纵子的基因以及糖基化基因。菌株M5由于丢失了包含溶剂形成所需所有基因的大质粒pSOL1，表现出无芽孢和非溶剂生成表型。因此，M5表现出WT中表达的所有pSOL1基因的下调。在WT中比在M5中表达更高的其他基因中，值得注意的有sigF、几个双组分组氨酸激酶、spo0A、cheA、cheC、许多应激反应基因、fts家族基因、DNA拓扑异构酶基因和中心碳代谢基因。在M5中表达更高的基因包括电子传递基因（但与SKO1中下调的基因不同）以及几个运动性和趋化性基因。这些表达模式大多与表型特征一致。其中一些表达模式是新的，或者与枯草芽孢杆菌中已知的不同，可用于检验一些功能基因组学假说。
