Protein Phosphatases in N Response and NUE in Crops

Kumari, Supriya; Raghuram, Nandula

doi:10.1007/978-3-030-48733-1_12

Cited by 7 publications

(6 citation statements)

References 69 publications

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“…Protein kinases and phosphatases are known to play an important role in N-response and NUE in crops (Fataftah et al, 2018 ; Hsieh et al, 2018 ; Jiang et al, 2018 ; Xiong et al, 2019 ; Kumari and Raghuram, 2020 ). In this study, we identified 91 NUE-related gene-encoding kinases and 9 other gene-encoding phosphatases.…”

Section: Resultsmentioning

confidence: 99%

“…All the 91 kinases we reported here are novel candidates hitherto unknown for their role in NUE ( Supplementary Table S18 ). Phosphatases are also known to be N-responsive in many crops (Kumari and Raghuram, 2020 ). We identified nine phosphatase-encoding genes, including fructose-1,6-bisphosphatase, which was recently reported to be potentially involved in NUE (Waqas et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…Some of the important functional classes of genes involved or implicated in NUE include transporters, kinases, and transcription factors (TFs) (Vidal et al, 2020 ; Yang et al, 2020 ; Zhang et al, 2020b ). Recently, Kumari and Raghuram ( 2020 ) compiled a comprehensive list of phosphatases involved in the N-response and/or NUE in crops. MicroRNAs (miRNAs) also regulate the use of nitrogen in crop plants and participate in the adaptation of crops to nitrogen deficiency (Zuluaga and Sonnante, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

2021

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Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein–protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

2021

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“…An important caveat of transcriptome-based inferences is that they often ignore the role of post-translational modifications (PTMs). Recently, PTMs have been reported to play roles in nitrogen utilization, signal transduction, and response to sudden changes in nitrogen availability ( Kumari and Raghuram, 2020 ). Our study revealed PTMs related to phosphorylation and ubiquitination among others, which could play their role in NUE.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

et al. 2022

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The genetic basis for nitrogen (N)-response and N use efficiency (NUE) must be found in N-responsive gene expression or protein regulation. Our transcriptomic analysis of nitrate response in two contrasting rice genotypes of Oryza sativa ssp. Indica (Nidhi with low NUE and Panvel1 with high NUE) revealed the processes/functions underlying differential N-response/NUE. The microarray analysis of low nitrate response (1.5 mM) relative to normal nitrate control (15 mM) used potted 21-days old whole plants. It revealed 1,327 differentially expressed genes (DEGs) exclusive to Nidhi and 666 exclusive to Panvel1, apart from 70 common DEGs, of which 10 were either oppositely expressed or regulated to different extents. Gene ontology analyses revealed that photosynthetic processes were among the very few processes common to both the genotypes in low N response. Those unique to Nidhi include cell division, nitrogen utilization, cytoskeleton, etc. in low N-response, whereas those unique to Panvel1 include signal transduction, protein import into the nucleus, and mitochondria. This trend of a few common but mostly unique categories was also true for transporters, transcription factors, microRNAs, and post-translational modifications, indicating their differential involvement in Nidhi and Panvel1. Protein-protein interaction networks constructed using DEG-associated experimentally validated interactors revealed subnetworks involved in cytoskeleton organization, cell wall, etc. in Nidhi, whereas in Panvel1, it was chloroplast development. NUE genes were identified by selecting yield-related genes from N-responsive DEGs and their co-localization on NUE-QTLs revealed the differential distribution of NUE-genes between genotypes but on the same chromosomes 1 and 3. Such hotspots are important for NUE breeders.

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“…The role of post translational modifications (PTMs) in NUE has largely been ignored, as gene expression and protein expression dominated the literature. However, their roles in N-response, utilization, signal transduction are known (Kumari and Raghuram, 2020). Our study revealed 7 types of urea-responsive PTMs in 1286 proteins, of which phosphorylation emerged as most predominant followed by acetylation for their potential role in NUE, though ubiquitination was also found, which was linked to source-to-sink nitrate remobilization in Arabidopsis (Liu et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Genomewide basis for nitrogen use efficiency in contrasting genotypes of rice

Sharma

Jaiswal

Kumari

et al. 2022

Preprint

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Rice is an ideal crop with huge germplasm diversity and post-genomic resources for improvement of nitrogen (N) use efficiency (NUE). There is a paucity of comparative studies on rice genotypes contrasting for NUE, especially with urea, the predominant fertilizer in rice growing countries. In this study, low urea-responsive transcriptomes of contrasting rice genotypes namely Nidhi (low NUE) and Panvel1 (high NUE) were compared. They were based on whole plants grown for 21 days in pots containing nutrient-depleted soil fertilized with normal (15 mM) and low urea (1.5 mM) media. There were 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors and better photosynthesis, water use efficiency and post translational modifications. Many of their genes co-localized to NUE QTLs on chromosomes 1, 3 and 9. Field evaluation of the contrasting genotypes under different doses of urea revealed better performance of Panvel1 in different agronomic parameters including grain yield, transport/uptake efficiencies and NUE. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes from the same contrasting rice genotypes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and transcription factors among others contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.SummaryRice genotypes with contrasting urea use efficiency differ in the role of transporters, transcription factors, miRNAs, post-translational modifications, photosynthesis and water use efficiency

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Protein Phosphatases in N Response and NUE in Crops

Cited by 7 publications

References 69 publications

Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

Genomewide basis for nitrogen use efficiency in contrasting genotypes of rice

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