Glutamine synthetase mRNA releases sRNA from its 3′UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Japan
- Transborder Medical Research Center, University of Tsukuba, Japan
- International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of Tsukuba, Japan
- Institute for Advanced Biosciences, Keio University, Japan
- Graduate School of Media and Governance, Keio University, Japan
- Medical Mycology Research Center, Chiba University, Japan
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Japan
Figures
Figure 1
glnA mRNA expresses both GlnA protein and GlnZ sRNA.
(A) The genetic structure of glnALG operon and nitrogen assimilation pathway. The transcription of glnA mRNA from σ54-dependent promoter glnAp2 is activated by the NtrB/NtrC two-component system, …
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Figure 1—source data 1
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig1-data1-v3.pdf
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Figure 1—source data 2
The original files of the full raw unedited northern blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig1-data2-v3.zip
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Figure 1—source data 3
The original files of the full raw unedited westen blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig1-data3-v3.zip
Figure 2
Variation of GlnZ sRNAs in the Enterobacteriaceae family.
(A) Multiple sequence alignment of glnA 3′UTRs using CLUSTALW program (https://www.genome.jp/tools-bin/clustalw). (B) The location of conserved seed region and Rho-independent terminator in …
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Figure 2—source data 1
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig2-data1-v3.pdf
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Figure 2—source data 2
The original files of the full raw unedited northern blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig2-data2-v3.zip
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Figure 2—source data 3
The original files of the full raw unedited western blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig2-data3-v3.zip
Figure 3 with 2 supplements
Post-transcriptional regulation mediated by Salmonella enterica and Escherichia coli GlnZ.
Predicted interactions of GlnZ with the target mRNAs are shown in the panels, (A) S. enterica sucA, (B) E. coli sucA, (C) S. enterica glnP, (D) S. enterica deoD, (E) E. coli aceE, and (F) S. …
Figure 3—figure supplement 1
Post-transcriptional regulation of sucA involves a purine-rich sequence.
(A) Predicted interaction of GlnZ with sucA mRNA in Salmonella and Escherichia coli. The nucleotide numbers relative to the start codon of sucA (bold) and the stop codon of glnA are shown above and …
Figure 3—figure supplement 2
Post-transcriptional regulation of aceE by GlnZO157.
(A) Escherichia coli ΔglnZ strain was transformed by pXG30sf-aceEeco along with pJV300 vector control or GlnZO157 expression plasmids (Supplementary file 5-7). Mean relative fluorescence units (RFU) …
Figure 4
Repression of SucA by endogenous GlnZ.
(A) GlnZ post-transcriptionally represses the expression of SucA in Salmonella during growth on glutamine (Gln) as the nitrogen source. Salmonella wild-type (WT) and ΔglnZ strains were grown to …
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Figure 4—source data 1
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig4-data1-v3.pdf
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Figure 4—source data 2
The original files of the full raw unedited northern blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig4-data2-v3.zip
Figure 5
Hfq is essential for GlnZ biogenesis and target regulation.
(A) Expression profiles of glnA gene products in Escherichia coli and its hfq mutant during growth on different nitrogen sources. E. coli BW25113 and its hfq mutant were grown to exponential phase …
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Figure 5—source data 1
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data1-v3.pdf
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Figure 5—source data 2
The original files of the full raw unedited western blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data2-v3.zip
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Figure 5—source data 3
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data3-v3.pdf
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Figure 5—source data 4
The original files of the full raw unedited northern blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data4-v3.zip
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Figure 5—source data 5
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data5-v3.pdf
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Figure 5—source data 6
The original files of the full raw unedited western blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data6-v3.zip
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Figure 5—source data 7
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data7-v3.pdf
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Figure 5—source data 8
The original files of the full raw unedited western blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig5-data8-v3.zip
Figure 6 with 1 supplement
GlnZ release from the glnA mRNA is necessary for target repression.
(A) RNase E is essential for the processing of glnA mRNA. Escherichia coli ΔglnZ (wild-type [WT]) and ΔglnZ ams-1 (TS) strains harboring pBAD-glnAsal or pBAD-glnAeco were grown to OD600 ~0.5 at 30°C …
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Figure 6—source data 1
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig6-data1-v3.pdf
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Figure 6—source data 2
The original files of the full raw unedited northern blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig6-data2-v3.zip
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Figure 6—source data 3
Figure with the uncropped blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig6-data3-v3.pdf
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Figure 6—source data 4
The original files of the full raw unedited northern and western blots.
- https://cdn.elifesciences.org/articles/82411/elife-82411-fig6-data4-v3.zip
Figure 6—figure supplement 1
Expression of GlnZ and its targets in Escherichia coli rnc14 mutant.
(A) E. coli wild-type (WT) and rnc14 strains were grown to exponential phase (OD600 ~0.5) in MOPS minimal medium containing 0.2% glucose or 20 mM pyruvate as the carbon source and 0.1% ammonium as …
Figure 7
GlnA and GlnZ expressed from glnA mRNA facilitate nitrogen assimilation independently.
The expression of GlnA and GlnZ is induced by the two-component system NtrBC upon nitrogen limitation. The glutamine synthetase (GS)-glutamine 2-oxoglutarate amidotransferase (GOGAT) (GlnA-GlnBD) …
Additional files
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Supplementary file 1
Genes downregulated upon GlnZ1 overexpression in Salmonella Typhimurium SL1344.
- https://cdn.elifesciences.org/articles/82411/elife-82411-supp1-v3.docx
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Supplementary file 2
Bacterial strains used in this study.
- https://cdn.elifesciences.org/articles/82411/elife-82411-supp2-v3.docx
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Supplementary file 3
Plasmids used in this study.
- https://cdn.elifesciences.org/articles/82411/elife-82411-supp3-v3.docx
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Supplementary file 4
DNA oligonucleotides used in this study.
- https://cdn.elifesciences.org/articles/82411/elife-82411-supp4-v3.docx
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Supplementary file 5
Inserts of GlnZ mutant plasmids.
- https://cdn.elifesciences.org/articles/82411/elife-82411-supp5-v3.docx
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Supplementary file 6
Details of GFP fusion plasmids.
- https://cdn.elifesciences.org/articles/82411/elife-82411-supp6-v3.docx
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Supplementary file 7
Inserts of GFP fusion plasmids.
- https://cdn.elifesciences.org/articles/82411/elife-82411-supp7-v3.docx
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MDAR checklist
- https://cdn.elifesciences.org/articles/82411/elife-82411-mdarchecklist1-v3.docx
