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Transcriptomic profile of Arabidopsis thaliana treated with exogenous Riboflavin

ABSTRACT: Transcriptomic profile of Arabidopsis thaliana treated with exogenous Riboflavin

PROVIDER: PRJNA1089574 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28387264_1.fastq.gz	Fastqsanger.gz
	SRR28387264_2.fastq.gz	Fastqsanger.gz
	SRR28387265_1.fastq.gz	Fastqsanger.gz
	SRR28387265_2.fastq.gz	Fastqsanger.gz
	SRR28387266_1.fastq.gz	Fastqsanger.gz

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Transcriptomic profile of Arabidopsis thaliana treated with exogenous Riboflavin

Project description:Riboflavin, also known as vitamin B2, is crucial for cell function as it is the central component of FMN and FAD cofactors. These flavocoenzymes are essential for various cellular processes including the control of flavoproteins activity. Flavins are vital for growth and cellular metabolism of plants, supporting functions like photosynthesis, mitochondrial electron transport, and fatty acid oxidation. Further, previous studies have shown that exogenous application of riboflavin enhances plant defenses against abiotic and biotic stresses. In this study, to identify and implicate genes and signaling pathways involved in these processes, a holistic transcriptome analysis was conducted on Arabidopsis wild-type plants treated with Riboflavin and the mutant called “melin” which accumulates Riboflavin at exceptionally high levels.

2024-11-25 | GSE261916 | GEO

Arabidopsis transcriptome changes caused by ectopic production of a turtle riboflavin-binding protein

Project description:Leaf contents of free riboflavin were modulated by ectopic expression of the turtle gene encoding riboflavin-binding protein (RfBP). Compared to Arabidopsis thaliana (L.) ecotype Col-0 (wild type), REAT (modified type) that constitutive express RfBP had 71%-77% less flavins of free form. We used microarray to investigate the influence on plants due to the reduced free flavin. One modified line (REAT11) and wild type (WT) were tested by microarray, and the experiments data revealed that abundance of transcripts for 950 genes in REAT was altered compared to the wild type.

2010-01-01 | GSE18417 | GEO

Arabidopsis transcriptome changes caused by ectopic production of a turtle riboflavin-binding protein

2010-01-01 | E-GEOD-18417 | biostudies-arrayexpress

Transcriptomics and Real-Time PCR analysis reveals a cross-modulatory effect between riboflavin and iron and outlines common and specific responses to riboflavin biosynthesis and uptake in Vibrio cholerae

Project description:Riboflavin-derived molecules such as flavin mononucleotide and flavin adenine dinucleotide comprise the most important redox coenzymes all across life kingdoms. Vibrio cholerae, a pandemic diarrheagenic bacterium, is able to synthesize riboflavin through the riboflavin biosynthetic pathway (RBP) and to internalize exogenous riboflavin using the RibN importer. This bacterium thrives in different environments such as estuarine waters and the human intestinal tract. The presence of two independent riboflavin supply pathways in this species may be related to the variable riboflavin availability and requirements across different niches. In order to gain insights into the role of the riboflavin provision pathways in the physiology of V. cholerae, we analyzed the bacterial transcriptomics response to extracellular riboflavin and to the deletions of ribD (RBP-deficient strain) or ribN. Notably, many genes responding to riboflavin have been previously reported to belong to the iron regulon. Real time PCR analysis confirmed this effect and further documented that reciprocally, iron regulates RBP and ribN genes in a riboflavin-dependent way. A subset of genes were responding to both ribD and ribN deletions. Nonetheless, a group of genes was specifically affected in the ∆ribD strain, on which the functional terms protein folding and oxidation reduction process were enriched. Also, a subset of genes was affected specifically in the ∆ribN strain, on which the cytochrome complex assembly functional term was enriched. Results indicate that iron and riboflavin interrelate to regulate its respective provision genes and suggest that both common and specific effects of biosynthesized and internalized riboflavin exist.

2018-02-21 | GSE107538 | GEO

Effects of exogenous auxin on the Arabidopsis thaliana root proteome

Project description:This study evaluates the effects of exogenous auxin on the Arabidopsis thaliana root proteome at 8, 12, and 24 hours post-treatment.

