Integrative analyses of transcriptome and proteome provides new insights into energy metabolism and light utilzation in cigar tobacco during different light intensities
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ABSTRACT:
ORGANISM(S): Nicotiana tabacum
PROVIDER: GSE211923 | GEO | 2022/08/26
REPOSITORIES: GEO
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Project description:Low light (LL) or shading is detrimental one among other abiotic stresses that limit plant growth and suppress the crop plants' productivity. However, shading is one of the key cultivation techniques in cigar wrapper tobacco production. A gap of knowledge is present related to transcriptional and translational regulatory networks under such conditions. Herein, this work is planned for the integrative profiling of transcriptome and proteome along with some biochemical and physio-anatomical analyses under different light intensities [T200 (200 μmol m−2 s−1), T100 (100 μmol m−2 s−1), and T50 (50 μmol m−2 s−1)] to uncover the underlying molecular response mechanisms. The result showed that the leaf anatomical structure has a relationship with leaf photosynthetic capacity; as LL intensities (particularly T50) decreased the leaf thickness and thickness of palisade, and spongy tissues resulting in a lower photosynthesis rate and eventually decreased the plant biomass compared with T200. Furthermore, 3045 differentially expressed genes (DEGs) and 966 differentially expressed proteins (DEPs) were identified in the transcriptome and proteome of cigar tobacco. Furthermore, the integrative analysis between both omics revealed a total of 160 correlated DEGs and DEPs. The integrated analysis of both omics showed that the shared DEGs and DEPs were upregulated in photosynthesis-antenna proteins, photosynthesis, and defense/detoxification-related pathways. While the correlated DEGs and DEPs were downregulated in glycolysis, starch and sucrose metabolism, tyrosine metabolism, and mitochondrial electron transport chain pathways along with decreased activities of glyceraldehyde-3-phosphate dehydrogenase, starch phosphorylase, and pyruvate kinase enzymes related to glycolysis. These results showed that cigar tobacco efficiently utilized low light and reconfigured its energy metabolism. Collectively, this study can offer profound insights into the response mechanism at the physio-anatomical, biochemical, and molecular levels and showcases valuable resources of genes and proteins for future functional studies underlying LL response.
2022-09-01 | PXD036470 | iProX
Project description:The test result showed that ribosome, photosynthesis, cysteine and methionine metabolism, photosynthesis antenna proteins pathway enriched more genes in LW treatment. It was found that 5 genes included PsbE, PsbA, atpH, psaB, Zm00001d045620. it was found that four genes were highly downregulated in the photosynthesis antenna proteins pathway included Zm00001d044396, Zm00001d044399, Zm00001d044401, Zm00001d044402, these high-fold down-regulation genes related to inhibit maize growth. There was four highly upregulated in the ribosome pathway included Zm00001d006924, Zm00001d023293, Zm00001d036464, Zm00001d051662, these genes are closely related to maize adaptation to the drought conditions with negative pressure continuous water supply environment.
2021-12-03 | GSE189392 | GEO
Project description:In the study, two soybean genotypes were selected to conduct high and low P, high and low Mg, and AM fungal inoculation treatments, combined with RNA-seq sequencing technique in order to investigate the physiological and molecular mechanisms of the symbiosis between soybean and AM fungi affected by P and Mg treatments. The results showed that both Mg application and AM fungal inoculation were beneficial to promote soybean growth under low P condition. And there was a synergistic effect between the Mg concentration and the P concentration in the root of HN112 under the inoculation condition. RNA-seq sequencing was carried out using the roots of P-efficient soybean HN89 under different Mg and inoculation treatments with low P condition, and the difference of gene expression profiles was analyzed between high and low Mg treatments, and different inoculation treatments. According to the analysis of GO function classification and KEGG enrichment, under high Mg condition, the metabolic pathway was mainly enriched in lipid metabolism and glucose metabolism pathway under the inoculation treatment compared with the non-inoculation treatment, which regulated carbon metabolism pathway. Under the low Mg condition, the metabolic pathway was mainly enriched in the photosynthesis- antenna protein pathway to regulate the photosynthesis pathway under the inoculation treatment compared with the non-inoculation treatment. At the same time, the inoculation treatment significantly increased soybean root starch concentration under low Mg condition, compared with the non-inoculation treatment, suggesting that the significant up-regulation of a large number of photosynthesis related genes might be related to the significant increase of starch concentration at this treatment.
