Dataset Information

HCN regulates cellular processes through posttranslational modification of proteins by S-cyanylation

ABSTRACT: Hydrogen cyanide (HCN) is coproduced with ethylene in plant cells and primarily enzymatically detoxified by the mitochondrial ß-cyanoalanine synthase (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis results in physiological alterations in the plant that suggest that the function of HCN is a gasotransmitter molecule. Label-free quantitative proteomic analysis of enriched mitochondrial samples isolated from the wild type and cas-c1 mutant revealed significant changes in protein content, identifying 451 proteins that are absent or less abundant in cas-c1 and 353 proteins that are only present or more abundant in the mutant background. Gene ontology classification of these proteins highlights proteomic changes that explains the root hairless phenotype and the altered immune response observed in the cas-c1 mutant. The mechanism of action of cyanide as a signaling molecule has been addressed using two proteomic approaches focused on identifying the S-cyanylation of cysteine as a posttranslational modification of proteins. Both the 2-imino-thiazolidine chemical method and the direct untargeted analysis of proteins using LC-MS/MS identified a set of 163 proteins susceptible to S-cyanylation that included sedoheptulose 1, 7-bisphosphatase (SBPase), the peptidyl-prolyl cis-trans isomerase (CYP20-3) and enolase 2 (ENO2). In vitro analysis of these proteins identified that this modification in the SBPase Cys74, CYP20-3 Cys259 and ENO2 Cys346 residues affected the enzymatic activity of the enzymes. GO classification and protein-protein interaction cluster analysis revealed the function of S-cyanylation in the regulation of primary metabolic pathways, such as glycolysis, and the Calvin and S-adenosylmethionine cycles.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Root

SUBMITTER: Luis C. Romero

LAB HEAD: Luis C Romero

PROVIDER: PXD009929 | Pride | 2019-01-09

REPOSITORIES: Pride

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			Action	DRS
	2016034-PVMVt-test.xlsx	Xlsx
	20160730-08_2016034-LIBRERIA_IMIBIC.group	Other
	20160730-08_2016034-LIBRERIA_IMIBIC.mgf	Mgf
	20160730-08_2016034-wt1_slow.wiff	Wiff
	20160730-08_2016034-wt1_slow.wiff.scan	Wiff

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HCN Regulates Cellular Processes through Posttranslational Modification of Proteins by S-cyanylation.

García Irene I Arenas-Alfonseca Lucía L Moreno Inmaculada I Gotor Cecilia C Romero Luis C LC

Plant physiology 20181030 1

Hydrogen cyanide (HCN) is coproduced with ethylene in plant cells and is primarily enzymatically detoxified by the mitochondrial β-CYANOALANINE SYNTHASE (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis (Arabidopsis thaliana) results in physiological alterations in the plant that suggest that HCN acts as a gasotransmitter molecule. Label-free quantitative proteomic analysis of mitochondrially enriched samples isolated from the wild type and cas-c1 mutant ...[more]

