Dissecting nutrient-related co-expression networks in phosphate starved poplars

Phosphorus (P) is an essential plant nutrient, but its availability is often limited in soil. Here, we studied changes in the transcriptome and in nutrient element concentrations in leaves and roots of poplars (Populus × canescens) in response to P deficiency. P starvation resulted in decreased concentrations of S and major cations (K, Mg, Ca), in increased concentrations of N, Zn and Al, while C, Fe and Mn were only little affected. In roots and leaves >4,000 and >9,000 genes were differently expressed upon P starvation. These genes clustered in eleven co-expression modules of which seven were correlated with distinct elements in the plant tissues. One module (4.7% of all differentially expressed genes) was strongly correlated with changes in the P concentration in the plant. In this module the GO term “response to P starvation” was enriched with phosphoenolpyruvate carboxylase kinases, phosphatases and pyrophosphatases as well as regulatory domains such as SPX, but no phosphate transporters. The P-related module was also enriched in genes of the functional category “galactolipid synthesis”. Galactolipids substitute phospholipids in membranes under P limitation. Two modules, one correlated with C and N and the other with biomass, S and Mg, were connected with the P-related module by co-expression. In these modules GO terms indicating “DNA modification” and “cell division” as well as “defense” and “RNA modification” and “signaling” were enriched; they contained phosphate transporters. Bark storage proteins were among the most strongly upregulated genes in the growth-related module suggesting that N, which could not be used for growth, accumulated in typical storage compounds. In conclusion, weighted gene coexpression network analysis revealed a hierarchical structure of gene clusters, which separated phosphate starvation responses correlated with P tissue concentrations from other gene modules, which most likely represented transcriptional adjustments related to down-stream nutritional changes and stress.磷（Phosphorus, P）是植物必需的营养元素，但其在土壤中的生物有效性往往受限。本研究针对灰杨（Populus × canescens）在磷缺乏条件下的叶片与根系转录组及营养元素浓度变化展开分析。磷饥饿会导致植株体内硫（S）及主要阳离子（钾K、镁Mg、钙Ca）浓度降低，同时使氮（N）、锌（Zn）与铝（Al）浓度升高，而碳（C）、铁（Fe）及锰（Mn）仅受轻微影响。在根系与叶片中，分别有超过4000个和9000个基因在磷饥饿条件下发生差异表达。这些基因可聚类为11个共表达模块，其中7个模块与植物组织中的特定元素含量显著相关。有一个模块（占所有差异表达基因的4.7%）与植株体内磷浓度的变化呈强相关。该模块中，基因本体（Gene Ontology, GO）术语“磷饥饿响应”显著富集，所包含的基因涵盖磷酸烯醇式丙酮酸羧化酶激酶、磷酸酶、焦磷酸酶以及SPX调控结构域，但未包含磷酸盐转运蛋白。该磷相关模块同时还富集了“半乳糖脂合成”功能类别的基因，在磷限制条件下，半乳糖脂可替代膜结构中的磷脂。另有两个模块，其一与碳、氮含量相关，另一与生物量、硫及镁含量相关，二者通过共表达网络与磷相关模块产生关联。在这两个模块中，富集了代表“DNA修饰”“细胞分裂”“防御反应”“RNA修饰”及“信号转导”的GO术语，且包含磷酸盐转运蛋白。树皮贮藏蛋白是生长相关模块中上调表达幅度最为显著的基因之一，这表明原本可用于植株生长的氮元素以典型贮藏化合物的形式累积。综上，加权基因共表达网络分析揭示了基因簇的层级结构：将与植株组织磷浓度相关的磷饥饿响应基因簇，与其他大概率代表下游营养状态改变及胁迫相关的转录调控应答的基因模块区分开来。