School of Biological Sciences, University of Reading, Reading, RG6 6AJ, UK.
Genome Biol. 2011 Oct 21;12(10):R106. doi: 10.1186/gb-2011-12-10-r106.
The rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere.
Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere.
Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants.
根际是植物根系周围富含微生物的区域，是生物圈生产力的关键决定因素。比较转录组学被用来研究根际定殖过程中的一般和植物特异性适应。根瘤菌属生物变种 viciae 在豌豆（其豆科结瘤宿主）、紫花苜蓿（非宿主豆科植物）和甜菜（非豆科植物）的根际中生长。将基因表达数据与代谢和转运组图谱进行比较，以了解对根际的适应。
碳代谢主要由有机酸主导，强烈偏向芳香族氨基酸、C1 和 C2 化合物。这在所有根际中都得到了证实，即需要诱导乙醛酸循环来进行 C2 代谢和糖异生。在根瘤菌中，糖抑制糖异生，这表明尽管在根际中诱导了许多糖和潜在的复杂碳水化合物转运系统，但它们不如有机酸重要的碳源。确定了一个共同的根际诱导基因核心，其中 66%的基因功能未知。许多基因在豆科植物的根际中被诱导，但在甜菜中没有，其中一些是植物特异性的。质粒 pRL8 可以被认为是豌豆根际特异性的，使根瘤菌能够适应其宿主。许多上调基因的突变降低了其在豌豆根际定殖的竞争力，而在豌豆根际中特异性上调的两个基因则降低了其在豌豆根际的定殖能力，但对紫花苜蓿根际的定殖没有影响。
比较转录组分析能够区分在植物根际定殖中保守的因素，以及对宿主植物的精细特异性适应。