PMID: 30377236

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Project description:Differential gene expression analysis of Leptospirillum ferriphilum DSM 14647 cells treated with quorum sensing singnal compounds. Briefly, Leptospirillum ferriphilum DSM 14647 cells were grown to early stationary phase in Mackintosh basal salt solution (Mac medium) pH 1.8 (Mackintosh 1978) with 71.6 mM Fe2+ (supplied as FeSO4•7H2O). Cultures were incubated under constant shaking at 140 rpm and 37 °C. Cells were harvested by centrifugation (7.000 g, 10 min). Subsequently cells were inoculated at 10^8 cells/mL in 100 mL Erlenmeyer flasks with 50 mL Mac medium (pH 1.8) and amended with combined DSF (cis-11-methyl-2-dodecenoic acid, CAS 677354-23-3; Sigma) and BDSF (cis-2-dodecenoic acid, CAS 55928-65-9; Sigma) at 2 µM per compound or with a mixture of N-acyl-homoserine-lactones, namely N-dodecanoyl-DL-homoserine lactone (C12-AHL, CAS 8627-38-8, Sigma), N-tetradecanoyl-DL-homoserine lactone (C14-AHL, CAS 98206-80-5, Sigma), N-(3-hydroxydodecanoyl)-DL-homoserine (3-OH-C12-AHL, CAS 182359-60-0), N-(3-hydroxytetradecanoyl)-DL-homoserine lactone (3-OH-C14-AHL, CAS 172670-99-4) at 5 µM per compound. Controls were supplemented with DMSO as used as solvent for signal compound stock solutions. After inoculation 32 mM iron(II) ions were added. The assay flasks were incubated for two hours at 37 °C and 140 rpm. Assays were periodically sampled for determination of Fe2+ concentrations using the phenantroline method (Harvey, Smart et al. 1955). Within this time the inhibitory effect of DSF/BDSF on Fe2+ oxidation was confirmed and subsequently the flasks were rapidly cooled on ice and by addition of 1 volume ice-cold Mac medium (pH 1.8). The cultures (n = 4 per condition) were centrifuged at 12,500 × g for 10 min at 4° C. The cell pellet was washed twice by re-suspending in 2 mL of sterile, ice-cold Mac medium (pH 1.8) and then flash frozen in liquid nitrogen and stored at -80 °C. The nucleic acid extraction was conducted as described by (Christel, Fridlund et al. 2016) with modifications. Briefly, the cells were re-suspended in lysis buffer (0.02 % sodium acetate, 2 % sodium dodecyl sulfate, 1 mM EDTA, pH 5.5) and lysed using Tri-reagent (Ambion) and the lysate was treated with bromo-chloro propane. Nucleic acids were precipitated with isopropanol, cleaned with 80% ethanol, dried at room temperature and subsequently treated with DNAse I (Thermo Fisher Scientific®). Ribosomal RNA depletion was conducted using the QIAseq® FastSelect™ −5S/16S/23S kit for bacterial RNA samples without fragmentation. Nucleic acid quantification and quality control were assessed by agarose gel electrophoresis, NanoDrop, Qubit™ RNA HS Assay kit (Invitrogen®) and the Agilent 2100 Bioanalyzer . Libraries (12 in total) were prepared by SciLifeLab, Stockholm, Sweden using the Illumina TruSeq stranded mRNA Kit. Paired-end sequencing (2 × 151 bp) was performed on one Illumina NovaSeq6000 lane using 'NovaSeqXp' workflow in 'S4' mode flowcell. Bioinformatics and statistics The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. at SciLifeLab, Stockholm, Sweden. The quality of the raw sequencing reads was assessed with FastQC/MultiQC (Andrews 2010, Ewels, Magnusson et al. 2016). Subsequently adapter sequences were removed using Cutadapt/TrimGalore 0.6.1 (Martin 2011, Krueger 2019). Paired-end transcript reads were mapped against the reference genome with the accession number GCA_900198525 (Christel, Herold et al. 2017) using Bowtie2 (Langmead and Salzberg 2012), sorted by their genomic location using the samtools sort function (Liao, Smyth et al. 2019) and counted using feautureCounts of the Rsubreads package (Liao et al. 2019). Raw counts were then processed for assessment of statistically significant differential gene expression with DESeq2 (Love, Huber et al. 2014) by determination of Log2-fold changes (LFC) and corresponding p-values (padj, adjusted p-values).

