Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Global expression profiles of the wild-type and overexpression of OsNMD3ΔNLS transgenic plants

ABSTRACT: Plants have mechanisms that coordinate protein synthesis and gene transcription, although they operate at different cellular sites. The altered translational efficiency may have a feedback effect on gene expression. To determine the global changes in ribosome biogenesis, we used an Illumina RNA sequencing approach to investigate the global expression profiles of the wild-type,OsNMD3ΔNLSL1,and OsNMD3ΔNLSL2 plants.These expression profiles suggested that overexpression of OsNMD3ΔNLS affected ribosome biogenesis and certain basic pathways, leading to pleotropic abnormalities in plant growth. The mRNA profiles of the 2nd internodes of development-matched wild-type and overexpression of OsNMD3ΔNLS transgenic plants.

ORGANISM(S): Oryza sativa

SUBMITTER: Baocai Zhang

PROVIDER: E-GEOD-55234 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Retention of OsNMD3 in the cytoplasm disturbs protein synthesis efficiency and affects plant development in rice.

Shi Yanyun Y Liu Xiangling X Li Rui R Gao Yaping Y Xu Zuopeng Z Zhang Baocai B Zhou Yihua Y

Journal of experimental botany 20140410 12

The ribosome is the basic machinery for translation, and biogenesis of ribosomes involves many coordinated events. However, knowledge about ribosomal dynamics in higher plants is very limited. This study chose a highly conserved trans-factor, the 60S ribosomal subunit nuclear export adaptor NMD3, to characterize the mechanism of ribosome biogenesis in the monocot plant Oryza sativa (rice). O. sativa NMD3 (OsNMD3) shares all the common motifs and shuttles between the nucleus and cytoplasm via CRM ...[more]

PMID: 24723395

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of C. albicans ATCC 10231 (RNA-seq) to transcriptome profiling of garlic oil-treated C. albicans ATCC 10231 and to evaluate protocols for optimal high-throughput data analysis Methods:SDB medium, C. albicans cells and garlic oil were added to two separate 50 mL conical flasks. The initial cell concentrations in culture were both 105 CFU/mL. The cultures were incubated in a water bath shaker at 28 ºC with shaking at 150 rpm for 12 h. Garlic oil or PBS buffer were then added to the cultures to make the concentrations of garlic oil arrived at 0 (control) and 1.25 ?l/mL, respectively. The cultures were continuously incubated at the same conditions for 5 h. The cells were then sampled and centrifuged. The cell precipitates in the control and 1.25 ?l/mL garlic oil groups were quickly separately frozen at -80 ºC. Then total RNA were repared from the cell pellets. Results:The RNA sequencing results showed that many genes in C. albicans exposed to garlic oil were differentially expressed. Nearly three thousand genes were differentially expressed, with either an increase or decrease of more than twofold. Most of them were down regulated while a small number were upregulated. Conclusions: Our study indicated that garlic oil induced differential expression of some critical genes, such as genes for cellular response to drugs, oxidation-reduction processes, pathogenesis, and the cellular response to starvation. Moreover, the differentially expressed genes were mainly clustered in 19 KEGG pathways, such as oxidative phosphorylation, spliceosome, cell cycle, protein processing in endoplasmic reticulum, pyrimidine metabolism, meiosis, RNA transport, ribosome biogenesis, and RNA degradation. The mRNA profiles of C. albicans ATCC 10231 (ck) and garlic oil-treated C. albicans ATCC 10231 (sample1) were generated by deep sequencing, in one time, using Illumina Higseq 2500.

Dataset Information

Global expression profiles of the wild-type and overexpression of OsNMD3ΔNLS transgenic plants

Publications

Retention of OsNMD3 in the cytoplasm disturbs protein synthesis efficiency and affects plant development in rice.

Similar Datasets

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