Transcriptomic analysis of salt stress responsive genes related pigment metabolism in photoheterotrophic Arabidopsis calli
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE188818 | GEO | 2023/12/31
REPOSITORIES: GEO
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Project description:Improvement in the photosynthetic efficiency is a major approach to improve crop yield potential. So far, most of the demonstrated cases of photosynthesis improvement was achieved through manipulation of one or a few photosynthesis related genes. Present study found that over-expression of one maize transcription factor, mEmBP-1 gene, led to simultaneously increased expression of nearly all genes in photosynthesis pathway, including genes encoding chlorophyll a and b-binding proteins (Lhca and Lhcb), photosystem II (PsbR3 and PsbW) and PS I reaction center subunits (PsaK and PsaN), genes encoding for chloroplast ATP synthase subunit and electron transport reaction (Fd1 and PC), and also major genes in the Calvin Benson Bassham cycle, Rubisco, GAPDH, FBA, TK and PRK. This increased photosynthesis gene expression resulted in increased leaf chlorophyll pigment, photosynthetic rate, quantum yields, biomass growth and grain yield both in the greenhouse and also in natural field conditions. Using DNA-Protein binding experiment, we found that mEmBP-1a protein can directly bind to the promoter regions of photosynthesis genes, suggesting that the direct binding of mEmBP-1a to the G-box domain of photosynthetic genes upregulates expression of these genes. Hence, this study shows that mEmBP-1a is a major regulator of photosynthesis.
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Project description:The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line âFTâ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line âFTâ, the drmâs chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between âFTâ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between âFTâ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage. The RNA from the third true leaves (day 15 to day 24 after the appearance of the third true leaves) of a developmentally retarded mutant (drm) and its wild type âFTâ in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
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Project description:The molecular response to salt exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed, whereas cell rescue and transcription factor-related genes were mostly up-regulated. A strong down-regulation of several functional categories including primary metabolism, detoxication apparatus and signal transduction was also observed. Gene expression has been followed three days after salinity treatment (150 mM NaCl). For each condition, 4 independent biological replicates were sampled. Dye-swaps were performed.
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Project description:The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line ‘FT’ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line ‘FT’, the drm’s chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between ‘FT’ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between ‘FT’ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage.
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Project description:Ananas comosus var. bracteatus has high ornamental value and widespread application because of its chimeric leaves. However, little is known about the molecular mechanism regulating this characteristic. Here, comparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of the chimeric leaves were performed to identify differentially expressed genes (DEGs) and differentially expressed proteins (DEPs). In total, 1,685 DEGs, including 712 up- and 973 down-regulated ones, and 5,428 DEPs, including 1,018 up- and 795 down-regulated ones, were identified between the Whs and Grs. Comparisons with the GO and KEGG annotations revealed that the DEGs were involved mostly in carbon fixation, porphyrin and chlorophyll metabolism and oxidative phosphorylation. The DEPs were mainly involved in ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed that nine proteins related to chlorophyll biosynthesis, photosynthetic pigments, and photosynthesis were unchanged at mRNA level but suppressed at protein level. These results indicated that the albino phenotype of the Whs was caused by the proteomic-level suppression of key enzymes involved in the chlorophyll biosynthesis pathway and that translational and post-translational regulation may play important roles in both the biosynthesis of photosynthetic pigments and photosynthesis. Biological significance: Leaves of Ananas comosus var. bracteatus serve as the best materials for the study of albino mechanism. Because the chemic trait of A. comosus var. bracteatus is unstable and the molecular mechanism of the albino cells was poorly understood, we performed comparative analyses both at the transcriptome and proteome levels. This work revealed suppressed proteomic-level and translational and post-translational regulation contribute to the albino phenotype formation. Our results provide better information concerning the molecular mechanism within the chimeric leaves of A. comosus var. bracteatus.
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Project description:This SuperSeries is composed of the SubSeries listed below. NIH grant(s): Grant ID: 5 P30 CA016672-44 Grant title: Cancer Center Support Grant Affiliation: The University of Texas MD Anderson Cancer Center Grantor: NCI
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