Project description:MicroRNA399-mediated regulation of the ubiquitin-conjugating enzyme UBC24/PHO2 is crucial for phosphate (Pi) acquisition and translocation in plants. Because of a potential role for PHO2 in protein degradation and its association with membranes, an iTRAQ-based quantitative membrane proteomic method was employed to search for components downstream of PHO2. A total of 7491 proteins were identified from Arabidopsis roots by mass spectrometry, 35.2 % of which were predicted to contain at least one transmembrane helix. Among the quantifiable proteins, 5 were significantly differentially expressed between the wild-type and pho2 mutant under 2 growth conditions. Using immunoblot analysis, we validated the upregulation of several PHT1 Pi transporters and PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (PHF1) in pho2 and demonstrated that PHO2 mediates the degradation of PHT1 proteins. Genetic evidence that loss of PHF1 or PHT1;1 alleviated Pi toxicity in pho2 further suggests their roles as downstream components of PHO2. Moreover, we showed that PHO2 interacts with PHT1s in the post-endoplasmic reticulum compartments and mediates the ubiquitination of endomembrane-localized PHT1;1. This study not only uncovers a mechanism by which PHO2 modulates Pi acquisition by regulating the abundance of PHT1s in the secretory pathway destined for plasma membranes, but also provides a database of the membrane proteome that will be widely applicable in root biology research. Spectra Processing: The MS/MS raw spectra generated from the Waters Q-TOF Premier (the first replicate) and the AB SCIEX TripleTOF 5600 (the second and third replicates) instruments were processed to detect MS/MS peaks using UniQua (Chang et al., 2013). For the UniQua processing, the spectra were converted into mzXML format using massWolf (version 4.3.1) and ProteoWizard (version 3.0.4623) for the raw data generated from the Waters and AB SCIEX instruments, respectively. The UniQua parameters for Waters Q-TOF Premier were: smoothing = 9, centroiding high = 80%, maximum resolution = 16,000, baseline cutoff = 1.5 counts, reporter m/z range = 114-117, and reporter dynamic range = 5-1,000. The UniQua parameters for AB SCIEX TripleTOF 5600 were: smoothing = 11, centroiding high = 80%, maximum resolution = 25,000, baseline cutoff = 4 counts, reporter m/z range= 114-117 and reporter dynamic range = 5-100,000. The processed MS/MS spectra were then converted into Mascot generic format (.mgf) using mzXML2Search in Trans Proteomics Pipeline (TPP)1 (Deutsch et al., 2010) version 4.4 rev. 1. To obtain better quantification results, the MS/MS spectra with peak number less than 10, average intensity of the top 10 abundant peaks less than 15 counts and iTRAQ average intensity less than 30 counts were further removed from the peaklist file. Protein Qualification and Quantitation: The processed spectra were searched against the TAIR10 database (December 2011, 27,416 sequences) using the Mascot version 2.3 (Matrix Science, London, UK). For the MASCOT search, the mass tolerance for peptide precursor and MS/MS fragments was 0.1 Da. Only one missed cleavage was allowed for tryptic peptides. The methylthiolation (C), iTRAQ4plex (N-term) and iTRAQ4plex (K) were set as fixed modification. The Oxidation (M) and iTRAQ4plex (Y) were set as variable modification. The quantitation option was enabled and set to the iTRAQ4-plex approach. The peptide was considered to be identified if the MASCOT ion score greater than 27 (P less than 0.05). In addition, the protein was considered to be identified if the MASCOT protein score was greater than or equal to 27 with at least one unique and two different peptides identified. For the protein quantitation, only unique peptide was quantified in MASCOT and used to determine the protein ratio in MASCOT. To minimize the systematic ratio error due to sample preparation, the protein ratios were normalized by the mode of the overall protein ratios. For the data acquired by the Q-TOF Premier, 72,817 peptides and 3107 proteins were quantified. For the data acquired by the TripleTOF 5600, 41,885 peptides and 2893 proteins were quantified in the first replicate; 82,397 peptides and 4939 proteins were quantified in the second replicate.

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Dataset Information

HCN regulates cellular processes through posttranslational modification of proteins by S-cyanylation

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Publications

HCN Regulates Cellular Processes through Posttranslational Modification of Proteins by <i>S-</i>cyanylation.

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