Co-expression and regulation of photorespiratory genes in Arabidopsis thaliana: A bioinformatic approach

Laxa, Miriam; Fromm, Steffanie

doi:10.1016/j.cpb.2018.09.001

Cited by 13 publications

(15 citation statements)

References 148 publications

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“…Although no previous studies have identified coordinated transcriptional regulation of the genes associated with oxalate metabolism in plants, the subset of TFs identified in this study could help identify target genes for the manipulation of oxalate content in spinach or other plant species. Although analysis of the expression patterns of photorespiratory genes using a bioinformatic approach suggested strong co-expression, and conserved cis-elements in their 5′ upstream regions [ 55 ], this does not necessarily suggest co-regulation by common TFs. Several studies have identified transcription factors that conditionally regulate individual genes associated with intrinsic processes such as photorespiration, the glyoxylate cycle, or ascorbate metabolism.…”

Section: Discussionmentioning

confidence: 99%

Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis

Joshi

Penalosa

Joshi³

et al. 2021

IJMS

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Although spinach (Spinacia oleracea L.) is considered to be one of the most nutrient-rich leafy vegetables, it is also a potent accumulator of anti-nutritional oxalate. Reducing oxalate content would increase the nutritional value of spinach by enhancing the dietary bioavailability of calcium and other minerals. This study aimed to investigate the proposed hypothesis that a complex network of genes associated with intrinsic metabolic and physiological processes regulates oxalate homeostasis in spinach. Transcriptomic (RNA-Seq) analysis of the leaf and root tissues of two spinach genotypes with contrasting oxalate phenotypes was performed under normal physiological conditions. A total of 2308 leaf- and 1686 root-specific differentially expressed genes (DEGs) were identified in the high-oxalate spinach genotype. Gene Ontology (GO) analysis of DEGs identified molecular functions associated with various enzymatic activities, while KEGG pathway analysis revealed enrichment of the metabolic and secondary metabolite pathways. The expression profiles of genes associated with distinct physiological processes suggested that the glyoxylate cycle, ascorbate degradation, and photorespiratory pathway may collectively regulate oxalate in spinach. The data support the idea that isocitrate lyase (ICL), ascorbate catabolism-related genes, and acyl-activating enzyme 3 (AAE3) all play roles in oxalate homeostasis in spinach. The findings from this study provide the foundation for novel insights into oxalate metabolism in spinach.

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Section: Discussionmentioning

confidence: 99%

Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis

Joshi

Penalosa

Joshi³

et al. 2021

IJMS

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“…Consequently, ALDase effectively catalyzed the conversion of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP) to fructose-1,6-bisphosphat (FBP) as well as the conversion of DHAP and erythrose 4-phosphate to sedoheptulose-1,7-bisphosphate (SBP) [ 78 ] ( Figure 2 ), after which SBPase catalyzed the dephosphorylation of SBP to S7P (sedoheptulose-7-phosphate). These reactions can lead to the formation of a metabolic flux that enhances the carbon partitioning in the cycle and avoids the negative feedback regulation due to metabolic intermediates (e.g., glycolate and glyoxylate) [ 79 , 80 ]. Additionally, up-regulated ALDase and SBPase gene expression might further activate Rubisco by promoting the regeneration of RuBP in the CBC [ 50 , 81 ], thereby accelerating the carbon turnover to achieve compensatory photosynthesis and to stimulate the restorative growth of S. grandis plants.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences

Dang

Jia

Tian

et al. 2021

IJMS

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Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Here, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. As a result, a total of 2357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified in RNA-Seq and qRT-PCR analyses that indicated the modulation of the Calvin–Benson cycle and photorespiration metabolic pathways. The key gene expression profiles encoding various proteins (e.g., ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase, etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection and identifying important questions to address in future transcriptome studies.

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“…Photorespiration is a highly conserved metabolic process that lies at the crossroads of primary metabolism, environmental stress response and crop improvement. Although, considerable progress has been made to biochemically characterize the genes involved in photorespiration the mechanism of regulation of these genes in response to unavoidable environmental cues is at its inception ( Laxa and Fromm, 2018 ). A number of recent reports have suggested that key photorespiratory genes, including PLGG1 , GOX1 , PGLP1 , HPR1 are differentially regulated by elevated temperature and high light intensity ( Song et al, 2014 ; Balfagón et al, 2019 ; Timm et al, 2019 ; Anderson et al, 2021 ; Moore et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

“…Since synthetic promoters are assembled linking cis -regulatory elements of various promoter regions upstream of the core promoter (TATA box), one can combine tissue specificity with heightened expression within the same promoter construct. Unfortunately, unlike yeast or animal genomics, very few studies have been devoted to identifying core cis -regulatory elements underlying developmental and biochemical pathways in plants to help us generate an array of synthetic promoters for gene stacking in crop plants ( Kaplan et al, 2006 ; Kaur et al, 2017 ; Laxa and Fromm, 2018 ; Eseverri et al, 2020 ; Jores et al, 2021 ; Kakei et al, 2021 ). In addition to promoters, upstream and downstream untranslated regions (UTRs) also have a profound effect on gene expression ( Diamos and Mason, 2018 ; Yamamoto et al, 2018 ; de Felippes et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Design and Analysis of Native Photorespiration Gene Motifs of Promoter Untranslated Region Combinations Under Short Term Abiotic Stress Conditions

Basu

South

2022

Front. Plant Sci.

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Quantitative traits are rarely controlled by a single gene, thereby making multi-gene transformation an indispensable component of modern synthetic biology approaches. However, the shortage of unique gene regulatory elements (GREs) for the robust simultaneous expression of multiple nuclear transgenes is a major bottleneck that impedes the engineering of complex pathways in plants. In this study, we compared the transcriptional efficacies of a comprehensive list of well-documented promoter and untranslated region (UTR) sequences side by side. The strength of GREs was examined by a dual-luciferase assay in conjunction with transient expression in tobacco. In addition, we created suites of new GREs with higher transcriptional efficacies by combining the best performing promoter-UTR sequences. We also tested the impact of elevated temperature and high irradiance on the effectiveness of these GREs. While constitutive promoters ensure robust expression of transgenes, they lack spatiotemporal regulations exhibited by native promoters. Here, we present a proof-of-principle study on the characterization of synthetic promoters based on cis-regulatory elements of three key photorespiratory genes. This conserved biochemical process normally increases under elevated temperature, low CO2, and high irradiance stress conditions and results in ∼25% loss in fixed CO2. To select stress-responsive cis-regulatory elements involved in photorespiration, we analyzed promoters of two chloroplast transporters (AtPLGG1 and AtBASS6) and a key plastidial enzyme, AtPGLP using PlantPAN3.0 and AthaMap. Our results suggest that these motifs play a critical role for PLGG1, BASS6, and PGLP in mediating response to elevated temperature and high-intensity light stress. These findings will not only enable the advancement of metabolic and genetic engineering of photorespiration but will also be instrumental in related synthetic biology approaches.

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Co-expression and regulation of photorespiratory genes in Arabidopsis thaliana: A bioinformatic approach

Cited by 13 publications

References 148 publications

Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis

Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis

Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences

Design and Analysis of Native Photorespiration Gene Motifs of Promoter Untranslated Region Combinations Under Short Term Abiotic Stress Conditions

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