2017-07-18 | PXD001400 | Pride

The RNA-seq data in riboflavin-treated alcoholic liver disease

Project description:Alcoholic liver disease (ALD) is a kind serious liver disease, which will develope into the cirrhosis, liver cancer and so on. The study results show that riboflavin has the protective effect against ALD. Then the study divides the C57BL/6 mice into the three groups that were Control (C), Alcohol, Alcohol with riboflavin (AR) groups respectively. And the study makes the mouse liver RNA sequencing (RNA-seq) to find the differential expression mRNAs among three groups futher and does the related analysis in riboflavin-treated alcoholic liver disease.

2024-08-28 | GSE273208 | GEO

The 16S RNA-seq data in riboflavin-treated alcoholic liver disease

Project description:Alcoholic liver disease (ALD) is a kind of liver disease that will result in liver cancer and some other high death rate liver disease. The study results show that riboflavin could protect the mouse against ALD. Then the study divides the C57BL/6 mice into the three groups including Control (C), Alcohol, Alcohol with riboflavin (AR) groups respectively. And the study makes the mouse stool samples 16S RNA sequencing (RNA-seq) to find the differential itestinal microbiota homeostasis among three groups futher and does the related analysis in riboflavin-treated alcoholic liver disease.

2024-08-28 | GSE273370 | GEO

Transcriptome analysis using Arabidopsis leaves after exogenous FAD treatment

Project description:Riboflavin (RF) and its cofactors (FMN and FAD) are essential molecules for vital metabolic processes in all organisms. Thus, the flavin metabolism must be tightly regulated in the cells. We previously demonstrated that the intracellular levels of flavins were tightly maintained by the enzymes involved in their synthesis and degradation, inducing a plastidic FAD hydrolase (AtNUDX23), in Arabidopsis. However, information of regulatory factors involved in the flavin homeostasis and transporters in each organelle are mostly limited. Terefore, we tried to identify novel factors involved in the flavin metabolism, such as transcription factors and transporters by a transcriptome analysis after exogenous FAD treatment.

2021-03-18 | GSE169061 | GEO

Riboflavin deficiency regulates inflammation-associated genes in rat esophageal intraepithelial neoplasia

Project description:Transcriptome analysis of RNA samples from riboflavin deficiency combined with NMBA-induced rat esophageal intraepithelial neoplasia tissues. Epidemiological studies suggest that dietary riboflavin deficiency and environmental exposure to N-nitrosomethylbenzylamine (NMBA) are common in China's high incidence area of esophageal cancer. Riboflavin deficiency has been documented as an important risk factor for esophageal cancer. In this study, we established a F344 rat esophageal tumor model that combines dietary riboflavin deficiency with exposure to NMBA. The results showed that riboflavin deficiency combined with NMBA (R0N+) enhanced the incidence of esophageal intraepithelial neoplasia, including in situ carcinoma, whereas normal levels of riboflavin combined with NMBA (RcN+) mainly induced the occurrence of esophageal benign hyperplasia and small amount of esophageal intraepithelial neoplasia. Oxidative DNA damage (8-OHdG) and DNA double-strand breaks (p-γH2AX) in R0N+ rats were higher than that in RcN+ rats. The aim of the present study is to analyze the mechanism of riboflavin deficiency-induced tumorigenesis. So, we used Affymetrix Clariom D(also known as Rat Transcriptome Array 1.0) to identify genes that were differentially expressed upon R0N+ esophageal intraepithelial neoplasia tissues.

2018-02-28 | GSE111207 | GEO

Riboflavin depletion regulates cell proliferation and cell cycle progression‑associated genes in HEK293T cells

Project description:Transcriptome analysis of RNA samples from riboflavin-depleted HEK293T cells. Riboflavin is an essential component of the human diet and its derivative cofactors have an established role in oxidative metabolism. Riboflavin deficiency has been linked with various human diseases. In this study, we have modelled riboflavin deficiency in HEK293T cell line, shown remarkable increase of cell proliferation. The aim of the present study is to develop a cell culture model of riboflavin depletion and analyze its molecular mechanism of acceleration cell proliferation. So, we used Affymetrix Human Transcriptome Array 2.0 to identify genes that were differentially expressed upon riboflavin-depleted HEK293T cells.

2017-05-16 | GSE98927 | GEO

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