Transcriptomic Analysis of Responses to Imbalanced Carbon: Nitrogen Availabilities in Rice Seedlings

Abstract

The internal C:N balance must be tightly controlled for the normal growth and development of plants. However, the underlying mechanisms, by which plants sense and balance the intracellular C:N status correspondingly to exogenous C:N availabilities remain elusive. In this study, we use comparative gene expression analysis to identify genes that are responsive to imbalanced C:N treatments in the aerial parts of rice seedlings. Transcripts of rice seedlings treated with four C:N availabilities (1:1, 1:60, 60:1 and 60:60) were compared and two groups of genes were classified: high C:low N responsive genes and low C:high N responsive genes. Our analysis identified several functional correlated genes including chalcone synthase (CHS), chlorophyll a-b binding protein (CAB) and other genes that are implicated in C:N balancing mechanism, such as alternative oxidase 1B (OsAOX1B), malate dehydrogenase (OsMDH) and lysine and histidine specific transporter 1 (OsLHT1). Additionally, six jasmonate synthetic genes and key regulatory genes involved in abiotic and biotic stresses, such as OsMYB4, autoinhibited calcium ATPase 3 (OsACA3) and pleiotropic drug resistance 9 (OsPDR9), were differentially expressed under high C:low N treatment. Gene ontology analysis showed that high C:low N up-regulated genes were primarily enriched in fatty acid biosynthesis and defense responses. Coexpression network analysis of these genes identified eight jasmonate ZIM domain protein (OsJAZ) genes and several defense response related regulators, suggesting that high C:low N status may act as a stress condition, which induces defense responses mediated by jasmonate signaling pathway. Our transcriptome analysis shed new light on the C:N balancing mechanisms and revealed several important regulators of C:N status in rice seedlings.

Nitrate deficiency decreased photosynthesis and oxidation-reduction processes, but increased cellular transport, lignin biosynthesis and flavonoid metabolism revealed by RNA-Seq in Oryza sativa leaves

“…This is consistent with the decreased CO 2 assimilation, maximum efficiency of light energy conversion (F v /F m ), and increased intercellular CO 2 and chlorosis symptom in O. sativa leaves under N limitation (Figs 1 and 3A-3C). Similarly, Huang et al (2016) reported that a chlorophyll a-b binding protein 2 (CAB2) encoding gene (Os01g0720500) was downregulated by low N [39]. The decreased photosynthesis is probably a direct effect of accumulated soluble carbohydrates and starch due to their metabolite feedback regulation, as revealed by increased contents of starch, sucrose and fructose in O. sativa leaves (Fig 3E and 3F).…”

“…Here, our RNA-Seq data showed that the expression levels of genes such as anthocyanidin reductase, bisdemethoxycurcumin synthase-like, chalcone synthase (CHS), chalcone-flavonone isomerase (CHFI), flavanone 3-dioxygenase 2-like, etc., which implicated in flavonoids biosynthesis were apparently upregulated by N deficiency in O. sativa leaves (S4 and S5 Tables; Fig 5). Huang et al (2016) also reported that the expression level of CHS was induced by low N in rice by microarray hybridization technique [39]. Peng et al reported that N limitation could channel the phenylpropanoid metabolic flux to the induced anthocyanin synthesis, which facilitated the adaptation of Arabidopsis seedlings to N limitation [67].…”

Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation

“…Transcription factors are important for controlling the expression of other genes in plant exposed to limited N condition or in complete starvation (Krapp et al ., 2011; Yang et al ., 2015; Curci et al ., 2017) and, accordingly, our results showed as the regulation of transcripts was highly different and, in some case, with an opposite trend between emmer and durum wheat. In addition, some GO categories were only enriched for the DEGs in durum wheat, such as: the cellular amino acids, oxoacid or organic acids metabolism which were also highlighted by Huang et al (2016) in their study on the transcriptomic evaluation in response to the imbalance of carbon: nitrogen ratio in rice seedling.…”

Genome-wide Analysis In Response to N and C Identifies New Regulators for root AtNRT2 Transporters

“…For root NRT2s genes and HATS activity in Arabidopsis , it enabled the identification of CIPK23 and CIPK8 in response to NO 3 - , LBDs transcription factors in response to high N and BT2, a negative regulator of NRT2.1 and NRT2.4 under low N conditions (Figure 7) (Ho et al, 2009; Hu et al, 2009; Rubin et al, 2009; Araus et al, 2016). For C and N signaling, previous microarray studies in response to transient treatments with NO 3 - , sucrose or NO 3 - plus sucrose have been used to reveal, at the level of the genome, the existence of interaction between C and N signaling (Wang et al, 2003; Price et al, 2004; Scheible et al, 2004; Wang et al, 2004; Gutierrez et al, 2007; Huang et al, 2016). In Arabidopsis, over 300 genes have been found differentially expressed by combined C:N treatments compared to C or N treatments (Palenchar et al, 2004).…”