Dataset Information

Study of the Salmonella enterica strains using the TMT-based proteomics

ABSTRACT: Tandem mass tags were used to performed the multiplexed proteomic study on the Salmonella enterica cell cultures corresponding to various strains of the bacterium.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. Sdt1291

TISSUE(S): Cell Culture

SUBMITTER: Egor Vorontsov

LAB HEAD: Joakim Näsvall

PROVIDER: PXD013041 | Pride | 2020-02-26

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2234_ProteomeDiscoverer14_TMT10_SET1_0mc_1pFDR_160120.msf	Msf
	2234_ProteomeDiscoverer14_TMT10_SET2_0mc_1pFDR_160119.msf	Msf
	2290_ProteomeDiscoverer14_0mc_160329-01.msf	Msf
	Fusion_160115_22.raw	Raw
	Fusion_160115_23.raw	Raw

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Publications

Synonymous Mutations in rpsT Lead to Ribosomal Assembly Defects That Can Be Compensated by Mutations in fis and rpoA.

Knöppel Anna A Andersson Dan I DI Näsvall Joakim J

Frontiers in microbiology 20200306

We previously described how four deleterious synonymous mutations in the Salmonella enterica rpsT gene (encoding ribosomal protein S20) result in low S20 levels that can be compensated by mutations that restore [S20]. Here, we have further studied the cause for the deleterious effects of S20 deficiency and found that the S20 mutants were also deficient in four other 30S proteins (S1, S2, S12, and S21), which is likely due to an assembly defect of the S20 deficient 30S subunits. We examine ...[more]

PMID: 32210939

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Project description:Cardiac amyloidosis is a severe clinical condition leading to restrictive cardiomyopathy and heart failure. With increasing options for specific treatment of different cardiac amyloid diseases, correct amyloid subtyping is essential for clinical outcome. Mass spectrometry-based methods for cardiac amyloid subtyping have become important diagnostic tools but are currently used only in a few reference laboratories. Such methods typically include laser-capture microdissection to ensure the specific analysis of amyloid deposits. While this strategy effectively reduces background signals, it is a labor-intensive and costly procedure hampering the implementation of these methods into a wider group of laboratories. Here we introduce a more direct proteomics-based method for subtyping of cardiac amyloids. Endomyocardial biopsies were retrospectively analyzed from fresh frozen material of 78 patients with cardiac amyloidosis and from 12 biopsies of unused donor heart explants. Cryostat sections were directly digested with trypsin and analyzed with the nano-liquid chromatography (nLC-MS/MS), and the data were evaluated by a proteomic software. With a diagnostic threshold set to 70% for each of the four most common amyloid proteins affecting the heart (LC k, LC l, TTR and SAA), 65 of the cases (87%) could be diagnosed, and of these, 61 cases (94%) were in concordance with the original diagnoses. The specimens were also analyzed for the summed intensities of the amyloid signature proteins (ApoE, ApoA-IV and SAP). The summed intensities were significantly higher (p<0.001) for all assigned amyloid cases, whereas unassigned cases were not significantly different from controls and had lower signals than the assigned cases (p<0.001), suggesting that signature proteins can serve as in situ quality markers of cardiac amyloid deposits. We argue that this efficient workflow can be useful for disseminating proteomics for cardiac amyloid subtyping into accredited clinical laboratories.

Project description:The protein secretory pathway must maintain homoeostasis while producing a wide assortment of proteins in different conditions. It is also used extensively to produce many useful proteins in biotechnology. As such, secretory pathway dysfunction can be highly detrimental to the cell, resulting in the molecular basis for many human diseases, and can drastically inhibit product titers in biochemical production. Because the secretory pathway is a highly-integrated, multi-organelle system, dysfunction can happen at many levels and dissecting the root cause can be challenging. To better understand some of these dysfunctions, we measured multiple systems-level states of the cell (physiology, transcriptome, metabolism) while secreting a small protein (insulin precursor) or a large protein (?-amylase). This was carried out in the presence and absence of HAC1, a key transcription factor in maintaining secretory homeostasis. Clear trends in cellular stress were apparent across multiple data resulting from our perturbations. In particular, processes involving (1) degradation of protein / recycling amino acids, (2) overall transcription/translation repression, and (3) oxidative stress. Apparent runaway oxidative radical production was explained by a thermodynamic model that we put forward for disulfide formation in the endoplasmic reticulum. This model predicts that balancing the relative rates of protein folding and disulfide bond formation are key to easing oxidative stress. These predictions have direct implications in how to engineer a broad range of recombinant proteins for secretion and provide potential hypotheses for the root causes of several secretory-associated diseases. Yeast strains were constructed that produce and secrete (a) IP or (b) ?-amylase and were compared to yeast strains containing (c) an empty vector in both wild-type and HAC1 deletion backgrounds. These strains are named WN (WT with empty vector), WI (WT secreting IP), WA (WT secreting ?-amylase), dN (?hac1 with empty vector), dI (?hac1 secreting IP), and dA (?hac1 secreting ?-amylase). Strains were characterized in batch fermentation and samples were taken in mid-exponential phase. Triplicate fermentations were carried out for each strain.

Dataset Information

Study of the Salmonella enterica strains using the TMT-based proteomics

Dataset's files

Publications

Synonymous Mutations in <i>rpsT</i> Lead to Ribosomal Assembly Defects That Can Be Compensated by Mutations in <i>fis</i> and <i>rpoA</i>.

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