Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA118211 | ENA |
REPOSITORIES: ENA
Similar Datasets
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. Four samples were analyzed. Two WT and two REAT11 biological replicates were analyzed (one array each).
2010-01-01 | E-GEOD-18417 | biostudies-arrayexpress
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
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
Project description:An investigation into transcriptional changes in developing Arabidopsis leaf caused by novel signalling protein, SPH1.
| PRJNA100647 | ENA
Project description:Bacteria are known to cope with environmental changes by using alternative sigma factors binding to RNA polymerase core enzyme. Sigma factor is one of the targets to modify transcription regulation in bacteria and to influence production capacities. In this study, the effect of overexpressing all annotated sigma factor genes on C. glutamicum WT was assayed using an IPTG inducible plasmid system and different IPTG concentrations. It was revealed that growth was severely decreased when sigD or sigH were overexpressed with IPTG concentrations higher than 50 μM. Overexpression of sigH led to an obvious phenotypic change, a yellow-colored supernatant. HPLC analysis revealed that riboflavin was excreted to the medium when sigH was overexpressed and DNA Microarray analysis confirmed increased expression of riboflavin biosynthesis genes. In addition, genes for enzymes of the pentose phosphate pathway and for enzymes dependent on FMN, FAD or NADPH as cofactor were upregulated when sigH was overexpressed. To test if sigH overexpression can be exploited for production of riboflavin-derived FMN or FAD, the endogenous gene for bifunctional riboflavin kinase/FMN adenyltransferase was co-expressed with sigH from a plasmid. Balanced expression of sigH and ribF improved accumulation of riboflavin (19.8 ± 0.3 μM) and allowed for its conversion to FMN (33.1 ± 1.8 μM) in the supernatant. While a proof-of-concept was reached, conversion was not complete and titers were not high. This study revealed that inducible and gradable overexpression of sigma factor genes is an interesting approach to switch gene expression profiles and to discover untapped potential of bacteria for chemical production. Endogenous sigma factor gene, sigH, was overexpressed in C. glutamicum ATCC13032 from IPTG inducible vector, pEKEx3. Two different concentration of IPTG (10 μM and 15 μM) was used for induction of SigH expression.
2015-06-20 | E-GEOD-70017 | biostudies-arrayexpress
Project description:Genome wide binding sites of the Arabidopsis B3 domain protein FUSCA3
| PRJNA185307 | ENA
Project description:The transcriptome profiles of a riboflavin-producing recombinant Bacillus subtilis RH33 and wild type Bacillus subtilis 168 were compared using DNA microarrays to identify the target genes for further enhancing riboflavin production. Transcriptome profiles of a riboflavin-producing B. subtilis RH33 were compared with those of the wild-type B. subtilis 168 as a control strain during exponentially growing period on LBG medium. These conditions corresponded to the state of high riboflavin production, which was growth related. For each comparison, two independent cultivations on LB medium with 1% glucose were performed, and exponentially growing cells (OD600 3â6) were harvested. The synthesis of cDNA and biotin-labeled cRNA were carried out exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual (2000).
2010-05-05 | E-GEOD-12873 | biostudies-arrayexpress
Project description:Bacteria are known to cope with environmental changes by using alternative sigma factors binding to RNA polymerase core enzyme. Sigma factor is one of the targets to modify transcription regulation in bacteria and to influence production capacities. In this study, the effect of overexpressing all annotated sigma factor genes on C. glutamicum WT was assayed using an IPTG inducible plasmid system and different IPTG concentrations. It was revealed that growth was severely decreased when sigD or sigH were overexpressed with IPTG concentrations higher than 50 μM. Overexpression of sigH led to an obvious phenotypic change, a yellow-colored supernatant. HPLC analysis revealed that riboflavin was excreted to the medium when sigH was overexpressed and DNA Microarray analysis confirmed increased expression of riboflavin biosynthesis genes. In addition, genes for enzymes of the pentose phosphate pathway and for enzymes dependent on FMN, FAD or NADPH as cofactor were upregulated when sigH was overexpressed. To test if sigH overexpression can be exploited for production of riboflavin-derived FMN or FAD, the endogenous gene for bifunctional riboflavin kinase/FMN adenyltransferase was co-expressed with sigH from a plasmid. Balanced expression of sigH and ribF improved accumulation of riboflavin (19.8 ± 0.3 μM) and allowed for its conversion to FMN (33.1 ± 1.8 μM) in the supernatant. While a proof-of-concept was reached, conversion was not complete and titers were not high. This study revealed that inducible and gradable overexpression of sigma factor genes is an interesting approach to switch gene expression profiles and to discover untapped potential of bacteria for chemical production.
2015-06-20 | GSE70017 | GEO
Project description:SARS-COV-2 caused COVID-19 has caused unprecedented global health crisis. Coronavirus have developed a variety of mechanisms to interfere host translation machinery to facilitate virus protein production. Here, we conducted Ribometh-seq to explore the effects of ectopic expression of SARS-COV-2 N protein on rRNA 2'-O-me modification profiles of host cells.
2022-10-28 | GSE199130 | GEO