A pentatricopeptide repeat protein DUA1 interacts with sigma factor 1 to regulate chloroplast gene expression in Rice

Du, Yutong; Mo, Weiping; Ma, Tingting; Tang, Weijiang; Tian, Lijin; Lin, Rongcheng

doi:10.1007/s11120-020-00793-0

Cited by 6 publications

(5 citation statements)

References 59 publications

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“…Contrary to this, the other six starch synthases in N22 showed only a 1.5-to 4.8-fold increase in gene expression. These are our work's main ndings and follow the previously published reports 70 .…”

Section: Discussionsupporting

confidence: 90%

“…In this pursuit, both plastid-and nuclear-encoded RNA polymerases (PEP and NEP, respectively) have been identi ed because of their crucial role in temperature-dependent effects on chlorophyll biosynthesis, photosystems, and chloroplast development [67][68][69] . Additionally, recent research has demonstrated that the sigma factor OsSIG1 interacts with DUA1 (a pentatricopeptide repeat protein) and strongly affects PEP-dependent chloroplast gene expression, resulting in an albino phenotype 70 . By analyzing the transcriptomes of N22 and the green-revertible albino mutant M-507, we found a signi cant three-fold increase in LOC_Os04g16820, which encodes DNA-directed RNA polymerase subunit beta.…”

Section: Discussionmentioning

confidence: 99%

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RNA-Seq, co-expression network and eQTL analysis identify key genes for chlorophyll and carbon metabolism in rice

Nehra¹,

Kaul²,

Jadhav³

et al. 2023

Preprint

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Leaf color mutations are excellent research tools for understanding the mechanics of pigment metabolism, chloroplast development, and photosynthesis. Chloroplasts and photosynthetic pigments in leaf cells of plants both play a significant role in determining the photosynthetic efficiency, as well as crop productivity to a greater extent. Leaf color has been regarded as an essential agronomic trait in rice (Oryza sativa L.) majorly because any changes in leaf color have an impact on rice yield. In this study, M-507, a green-revertible albino mutant of Nagina 22 (N22), was characterized and compared to wild-type in terms of anatomical, physiological, and molecular similarities. The mutant showed significantly lower chlorophyll content, defective chloroplast morphology, and reduced photosynthetic capacity than the wild-type. The differentially expressed genes (DEGs) were identified in M-507 with respect to wild-type using high-throughput transcriptome sequencing revealed downregulation of genes essential for the synthesis of chlorophyll, carotenoid, anthocyanin, and photosynthesis pathway. Whereas, genes associated with chlorophyll degradation, ion transport, and starch and sucrose metabolism were remarkably up-regulated in M-507. Co-expression networking revealed a substantial positive correlation between the expression profiles of the chloroplastic genes, transcription factors, and the genes involved in pigment metabolism and starch and sucrose metabolism. Furthermore, sequence similarity analysis revealed existing single-nucleotide polymorphism (SNP) and Insertions and Deletions (InDels) in M-507 as compared to N22. The identified SNPs and InDels candidate genes have been found to have strong associated positive and negative expression quantitative trait loci (eQTLs). Additionally, transcription factor family genes, including NAC, bHLH, WRKY, AP2/ERF, and MYB, were also identified. Real-time quantitative PCR (qPCR) was used to confirm the reliability of RNA sequencing results. These findings provide a possible pathway for the molecular mechanism associated with leaf color formation as well as a valuable resource for molecular marker development, that will be critical for improving rice crop production efficiency.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

RNA-Seq, co-expression network and eQTL analysis identify key genes for chlorophyll and carbon metabolism in rice