2022-06-13 | GSE132679 | GEO
Project description:Lobosphaera incisa is an oleaginous green microalga and a target organism of high biotechnological interest because it is the richest known plant source of arachidonic acid (ARA), a pharmaceutically and nutraceutically valuable omega-6 long-chain polyunsaturated fatty acid. ARA is deposited in considerable amounts in storage lipid triacylglycerols, most profoundly when L. incisa is exposed to nitrogen starvation. To get insights into genome-wide gene expression in L. incisa under nitrogen starvation, the whole transcriptome was sequenced by RNA-Seq. Total RNA was isolated under four growth conditions: exponential growth (control) and growth in nitrogen-depleted medium for 12 or 72 hours at normal or high light intensities. Statistical and differential gene expression analyses were conducted by comparing the various samples. The results of this study were used to identify patterns of gene regulation with special emphasis on genes involved in fatty acid and lipid metabolism.
2017-05-01 | GSE94666 | GEO
Project description:The effect of light during the development of freezing tolerance was studied in winter wheat (Triticum aestivum L. var. Mv Emese) and spring wheat variety Nadro. Ten-day-old plants were cold hardened at 5°C for 12 days either under normal (250 mmol m-2 s-1) or low light (20 mmol m-2 s-1) conditions. Samples of Emese (E) and Nadro (N) plants grown at 18°C under normal (NL) and low (LL) light fluences were compared to each other in a simple loop design and E-NL vs. E-LL; N-NL vs. N-LL; E-NL vs. NLL and E-LL vs. N-LL comparisons were made.
2012-01-31 | E-GEOD-29640 | biostudies-arrayexpress
Project description:Peripheral light harvesting (LH) antenna complexes have been studied extensively in the purple nonsulfur bacterium Rhodopseudomonas palustris because it produces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complex). The ability of R. palustris to alter its peripheral LH complexes in response to changes in light intensity is attributed to the multiple operons that encode the a and b peptides that make up these complexes, whose expression is affected by light intensity, light quality, and oxygen tension. However, low resolution structures, amino acid similarities between the complexes, and a lack of transcriptional analysis made it difficult to determine the LH complexes composition and functions under different light intensities. It was also unclear how much diversity of the R. palustris LH complexes exists in nature.Results: To gain insight into the composition of the LH complexes, their function under high light intensities and low light intensities, and their prevalence in the environment we undertook an integrative genomics approach using 15 closely related R. palustris strains isolated from the environment and 5 R. palustris ecotypes whose genomes have been sequenced. We sequenced the genomes for the 15 closely related strains and using RNA-seq carried out transcriptomic analysis on all 20 strains grown under high light intensity and low light intensity. We were able to determine that even closely related R. palustris strains had differences in their pucBA gene content and expression, even under the same growth conditions. We also found that the LH2 complex could compensate for the lack of an LH4 complex under LL intensities but not under extremely LL intensities. Conclusions: This is the first time an integrative genomics approach has been used to study light harvesting in the environment. The variation observed in LH gene composition and expression in environmental isolates of R. palustris likely reflects how these strains have adapted to specific light conditions in the environment. We have also shown that there is redundancy between some of the LH complexes under certain light intensities, which may partially explain why multiple operons encoding LH complexes have evolved and been maintained in R. palustris. Examing the variation observed in LH gene composition and expression in various environmental isolates
2015-03-01 | E-GEOD-59544 | biostudies-arrayexpress
Project description:Peripheral light harvesting (LH) antenna complexes have been studied extensively in the purple nonsulfur bacterium Rhodopseudomonas palustris because it produces different types of LH complexes under high light intensities (LH2 complex) and low light intensities (LH3 and LH4 complex). The ability of R. palustris to alter its peripheral LH complexes in response to changes in light intensity is attributed to the multiple operons that encode the a and b peptides that make up these complexes, whose expression is affected by light intensity, light quality, and oxygen tension. However, low resolution structures, amino acid similarities between the complexes, and a lack of transcriptional analysis made it difficult to determine the LH complexes composition and functions under different light intensities. It was also unclear how much diversity of the R. palustris LH complexes exists in nature.Results: To gain insight into the composition of the LH complexes, their function under high light intensities and low light intensities, and their prevalence in the environment we undertook an integrative genomics approach using 15 closely related R. palustris strains isolated from the environment and 5 R. palustris ecotypes whose genomes have been sequenced. We sequenced the genomes for the 15 closely related strains and using RNA-seq carried out transcriptomic analysis on all 20 strains grown under high light intensity and low light intensity. We were able to determine that even closely related R. palustris strains had differences in their pucBA gene content and expression, even under the same growth conditions. We also found that the LH2 complex could compensate for the lack of an LH4 complex under LL intensities but not under extremely LL intensities. Conclusions: This is the first time an integrative genomics approach has been used to study light harvesting in the environment. The variation observed in LH gene composition and expression in environmental isolates of R. palustris likely reflects how these strains have adapted to specific light conditions in the environment. We have also shown that there is redundancy between some of the LH complexes under certain light intensities, which may partially explain why multiple operons encoding LH complexes have evolved and been maintained in R. palustris.
