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Investigating the impact of heterologous expression of the Micrococcus luteus FabH on global transcription in Escherichia coli

ABSTRACT: Investigation of whole genome gene expression level changes in a E. coli fatty acid overproducing strain with or without heterologous expression of the M. luteus FabH. The strain expressing M. luteus FabH produces more methyl ketones. This study will be further described in Goh, E.B., E.E.K. Baidoo, J.D. Keasling, and H.R. Beller. Engineering of bacterial methyl ketone synthesis for biofuels.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE32561 | GEO | 2012/01/26

SECONDARY ACCESSION(S): PRJNA147115

REPOSITORIES: GEO

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Investigating the impact of heterologous expression of the Micrococcus luteus FabH on global transcription in Escherichia coli

Project description:Investigation of whole genome gene expression level changes in a E. coli fatty acid overproducing strain with or without heterologous expression of the M. luteus FabH. The strain expressing M. luteus FabH produces more methyl ketones. This study will be further described in Goh, E.B., E.E.K. Baidoo, J.D. Keasling, and H.R. Beller. Engineering of bacterial methyl ketone synthesis for biofuels. A 11 microarray study using total RNA recovered from six separate control cultures of Escherichia coli K-12 DH1 fatty acid overproducing strain with empty vector and five separate cultures of test strain, Escherichia coli K-12 DH1 fatty acid overproducing strain with vector overexpressing M. luteus FabH. Each chip measures the expression level of 4,254 genes from Escherichia coli K-12 with eight 60-mer probe pairs (PM/MM) per gene, with 2-fold technical redundancy.

2012-01-26 | E-GEOD-32561 | biostudies-arrayexpress

Transcription differences of Micrococcus luteus at late-exponential and stationary phase

Project description:Investigation of transcriptomic changes in M.luteus at 12hrs and 24hrs. Differences in fatty acid profiles of M. luteus at exponential and stationary phase is attributed to transcriptional changes of branched amino acid biosynthesis and degradation genes. This study is described by Pereira, J.H., E.B. Goh, J.D. Keasling, H.R. Beller and P.A. Adams in Crystal structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus, which has been submitted to Acta Crystallographica Section D A 6 microarray study using total RNA recovered from six separate control cultures of Micrococcus luteus NCTC2665 strain with 3 harvested after 12hrs of growth and the other 3 after 24hrs of growth. Each chip measures the expression level of 2,374 ORF based on the draft genome sequence of Micrococcus luteus with ten 60-mer probe pairs (PM/MM) per gene, with 3-fold technical redundancy.

2012-09-24 | E-GEOD-38040 | biostudies-arrayexpress

Transcription differences of Micrococcus luteus at late-exponential and stationary phase

2012-09-24 | GSE38040 | GEO

Gene expression changes in Suillus luteus- Pinus sylvestris ectomycorrhizal roots compared to Suillus luteus free-living mycelium

2015-02-06 | GSE63926 | GEO

Gene expression changes in Suillus luteus- Pinus sylvestris ectomycorrhizal roots compared to Suillus luteus free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Suillus luteus ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 40 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Suillus luteus ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.

2015-02-06 | E-GEOD-63926 | biostudies-arrayexpress

Dynamic miRNA-mRNA regulations are essential for maintaining Drosophila immune homeostasis during Micrococcus luteus infection

Project description:Pathogen bacteria infections can lead to dynamic changes of microRNA (miRNA) and mRNA expression profiles, which may control synergistically the outcome of immune responses. To reveal the role of dynamic miRNA-mRNA regulation in Drosophila innate immune responses, we have detailedly analyzed the paired miRNA and mRNA expression profiles at three time points during Drosophila adult males with Micrococcus luteus (M. luteus) infection using RNA- and small RNA-seq data. Our results demonstrate that differentially expressed miRNAs and mRNAs represent extensively dynamic changes over three time points during Drosophila with M. luteus infection. The pathway enrichment analysis indicates that differentially expressed genes are involved in diverse signaling pathways, including Toll and Imd as well as orther signaling pathways at three time points during Drosophila with M. luteus infection. Remarkably, the dynamic change of miRNA expression is delayed by compared to mRNA expression change over three time points, implying that the "time" parameter should be considered when the function of miRNA/mRNA is further studied. In particular, the dynamic miRNA-mRNA regulatory networks have shown that miRNAs may synergistically regulate gene expressions of different signaling pathways to promote or inhibit innate immune responses and maintain homeostasis in Drosophila, and some new regulators involved in Drosophila innate immune response have been identified. Our findings strongly suggest that miRNA regulation is a key mechanism involved in fine-tuning cooperatively gene expressions of diverse signaling pathways to maintain innate immune response and homeostasis in Drosophila. Taken together, the present study reveals a novel role of dynamic miRNA-mRNA regulation in immune response to bacteria infection, and provides a new insight into the underlying molecular regulatory mechanism of Drosophila innate immune responses.

2021-05-04 | GSE173733 | GEO

Preimplantation embryo ketone body exposure exerts sex-specific effects on mouse fetal and placental transcriptomes

Project description:Ketogenic diet consumption elevates circulating levels of the ketones β-hydroxybutyrate (βOHB) and acetoacetate (AcAc). In vitro ketone exposure perturbs preimplantation mouse embryo viability and female-specific fetal development post-transfer. Here we assessed whether transient exposure of preimplantation embryos to ketones impacts post-implantation fetal and placental gene expression. Blastocysts cultured in vitro with or without 2 mmol/L βOHB alone (‘βOHB’) or combined with 0.8 mmol/L AcAc (‘Keto’) underwent embryo transfer. Transcriptional profiles of sexed E14.5 placentae, liver, and brain were examined via RNA-Seq and DAVID functional analysis, revealing a sexually dimorphic transcriptomic response. βOHB and Keto exposure both downregulated genes related to oxidative phosphorylation specifically in female liver. βOHB downregulated female placental steroid biosynthetic processes, while Keto treatment upregulated genes relevant to blood vessel formation and cell migration in male placentae. Brain transcriptomes were minimally affected. X-linked genes and chromatin modifiers were identified as differentially expressed, alluding to a sex-specific regulatory mechanism. Transient preimplantation ketone exposure therefore perturbs sex-specific fetal liver and placental gene expression demonstrating a developmental programming effect that warrants future investigation of male and female offspring postnatal metabolic health.

2023-09-15 | GSE217821 | GEO

Micrococcus luteus ATCC 4698 = NCTC 2665 microbeMASST submission

Project description:HLB SPE extract from M. luteus ATCC 4698 grown in TSB for 24hrs at 37C. Media blank is included in supplementary files.

2022-07-31 | MSV000090033 | MassIVE

Oloplotosus luteus

Project description:Oloplotosus luteus

| PRJNA837941 | ENA

Expression of immune-inducible genes in Drosophila melanogaster whole fly samples upon Micrococcus luteus infection for 24h

Project description:Transcriptome profiling of immune-responsive genes in Drosophila melanogaster during Gram-positive bacterial infection was performed. The most highly induced gene by Micrococcus luteus infection was a novel gene CG44404, named Induced by Infection (IBIN). In the Flybase release FB2019_4 (22.8.2019) IBIN is annotated as coding for a short peptide. In the transcriptome analysis, fourteen immune-inducible long non-coding RNA (lncRNA) genes (Fold Change > 3) were also found.

2019-01-01 | GSE120387 | GEO

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