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Integrative analyses of transcriptome and proteome provides new insights into energy metabolism and light utilzation in cigar tobacco during different light intensities

ABSTRACT: Integrative analyses of transcriptome and proteome provides new insights into energy metabolism and light utilzation in cigar tobacco during different light intensities

PROVIDER: PRJNA872821 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21227807_1.fastq.gz	Fastqsanger.gz
	SRR21227807_2.fastq.gz	Fastqsanger.gz
	SRR21227808_1.fastq.gz	Fastqsanger.gz
	SRR21227808_2.fastq.gz	Fastqsanger.gz
	SRR21227809_1.fastq.gz	Fastqsanger.gz

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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.

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.

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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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