Phosphate-Starvation-Inducible S-Like RNase Genes in Rice Are Involved in Phosphate Source Recycling by RNA Decay

Abstract

The fine-tuning of inorganic phosphate (Pi) for enhanced use efficiency has long been a challenging subject in agriculture, particularly in regard to rice as a major crop plant. Among ribonucleases (RNases), the RNase T2 family is broadly distributed across kingdoms, but little has been known on its substrate specificity compared to RNase A and RNase T1 families. Class I and class II of the RNase T2 family are defined as the S-like RNase (RNS) family and have showed the connection to Pi recycling in Arabidopsis. In this study, we first carried out a phylogenetic analysis of eight rice and five Arabidopsis RNS genes and identified mono-specific class I and dicot-specific class I RNS genes, suggesting the possibility of functional diversity between class I RNS family members in monocot and dicot species through evolution. We then compared the in silico expression patterns of all RNS genes in rice and Arabidopsis under normal and Pi-deficient conditions and further confirmed the expression patterns of rice RNS genes via qRT-PCR analysis. Subsequently, we found that most of the OsRNS genes were differentially regulated under Pi-deficient treatment. Association of Pi recycling by RNase activity in rice was confirmed by measuring total RNA concentration and ribonuclease activity of shoot and root samples under Pi-sufficient or Pi-deficient treatment during 21 days. The total RNA concentrations were decreased by < 60% in shoots and < 80% in roots under Pi starvation, respectively, while ribonuclease activity increased correspondingly. We further elucidate the signaling pathway of Pi starvation through upregulation of the OsRNS genes. The 2-kb promoter region of all OsRNS genes with inducible expression patterns under Pi deficiency contains a high frequency of P1BS cis-acting regulatory element (CRE) known as the OsPHR2 binding site, suggesting that the OsRNS family is likely to be controlled by OsPHR2. Finally, the dynamic transcriptional regulation of OsRNS genes by overexpression of OsPHR2, ospho2 mutant, and overexpression of OsPT1 lines involved in Pi signaling pathway suggests the molecular basis of OsRNS family in Pi recycling via RNA decay under Pi starvation.

Characterization of contrasting rice (Oryza sativa L.) genotypes reveals the Pi-efficient schema for phosphate starvation tolerance

“…Moreover, the observed up-regulated expression of the genes involved in glycolysis is necessary to increase carbon supply for organic acid synthesis. Our observation on > 6.3-fold and > 2.4-fold up-regulated expression of LOC_Os08g33710 and LOC_Os01g67190 (the ribonuclease T2 family domain containing proteins), respectively, is in agreement with the findings of Gho et al [ 17 ]. Increased excretion of organic acids and Pi-releasing enzymes such as RNases and purple acid phosphatases (PAPs) results in larger rhizospheric Pi pool for uptake.…”

“…Thus, more efficient metabolic adjustments in NIL-23, compared to that in Pusa-44, are responsible better survival of NIL-23 under P-starvation stress. Phosphorus homeostasis between shoot and root under the stress has been reported to be maintained by modulating the expression of transporters, phosphatases, RNases, and the enzymes involved in metabolic processes [ 17 , 69 , 70 , 83 ].…”

“…Formation of root clusters has been observed in some plant species in response to low P in soil, which exudate organic acids to acidify/release the chelated ions around the roots, resulting in better availability of P and other micronutrients [ 13 – 15 ]. Plant releases phosphatase and RNase to enhance Pi availability and acquisition [ 16 , 17 ]. Plant possesses specialized transporters and other molecular mechanisms for remobilizing Pi across the intracellular compartments where the P might have been stored in organic (phytic acid) form.…”

Rice PIN Auxin Efflux Carriers Modulate the Nitrogen Response in a Changing Nitrogen Growth Environment

“…To perform a phylogenomic analysis of PIN-family proteins in rice, Arabidopsis, and maize, we collected 12 family members from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/accessed on 15 February 2021), as well as 8 Arabidopsis and 11 maize family members from GreenPhyl v5 (http://www.greenphyl.org/cgi-bin/index.cgi accessed on 15 February 2021) ( Table S1). The phylogenetic analysis used MEGA7 under the following parameters: neighbor joining, complete deletion, and bootstrap with 500 replicates ( Figure S1), as described previously [55,56]. We also generated a phylogenic tree for rice PINs, to integrate meta-expression data from data from 983 Affymetrix arrays (Figure 1).…”

“…cgi accessed on 15 February 2021) ( Table S1). The phylogenetic analysis used MEGA7 under the following parameters: neighbor joining, complete deletion, and bootstrap with 500 replicates (Figure S1), as described previously [55,56]. We also generated a phylogenic tree for rice PINs, to integrate meta-expression data from data from 983 Affymetrix arrays (Figure 1).…”