Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon:: Pyrococcus furiosus grown on carbohydrates or peptides
Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon:: Pyrococcus furiosus grown on carbohydrates or peptides
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DOI：
10.1128/jb.185.13.3935-3947.2003
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发表时间：
2003-07-01
影响因子：
3.2
通讯作者：
Adams, MWW
中科院分区：
文献类型：
--
作者：
Schut, GJ;Brehm, SD;Adams, MWW
第一个完整的基因组DNA微阵列是通过使用2,065个开放阅读框架（ORF），已被注释的基因组中的Pyrococcus furiosus（最佳生长温度，100 degreesC）的超嗜热菌或非嗜盐古菌构建的。这被用来确定在95 ℃下生长的细胞中的相对转录水平，其中肽或碳水化合物（麦芽糖）用作主要碳源。大约20%（398/2065）的ORF在两种生长条件下似乎都没有显著表达。在剩下的1，667个ORF中，其中125个（8%）的表达在两种培养物之间差异超过5倍，125个中的82个（65%）似乎是操纵子的一部分，表明广泛的协调调节。在27个受调控的操纵子中，有5个编码（保守的）假设蛋白质。在麦芽糖生长的细胞中，总共有18个操纵子被上调（大于5倍），包括负责麦芽糖转运和12种氨基酸、鸟氨酸和柠檬酸循环中间产物的生物合成的操纵子。在肽生长的细胞中，总共有9个操纵子被上调（超过5倍），包括编码参与酰基和芳基酸以及2-酮酸生产的酶的那些，这些酶用于能量保存。用过的生长培养基的分析证实了在肽上生长期间支链和芳香酸的产生。此外，糖代谢途径中的六种非连接酶被调节超过五倍--三种在麦芽糖生长的细胞中是不寻常的糖酵解途径所特有的，三种在肽生长的细胞中是异生所特有的。16种代谢酶的催化活性，其表达似乎在两种细胞类型中高度调节，与微阵列数据非常相关。微阵列数据揭示的协调调节程度是出乎意料的，表明激烈原杆菌可以很容易地适应其主要碳源的变化。
The first complete-genome DNA microarray was constructed for a hyperthermophile or a nonhalophilic archaeon by using the 2,065 open reading frames (ORFs) that have been annotated in the genome of Pyrococcus furiosus (optimal growth temperature, 100degreesC). This was used to determine relative transcript levels in cells grown at 95degreesC with either peptides or a carbohydrate (maltose) used as the primary carbon source. Approximately 20% (398 of 2065) of the ORFs did not appear to be significantly expressed under either growth condition. Of the remaining 1,667 ORFs, the expression of 125 of them (8%) differed by more than fivefold between the two cultures, and 82 of the 125 (65%) appear to be part of operons, indicating extensive coordinate regulation. Of the 27 operons that are regulated, 5 of them encode (conserved) hypothetical proteins. A total of 18 operons are up-regulated (greater than fivefold) in maltose-grown cells, including those responsible for maltose transport and for the biosynthesis of 12 amino acids, of ornithine, and of citric acid cycle intermediate products. A total of nine operons are up-regulated (greater than fivefold) in peptide-grown cells, including those encoding enzymes involved in the production of acyl and aryl acids and 2-ketoacids, which are used for energy conservation. Analyses of the spent growth media confirmed the production of branched-chain and aromatic acids during growth on peptides. In addition, six nonlinked enzymes in the pathways of sugar metabolism were regulated more than fivefold-three in maltose-grown cells that are unique to the unusual glycolytic pathway and three in peptide-grown cells that are unique to gluconeogenesis. The catalytic activities of 16 metabolic enzymes whose expression appeared to be highly regulated in the two cell types correlated very well with the microarray data. The degree of coordinate regulation revealed by the microarray data was unanticipated and shows that P. furiosus can readily adapt to a change in its primary carbon source.