Dataset Information

Mass spectrometry of Phage PhiKZ gp54 with the prohead protease gp175

ABSTRACT: Assay of recombinant Pseudomonas phage PhiKZ gp54 with the prohead protease gp175. The gene for each protein was cloned into the expression plasmid DH10B. The assay was conducted in a lysate of E. coli DH10B cells, conditions in which PhiKZ gp175 had previously been shown to be active. Analyses of gel slices identified C-terminal processing of gp54 via the semi-tryptic peptide 558-FITAMDAAAAAAGVTVTME-576 in the gp54-plus-gp175 slices (predominantly slice 3) provided convincing evidence for proteolysis of gp54 in the presence of gp175.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Pseudomonas Phage Phikz

SUBMITTER: Julie Thomas

LAB HEAD: Julie Thomas

PROVIDER: PXD011519 | Pride | 2018-11-21

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	171214JAT01_B1.raw	Raw
	171214JAT01_B1.rawF042205_B1.mzid.gz	Mzid
	171214JAT01_B1.rawF042205_B1.mzid_171214JAT01_B1.raw_F042205_B1.MGF	Mzid
	171214JAT02_B2.raw	Raw
	171214JAT02_B2.rawF042206_B2.mzid.gz	Mzid

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Publications

Global Proteomic Profiling of Salmonella Infection by a Giant Phage.

Weintraub Susan T ST Mohd Redzuan Nurul Humaira NH Barton Melissa K MK Md Amin Nur Amira NA Desmond Maxim I MI Adams Lily E LE Ali Bazla B Pardo Sammy S Molleur Dana D Wu Weimin W Newcomb William W WW Osier Michael V MV Black Lindsay W LW Steven Alasdair C AC Thomas Julie A JA

Journal of virology 20190219 5

The 240-kb Salmonella phage SPN3US genome encodes 264 gene products, many of which are functionally uncharacterized. We have previously used mass spectrometry to define the proteomes of wild-type and mutant forms of the SPN3US virion. In this study, we sought to determine whether this technique was suitable for the characterization of the SPN3US proteome during liquid infection. Mass spectrometry of SPN3US-infected cells identified 232 SPN3US and 1,994 Salmonella proteins. SPN3US p ...[more]

PMID: 30541839

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Project description:To investigate the developmental gradient of the third maize leaf, the light exposed area of the leaf (corresponding to 18cm of leaf) and 2cm shaded by the sheath were sampled in ten slices. Four replicates were collected, immediately shock frozen in liquid nitrogen and subsequently cut into 2cm slices. At least 10 plants were pooled for each biological replicate. We have systematically analyzed a developmental gradient of the third maize leaf from the point of emergence into the light to the tip in ten continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, delta-13C values, and photosynthetic rate measurements showed that the maize leaf undergoes a sink to source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All datasets are included within the publication to serve as a resource for maize leaf systems biology. For the transcriptional analysis, the goal of the study was to (i) identify whether the leaf contains binary switches for genes involved in photosynthesis, (ii)characterize the patterns of gene expression in the leaf, (iii) provide independent validation of maize leaf expression experiments published in Li et al. (2011) and (iv) determine transcripts co-expressed with key transcripts of C4 photosynthesis. To this end, changed transcripts were determined by ANOVA and characterized by K-means and hierachical clustering. Four replicates were collected for each of the ten consecutive leaf slices resulting in 40 one color arrays. Slice 1 represents the tip of the leaf, slice 10 the lowermost slice which is shaded by the sheath with all slices in between consecutively numbered.

Project description:Background: Evidence has recently accumulated suggesting that mature hepatocytes have the unique capacity to autonomously decide their replication fate. The molecular mechanism by which hepatocytes switch from an essentially quiescent state to rapidly proliferation after liver injury is not fully understood. To provide molecular insights into the self-renewal of mature hepatocytes, we have applied an ex vivo liver slice culture system. Results: After liver injury, activation of p38 and Erk1/2 began in mature hepatocytes within 5 min. Erk1/2 was activated at the edge of the cut as well as on the surface of liver slices. The number of hepatocytes that contain activated Erk1/2 increased within 1 h and then decreased. Concomitantly, immediate early genes (IEGs), such as Jun, early gene response 1 (Egr1) and Myc were induced and Ki67 positive hepatocytes appeared 24 h after liver injury in the slices. In agreement with in vivo studies, transcriptome analysis using 2 h slice culture reveals that 63% of upregulated genes were downstream of lipopolysaccharide (LPS) stimulation which induces interleukin 6 (IL 6) or tumor necrosis factor (TNF) alpha pathways. Furthermore, circadian clock regulator, such as members of the basic helix-loop-helix family, Bhlhe40 and Bhlhe41, were highly upregulated for 4 h after injury. Although upon injury Jun or Egr1 were induced in liver slices from proliferation-defective liver, no circadian clock regulator genes were upregulated. Moreover, using an in vitro cell culture system we show that Bhlhe40 is required for the G0-G1 transition. Conclusion: Our data suggest that the circadian clock regulator, Bhlhe40, is involved in the G0-G1 transition. An ex vivo system using normal and proliferation defective KO liver is a useful tool for identification of genes that trigger cell proliferation shortly after liver injury. This method may also be applied for measurement of the liver regeneration potential of individual livers at the priming phase. In one dual-color microarray hybridization, mRNA expression changes after 2h ex vivo incubation of liver slices were examined.

Dataset Information

Mass spectrometry of Phage PhiKZ gp54 with the prohead protease gp175

Dataset's files

Publications

Global Proteomic Profiling of <i>Salmonella</i> Infection by a Giant Phage.

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