Dataset Information

Proteomics of Pseudomonas putida PaW85 TruA and RluA deficient strains

ABSTRACT: Understanding the proteomic changes in Pseudomonas putida caused by the lack of pseudouridine synthases TruA or RluA.

INSTRUMENT(S): LTQ Orbitrap XL

ORGANISM(S): Pseudomonas Putida Kt2440

SUBMITTER: Karl Jürgenstein

LAB HEAD: Maia Kivisaar

PROVIDER: PXD022353 | Pride | 2021-01-06

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	190222_04_Orbi2_SK_SER_G240_T274_TYMRI_Kivisaar_rluA1.mgf	Mgf
	190222_04_Orbi2_SK_SER_G240_T274_TYMRI_Kivisaar_rluA1.raw	Raw
	190222_06_Orbi2_SK_SER_G240_T274_TYMRI_Kivisaar_truA2.mgf	Mgf
	190222_06_Orbi2_SK_SER_G240_T274_TYMRI_Kivisaar_truA2.raw	Raw
	190222_08_Orbi2_SK_SER_G240_T274_TYMRI_Kivisaar_PaW2.mgf	Mgf

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Publications

Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp.

Tagel Mari M Ilves Heili H Leppik Margus M Jürgenstein Karl K Remme Jaanus J Kivisaar Maia M

Microorganisms 20201223 1

Pseudouridines are known to be important for optimal translation. In this study we demonstrate an unexpected link between pseudouridylation of tRNA and mutation frequency in Pseudomonas species. We observed that the lack of pseudouridylation activity of pseudouridine synthases TruA or RluA elevates the mutation frequency in Pseudomonas putida 3 to 5-fold. The absence of TruA but not RluA elevates mutation frequency also in Pseudomonas aeruginosa. Based on the results of gene ...[more]

PMID: 33374637

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Project description:In this study we exploited next-generation Illumina sequencing technology (Wang et al., 2009) to refine the current annotation of the KT2440 genome. Transcriptome sequencing data were queried for yet undescribed small RNAs and ORFs and employed to validate predicted operons and gene coordinates. Expression profiles were measured at 10Â°C and 30Â°C to cover the physiologic temperature profile of this mesophilic bacterium. Moreover we compared the sensitivity and specificity of transcriptome data by taking the same RNA preparations for cDNA sequencing and hybridization of Progenika and Affymetrix microarrays. This SuperSeries is composed of the SubSeries listed below. P. putida KT2440 (strain DSM6125) (Bagdasarian et al., 1981) was obtained from the German Resource Centre for Biological Material (DSMZ, (Braunschweig, Germany). Bacterial cultures were inoculated from a frozen stock culture of P. putida wild type, and incubated at 30Â°C for 8 hours at 250 rpm in LB medium. An aliquot of 0.2 mL was added to 20 mL M9 medium (Na2HPO4 33.9 g/L, KH2PO4 15.0 g/L, NaCl 2.5 g/L, NH4Cl 5.0 g/L, MgSO4 2 mM, CaCl2 0.1 mM, FeSO4 x 7 H2O 0.01 mM, pH 6.8) supplemented with 15 mM succinate as sole carbon source in a 100 mL flask and incubated overnight at 30Â°C. For RNA extraction, bacteria were grown in a 1.5 L batch culture (M9 + 15 mM succinate) using the BioFlo 110 Fermenter (New Brunswick Scientific Co., Edison, NJ) to ensure constant pH, aeration and agitation. When cultures reached mid-exponential phase (OD600 ~ 0.8) the temperature was decreased from 30Â°C to 10Â°C. Three samples, each for parallel RNA extraction, were subsequently taken immediately before temperature downshift (30Â°C) and two hours after the media had been cooled to 10Â°C. The gene expression profiles of P. putida KT2440 at 30Â°C and 10Â°C were analyzed using three different transcriptome platforms: RNA-Seq (Illumina cDNA sequencing), Affymetrix microarrays and Progenika oligonucleotide microarrays. For a detailed description of sample preparation (RNA, cDNA , labelling, hybridization etc.) refer to individual Series.

Dataset Information

Proteomics of Pseudomonas putida PaW85 TruA and RluA deficient strains

Dataset's files

Publications

Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in <i>Pseudomonas</i> sp.

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