2015-03-01 | GSE59544 | GEO
Project description:Photosynthesis is affected by water deficiency (WD) stress, and nitric oxide (NO) is a free radical that participates in the photosynthesis process. Previous studies have suggested that NO regulates the excitation energy distribution of photosynthesis under WD stress. Here, quantitative phosphoproteomic profiling was conducted using isobaric tags for relative and absolute quantitation. Differentially phosphorylated protein species (DEPs) were identified in leaves of NO or polyethylene glycol (PEG)-treated wheat seedlings (D) and in control seedlings, 2,257 unique phosphorylated peptides and 2,416 phosphorylation sites were identified from 1,396 unique phosphoproteins. Of these, 96 DEPs displayed significant changes (≥ 1.50-fold, p < 0.01). These DEPs are involved in photosynthesis and signal transduction, etc. Furthermore, phosphorylation of several DEPs were up-regulated by both D and NO treatments, but down-regulated only in NO treatment. These differences affected the chlorophyll A-B binding protein, chloroplast post-illumination chlorophyll fluorescence increase protein, and SNT7, implying that NO indirectly regulated the absorption and transport of light energy in photosynthesis in response to WD stress. The significant difference of chlorophyll (Chl) content, Chl a fluorescence transient, photosynthesis index, and trapping and transport of light energy further indicated that exogenous NO under D stress enhanced the primary reaction of photosynthesis compared to D treatment. A putative pathway is proposed to elucidate NO regulation of the primary reaction of photosynthesis under WD.
2019-11-14 | PXD010724 | Pride
Project description:A comparative proteomic analysis of grapevine leaves from the resistant genotype V. davidii ‘LiuBa-8’ (LB) and susceptible genotype V. vinifera ‘Pinot Noir’ (PN) at 12 hpi was conducted to understand the complex relationship between grapevine and P. viticola and the molecular mechanisms between difference resistant vitis genotypes at the early stage of infection. A total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN respectively at 12 hpi by iTRAQ. MapMan analysis showed that the majority of these DEPs were related to photosynthesis, metabolism, stress and redox. More up-expressed DEPs involved in photosynthesis and less down-expressed DEPs involved in metabolism contribute to the resistance in LB. PR10.2, PR10.3, HSF70.2 and HSP90.6 are proposed to be key proteins in both compatible and incompatible interactions. Accumulation H2O2 established the ROS signaling in incompatible interaction and APXs, GSTs maybe associated with the resistance of grapevine against downy mildew. Moreover, we verified four proteins to ensure the accuracy of proteome data using PRM. Overall, these data provide new insights into molecular events and provide valuable candidate proteins that could be used to illuminate molecular mechanisms underlying the incompatible and compatible interaction in early stage and eventually to be exploited to develop new protection strategy against downy mildew in grapevine.
2021-09-09 | PXD018845 | Pride
Project description:A comparative proteomic analysis of grapevine leaves from the resistant genotype V. davidii ‘LiuBa-8’ (LB) and susceptible genotype V. vinifera ‘Pinot Noir’ (PN) at 12 hpi was conducted to understand the complex relationship between grapevine and P. viticola and the molecular mechanisms between difference resistant vitis genotypes at the early stage of infection. A total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN respectively at 12 hpi by iTRAQ. MapMan analysis showed that the majority of these DEPs were related to photosynthesis, metabolism, stress and redox. More up-expressed DEPs involved in photosynthesis and less down-expressed DEPs involved in metabolism contribute to the resistance in LB. PR10.2, PR10.3, HSF70.2 and HSP90.6 are proposed to be key proteins in both compatible and incompatible interactions. Accumulation H2O2 established the ROS signaling in incompatible interaction and APXs, GSTs maybe associated with the resistance of grapevine against downy mildew. Moreover, we verified four proteins to ensure the accuracy of proteome data using PRM. Overall, these data provide new insights into molecular events and provide valuable candidate proteins that could be used to illuminate molecular mechanisms underlying the incompatible and compatible interaction in early stage and eventually to be exploited to develop new protection strategy against downy mildew in grapevine.
2021-09-09 | PXD018868 | Pride