Nehra¹,

Kaul²,

Jadhav³

et al. 2023

Preprint

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show abstract

“…Similarly, several other PPR proteins such as seedling-lethal chlorosis 1 ( Lv et al, 2020 ), pale-green leaf 12 (PGL12) ( Chen et al, 2019 ), white stripe leaf 4 (WSL4) ( Wang et al, 2017 ), thermo-sensitive chlorophyll-deficient mutant 10 (TCD10) ( Wu et al, 2016 ), lovastatin insensitive 1 (LOI1) ( Tang et al, 2010 ), seedling-lethal albino 4 (OsSLA4) ( Wang et al, 2018 ), OsPPR16 ( Huang et al, 2020 ), and OsPPR4 ( Asano et al, 2013 ) were characterized to be involved in chloroplast development and function. Another report has shown that the DUA1 PPR protein is involved in regulating the chloroplast gene expression by interacting with the sigma factor, OsSIG1, in rice ( Du et al, 2021 ). It is well established that PPRs are involved in chloroplast-encoded RNA editing and processing.…”

Section: Discussionmentioning

confidence: 99%

An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection

Srikakulam

Guria²,

Karanthamalai³

et al. 2022

Front. Genet.

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Sheath blight (ShB) disease, caused by Rhizoctonia solani, is one of the major biotic stress-oriented diseases that adversely affect the rice productivity worldwide. However, the regulatory mechanisms are not understood yet comprehensively. In the current study, we had investigated the potential roles of miRNAs in economically important indica rice variety Pusa Basmati-1 upon R. solani infection by carrying out in-depth, high-throughput small RNA sequencing with a total data size of 435 million paired-end raw reads from rice leaf RNA samples collected at different time points. Detailed data analysis revealed a total of 468 known mature miRNAs and 747 putative novel miRNAs across all the libraries. Target prediction and Gene Ontology functional analysis of these miRNAs were found to be unraveling various cellular, molecular, and biological functions by targeting various plant defense-related genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate the miRNAs and their putative target genes. Out of the selected miRNA-specific putative target genes, miR395a binding and its cleavage site on pentatricopeptide were determined by 5’ RACE-PCR. It might be possible that R. solani instigated chloroplast degradation by modulating the pentatricopeptide which led to increased susceptibility to fungal infection.

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“…Additionally, DUA1 interacts with a multiple organellar RNA editing factor OsMORF9, a determinant of chloroplast development ( Zhang et al., 2021 ). The dua1 mutants exhibited defective chloroplast development, chlorophyll biosynthesis, and albino phenotype at low temperatures ( Cui et al., 2019 ; Du et al., 2021 ).…”

Section: Roles Of Ppr Proteins In Rice Chloroplast Developmentmentioning

confidence: 99%

PPR proteins in plants: roles, mechanisms, and prospects for rice research

Meng,

Du,

Zhu

et al. 2024

Front. Plant Sci.

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Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with over 300 members in various species. Nearly all PPR proteins are nuclear-encoded and targeted to the chloroplast and mitochondria, modulating organellar gene expression by participating in RNA metabolism, including mRNA stability, RNA editing, RNA splicing, and translation initiation. Organelle RNA metabolism significantly influences chloroplast and mitochondria functions, impacting plant photosynthesis, respiration, and environmental responses. Over the past decades, PPR proteins have emerged as a research focus in molecular biology due to their diverse roles throughout plant life. This review summarizes recent progress in understanding the roles and molecular mechanisms of PPR proteins, emphasizing their functions in fertility, abiotic and biotic stress, grain quality, and chloroplast development in rice. Furthermore, we discuss prospects for PPR family research in rice, aiming to provide a theoretical foundation for future investigations and applications.

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A pentatricopeptide repeat protein DUA1 interacts with sigma factor 1 to regulate chloroplast gene expression in Rice

Cited by 6 publications

References 59 publications

RNA-Seq, co-expression network and eQTL analysis identify key genes for chlorophyll and carbon metabolism in rice

RNA-Seq, co-expression network and eQTL analysis identify key genes for chlorophyll and carbon metabolism in rice

An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection

PPR proteins in plants: roles, mechanisms, and prospects for rice research

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