Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

Gho, Yun-Shil; Park, Sun‐A; Kim, Sung-Ruyl; Chandran, Anil Kumar Nalini; An, Gynheung; Jung, Ki‐Hong

doi:10.1186/s12284-017-0170-5

Cited by 11 publications

(10 citation statements)

References 64 publications

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“…S11 D and S12 ). The rice genome contains 10 members of the PRX genes with diversified spatiotemporal expression patterns, and one of which, PER1A (also called Os1-CysPrxA ), was preferentially expressed in the seeds ( 36 ). We also observed that PER1A was expressed far more pronounced than the other four identified DE members, with its allelic transcript level of Kasalath stronger than that of Jigeng88 ( SI Appendix , Fig.…”

Section: Resultsmentioning

confidence: 99%

A multiomic study uncovers a bZIP23-PER1A–mediated detoxification pathway to enhance seed vigor in rice

Wang

Sui

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Seed vigor in crops is important in terms of improving grain quality and germplasm conservation; however, little is known about its regulatory mechanisms through the encoded proteome and gene network. Comparative analyses of transcriptome (RNA sequencing [RNA-seq]) and broadly targeted metabolic profiling of two subspecific rice cultivars with distinct seed vigor during accelerated aging revealed various biological pathways and metabolic processes as key influences explaining trait differences. RNA-seq coexpression regulatory network analyses identified several transcription factors, including bZIP23 and bZIP42, that act as nodes in the gene network. Importantly, transgenic seeds of overexpression of bZIP23 enhanced seed vigor, whereas its gene knockout reduced seed vigor, suggesting that the protein it encodes functions as a positive regulator. Similarly, overexpression and knockout of PER1A that encodes a key player in the detoxification pathway enhanced and decreased seed vigor, respectively. We further demonstrated a direct interaction of the PER1A promoter with bZIP23 in seeds, which activates the expression of PER1A, and the genetic evidence suggested that bZIP23 most likely functions in a common pathway with and acts upstream of PER1A to modulate seed vigor. In addition, the control of seed vigor by the bZIP23-PER1A module was connected with that of the abscisic acid signaling pathway. Collectively, we revealed the genetic architecture of variation in seed vigor and uncovered the bZIP23-PER1A–mediated detoxification pathway that enhances the trait in rice.

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Section: Resultsmentioning

confidence: 99%

A multiomic study uncovers a bZIP23-PER1A–mediated detoxification pathway to enhance seed vigor in rice

Wang

Sui

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…The tandemly duplicated PRX genes in rice, Os1-CysPrxA and Os1-CysPrxB, also have different expression patterns. Although tandemly duplicated PRX genes in rice, Os1-CysPrxA and Os1-CysPrxB, might be functionally redundant due to high amino acid sequence similarity, their anatomical expression patterns are quite different (Gho et al, 2017). It has been reported that their promoters contain unique tissuepreferred CREs: the promoter of Os1-CysPrxA has CREs for endosperm preferred expression, while that of Os1-CysPrxB has embryo or root-preferred CREs.…”

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

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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.

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“…This case demonstrates that a phylogenetic heatmap is useful even in the case of partial or unequal functional redundancy because researchers are still able to check the degree of functional redundancy using three different colored boxes (yellow, orange, and red). Moreover, it can be used to identify cis ‐acting regulatory elements between two closest genes having different expression patterns, as in the research about the rice peroxiredoxin family (Gho et al ., 2017; Figure S2b).…”

Section: Resultsmentioning

confidence: 99%

CAFRI‐Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

Hong

Kim

et al. 2020

The Plant Journal

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Rice (Oryza sativa L.) is a staple crop with agricultural traits that have been intensively investigated. However, despite the variety of mutant population and multi-omics data that have been generated, rice functional genomic research has been bottlenecked due to the functional redundancy in the genome. This phenomenon has masked the phenotypes of knockout mutants by functional compensation and redundancy. Here, we present an intuitive tool, CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice (CAFRI-Rice; cafri-rice.khu.ac.kr). To create this tool, we generated a phylogenetic heatmap that can estimate the similarity between protein sequences and expression patterns, based on 2,617 phylogenetic trees and eight tissue RNA-sequencing datasets. In this study, 33,483 genes were sorted into 2,617 families, and about 24,980 genes were tested for functional redundancy using a phylogenetic heatmap approach. It was predicted that 7,075 genes would have functional redundancy, according to the threshold value validated by an analysis of 111 known genes functionally characterized using knockout mutants and 5,170 duplicated genes. In addition, our analysis demonstrated that an anther/pollen-preferred gene cluster has more functional redundancy than other clusters. Finally, we showed the usefulness of the CAFRI-Rice-based approach by overcoming the functional redundancy between two root-preferred genes via loss-of-function analyses as well as confirming the functional dominancy of three genes through a literature search. This CAFRI-Rice-based target selection for CRISPR/Cas9-mediated mutagenesis will not only accelerate functional genomic studies in rice but can also be straightforwardly expanded to other plant species.

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Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

Cited by 11 publications

References 64 publications

A multiomic study uncovers a bZIP23-PER1A–mediated detoxification pathway to enhance seed vigor in rice

A multiomic study uncovers a bZIP23-PER1A–mediated detoxification pathway to enhance seed vigor in rice

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

CAFRI‐Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice

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