Nuclease and ribonuclease activities in response to salt stress: Identification of PvRNS3, a T2/S-like ribonuclease induced in common bean radicles by salt stress

Diaz-Baena, Mercedes; Gálvez‐Valdivieso, Gregorio; Delgado-Garcia, Elena; Pineda, Manuel; Piedras, Pedro

doi:10.1016/j.plaphy.2019.12.016

Cited by 16 publications

(32 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…responding to abiotic stresses including heat, salt, and nutrient deficiencies (Huang et al, 2015;Kawa and Testerink, 2017;Matsui et al, 2019;Diaz-Baena et al, 2020). Here, we performed various analyses of RNA content, RNase activity, and RNA stability that suggest that RNS induced under Pi deficiency makes Pi acquisition by RNA degradation (Figures 3-5).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The elevated abundance of sRNAs has been associated with the up-regulation of two types of nucleases (endonuclease S1/P1 and 3'-5' exonuclease), which may catalyze the degradation of RNA into shorter fragments [123,124] and play a relevant role in nutrient mobilization under Pi-starvation. It seems likely that sRNA production upon Pi-starvation is an effect of RNA degradation by different types of nucleases.…”

Section: Discussionmentioning

confidence: 99%

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

show abstract

“…Other related RNA-Seq data published for either wheat (Triticum aestivum L.) [93], rice [94], soybean [95], Plantago major L. [96], and maize [97] demonstrated similar molecular patterns to those in our study. Interestingly, an elevated abundance of sRNAs has been associated with the upregulation of two types of nucleases (endonuclease S1/P1 and 3'-5' exonuclease), which may catalyze the degradation of RNA into smaller components [98,99] and play a relevant role in nutrient mobilization under Pi scarcity. Taken together, the 98 DEGs identified in our RNA-Seq analysis have broadened the landscape of low-Pi responsive genes modulating stress tolerance in barley (Fig.…”

Section: Identification Of Barley Genes Responsive To Pi Starvationmentioning

confidence: 99%

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Small RNAs (sRNAs) are 18–24 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, Bonferroni correction). In roots, a more abundant and diverse set of other sRNAs (1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are upregulated in both organs. Additionally, in barley shoots, upregulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identify 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi scarcity through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

show abstract

Nuclease and ribonuclease activities in response to salt stress: Identification of PvRNS3, a T2/S-like ribonuclease induced in common bean radicles by salt stress

Cited by 16 publications

References 43 publications

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

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

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Contact Info

Product

Resources

About