Antisense-Mediated Inhibition of Arginase (CAR1) Gene Expression in Saccharomyces cerevisiae.

Park, Heui-Dong; Shin, Min-Choul; Woo, Im-Sun

doi:10.1263/jbb.92.481

Cited by 13 publications

(8 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We observed similar correlations for antisense transcripts in S. cerevisiae, which together with their association to particular functional categories may suggest a possible regulatory role. There are experiments supporting this hypothesis: artificial antisense transcripts in S. cerevisiae had effects on expression of several genes (40)(41)(42), and overexpression of random genomic fragments antisense to ORFs has led in several cases to growth inhibition (43). In our data set, naturally occurring antisense transcripts were found for Ϸ20 of these cases.…”

Section: Resultssupporting

confidence: 58%

A high-resolution map of transcription in the yeast genome

David

Huber²,

Granovskaia³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

611

661

View full text Add to dashboard Cite

There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genomewide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3 and 5 UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.tiling array ͉ transcriptone survey ͉ gene architecture ͉ segmentation ͉ antisense regulation P roteins constitute most structural and functional components of cells. The assumption has been that protein-encoding genes are also the main controllers of cellular processes. Recent evidence challenges this assumption, suggesting a wide-spread involvement of noncoding RNA in regulation, including through the activity of untranslated regions of mRNAs (1), antisense transcripts (2, 3), and isolated noncoding RNAs such as microRNA that control transcript levels or their translation (4).High-resolution transcriptome analysis in higher eukaryotes using tiling arrays has improved ORF annotations and exonintron predictions and discovered many new transcripts of currently unknown function (5-7). However, these studies have encountered challenges, due to noise, limited resolution, lack of strand-specific signal, and drawbacks in the analysis methods (8). Sequencing of cloned cDNAs has also revealed a high level of transcriptional complexity, including the presence of many new transcripts, alternative promoter usage, splicing, and polyadenylation, as well as the presence of many sense-antisense transcript pairs (3, 9). However, because of the cost and labor of large-scale sequencing, this approach has been limited. Therefore, there is a need to develop high-throughput, precise, and high-re...

show abstract

Section: Resultssupporting

confidence: 58%

A high-resolution map of transcription in the yeast genome

David

Huber²,

Granovskaia³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

611

661

View full text Add to dashboard Cite

show abstract

“…There were two aspects to the experiments using the model rice wine system. On one hand, the effect of the UG strain on EC elimination was far superior to the effects of the other methods (9,10,32,33). On the other hand, the concentrations of the main components in rice wine changed very little (all of the changes were Ͻ5%).…”

Section: Discussionmentioning

confidence: 90%

Metabolic Engineering of the Regulators in Nitrogen Catabolite Repression To Reduce the Production of Ethyl Carbamate in a Model Rice Wine System

Zhao

Zhang

et al. 2014

Appl Environ Microbiol

View full text Add to dashboard Cite

Rice wine has been one of the most popular traditional alcoholic drinks in China. However, the presence of potentially carcinogenic ethyl carbamate (EC) in rice wine has raised a series of food safety issues. During rice wine production, the key reason for EC formation is urea accumulation, which occurs because of nitrogen catabolite repression (NCR) in Saccharomyces cerevisiae. NCR represses urea utilization by retaining Gln3p in the cytoplasm when preferred nitrogen sources are present. In order to increase the nuclear localization of Gln3p, some possible phosphorylation sites on the nuclear localization signal were mutated and the nuclear localization regulation signal was truncated, and the disruption of URE2 provided an additional method of reducing urea accumulation. By combining these strategies, the genes involved in urea utilization (DUR1,2 and DUR3) could be significantly activated in the presence of glutamine. During shake flask fermentations of the genetically modified strains, very little urea accumulated in the medium. Furthermore, the concentrations of urea and EC were reduced by 63% and 72%, respectively, in a model rice wine system. Examination of the normal nutrients in rice wine indicated that there were few differences in fermentation characteristics between the wild-type strain and the genetically modified strain. These results show that metabolic engineering of the NCR regulators has great potential as a method for eliminating EC during rice wine production.

show abstract

“…Specific glutamyl transferase activity was given as the number of moles of L-␥-glutamyl hydroxamate produced per min per mg of protein. Arginase activity was assayed essentially as described previously (6,34). Cells were grown in arginine-supplemented rich medium until exponential phase and treated for 6 h with either 250 M Dip or 100 M FeCl 3 .…”

Section: Methodsmentioning

confidence: 99%

Iron-Dependent Remodeling of Fungal Metabolic Pathways Associated with Ferrichrome Biosynthesis

Mercier

Labbé

2010

Appl Environ Microbiol

View full text Add to dashboard Cite

The fission yeast Schizosaccharomyces pombe excretes and accumulates the hydroxamate-type siderophore ferrichrome. The sib1 ؉ and sib2 ؉ genes encode, respectively, a siderophore synthetase and an L-ornithine N 5 -oxygenase that participate in ferrichrome biosynthesis. In the present report, we demonstrate that sib1 ؉ and sib2 ؉ are repressed by the GATA-type transcriptional repressor Fep1 in response to high levels of iron. We further found that the loss of Fep1 results in increased ferrichrome production. We showed that a sib1⌬ sib2⌬ mutant strain exhibits a severe growth defect on iron-poor media. We determined that two metabolic pathways are involved in biosynthesis of ornithine, an obligatory precursor of ferrichrome. Ornithine is produced by hydrolysis of arginine by the Car1 and Car3 proteins. Although car3 ؉ was constitutively expressed, car1 ؉ transcription levels were repressed upon exposure to iron, with a concomitant decrease of Car1 arginase activity. Ornithine is also generated by transformation of glutamate, which itself is produced by two separate biosynthetic pathways which are transcriptionally regulated by iron in an opposite fashion. In one pathway, the glutamate dehydrogenase Gdh1, which produces glutamate from 2-ketoglutarate, was repressed under iron-replete conditions in a Fep1-dependent manner. The other pathway involves two coupled enzymes, glutamine synthetase Gln1 and Fe-S cluster-containing glutamate synthase Glt1, which were both repressed under iron-limiting conditions but were expressed under iron-replete conditions. Collectively, these results indicate that under conditions of iron deprivation, yeast remodels metabolic pathways linked to ferrichrome synthesis in order to limit iron utilization without compromising siderophore production and its ability to sequester iron from the environment.

show abstract

Antisense-Mediated Inhibition of Arginase (CAR1) Gene Expression in Saccharomyces cerevisiae.

Cited by 13 publications

References 22 publications

A high-resolution map of transcription in the yeast genome

A high-resolution map of transcription in the yeast genome

Metabolic Engineering of the Regulators in Nitrogen Catabolite Repression To Reduce the Production of Ethyl Carbamate in a Model Rice Wine System

Iron-Dependent Remodeling of Fungal Metabolic Pathways Associated with Ferrichrome Biosynthesis

Contact Info

Product

Resources

About