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Sulfolobus islandicus HCD+ETD, including LFQ

ABSTRACT: Protein posttranslational methylation and acetylations have been reported to occur in archaea, including members of the genus Sulfolobus, but have not been characterized on a proteome-wide scale. Sulfolobus chromatin proteins are known to be methylated and acetylated on lysine side chains, resembling eukaryotic histones in this respect. We utilized bottom-up and top-down proteomic approaches to perform a global and deep methylation study in the hyperthermoacidophylic archaeon S. islandicus LAL 14/1 with a particular focus on chromatin proteins. Without specific enrichment, 1931 methylation sites on 731 protein were found by bottom-up proteomic analysis. The dynamics of protein methylation has been investigated on 424-526 proteins throughout 3 cell culture growth stages. We also confirm the relaxed specificity and steady abundance of the previously described methyltransferase aKMT4 which is implicated in the massive proteome methylation. We also detected an abundant N-terminal acetylation of S. islandicus proteins, with more than one third of the detected N-terminal peptides being acetylated

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Sulfolobus Islandicus Lal14/1

SUBMITTER: Egor Vorontsov

LAB HEAD: Julia Chamot-Rooke

PROVIDER: PXD003102 | Pride | 2022-03-01

REPOSITORIES: Pride

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			Action	DRS
	20141231_F_EV_Sisl-S3-late-exp_dig-SCX-fr100mM_HCD28.raw	Raw
	20141231_F_EV_Sisl-S3-late-exp_dig-SCX-fr1M_HCD28.raw	Raw
	20141231_F_EV_Sisl-S3-late-exp_dig-SCX-fr250mM_HCD28.raw	Raw
	20141231_F_EV_Sisl-S3-late-exp_dig-SCX-fr500mM_HCD28.raw	Raw
	20141231_F_EV_Sisl-S3-late-exp_dig-SCX-fr50mM_HCD28.raw	Raw

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Sulfolobus islandicus top-down LC-MSMS

Project description:Protein posttranslational methylation and acetylations have been reported to occur in archaea, including members of the genus Sulfolobus, but have not been characterized on a proteome-wide scale. Sulfolobus chromatin proteins are known to be methylated and acetylated on lysine side chains, resembling eukaryotic histones in this respect. We utilized bottom-up and top-down proteomic approaches to perform a global and deep methylation study in the hyperthermoacidophylic archaeon S. islandicus with particular interest in chromatin proteins. Without specific enrichment, 731 protein were found by bottom-up proteomic analysis. The methylation sites on >400 proteins were monitored throughout 3 cell culture growth stages: early exponential, late exponential and stationary. (The previously described aKMT4 is found to be a plausible methyltransferase responsible for the massive methylation.) The proteome-wide top-down study/approach revealed 3778 proteoforms of 681 proteins, including 292 methylated proteoforms, of which 85 were comprehensively characterized by high-resolution MS/MS. Methylated proteoforms of the five chromatin proteins were characterized in detail by combination of bottom-up and top-down data showing the differences between the closely related Sul7d proteins. The two Alba chromatin proteins are, for the first time, reported to be methylated in this work. Alba1 protein is shown to be mono-, di- and trimethylated at the lysine-16 side chain. Stage-wise top-down analysis shows that the relative abundance of the methylated proteoforms versus non-methylated ones significantly grows/increases for Alba1 and Cren7 chromatin proteins throughout the cell growth. These findings highlight the ubiquitous lysine methylation throughout the S. islandicus proteome and singificantly enrich our knowledge related aboutarchaeal chromatin proteins.

2016-09-13 | PXD003074 | Pride

Sulfolobus islandicus PTM and quantitative study using bottom-up proteomics

Project description:Protein posttranslational methylation and acetylation have been reported to occur in archaea, including the genus Sulfolobus, but have never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modifications are the chromatin proteins that have been described to be methylated and acetylated on lysine side chains, resembling eukaryotic histones in that aspect. To get more insight into the extent of these modifications and their dynamics during the different growth steps of the thermoacidophylic archaeon S. islandicus , we performed a global and deep proteomics analysis using a combination of high-throughput bottom-up and top-down proteomics approaches on a single high-resolution mass spectrometer. 1,931 methylation sites on 751 proteins were found by the bottom-up analysis, with methylation sites of 424-526 proteins monitored throughout three cell culture growth stages: Early, Mid and Late. The previously described aKMT4 methyltransferase was found to be potentially responsible for this massive modification.

2016-09-13 | PXD004179 | Pride

A single transcriptional factor Csa3b regulates CRISPR-Cas adaptation and interference in Sulfolobus

Project description:Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate CRISPR-Cas and DNA repair systems by Csa3b in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector,We find thatcmr-α (SiRe_0890 ~ SiRe_0895) and cmr-β (SiRe_0597 ~ SiRe_0603)、the DNA double strand break (DSB)repair genes, including nurA, rad50, mre11, and herA (SiRe_0061 ~ SiRe_0064), as well as two subunits of DNA polymerase II (SiRe_0615 and SiRe_0617) that function in DNA repair, were significantly up-regulated. Our data indicated that the Csa3b regulator couples transcriptional activation of cmr genes, DNA repair genes.

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RNA-seq data for Sulfolobus islandicus REY15A Δcbp1 strain and the parental strain E234

Project description:RNA-seq data for Sulfolobus islandicus REY15A Δcbp1 strain and the parental strain E234

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SIRV2infection

Project description:Archaeal viruses display unusually high genetic and morphologic diversity. The Sulfolobus islandicus Rod Shaped Virus 2 (SIRV2) is a model to study virus-host interactions in Archaea. It is a lytic virus that exploits a unique egress mechanism based on formation of remarkable pyramidal structures on the host cell envelope. The hyperthermophilic Sulfolobus islandicus LAL14/1 is the natural host for SIRV2. RNA was isolated at 0,1,2,3,5,7 and 9 hours after SIRV2 infection of two S.islandicus cultures and analysed with whole transcriptome sequencing (RNAseq). As a control RNA was isolated at the same time points from two uninfected cultures.

2013-05-25 | E-MTAB-1660 | biostudies-arrayexpress

Coupling transcriptional activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus

Project description:Transcriptome sequencing was carried out on an Illumina HiSeq platform to investigate the activation of CRISPR-Cas and DNA repair systems by Csa3a in Sulfolobus islandicus Rey15A. We compared the differently expressed genes in Sulfolobus islandicus Rey15A strain with csa3a overexpression vs. Sulfolobus islandicus Rey15A strain carrying an empty expression vector, cas1 deletion strain with csa3a overexpression vs. cas1 deletion strain carrying an empty expression vector, as well as interference-deficient strain with csa3a overexpression vs. interference-deficient strain carrying an empty expression vector. We find that cas genes (SiRe_0760, SiRe_0761, SiRe_0762, SiRe_0763), nucleotidyltransferase domain of DNA polymerase beta (SiRe_0459), chromosome segregation protein (SMC)-related ATPase (SiRe_0649), SMC-related protein (SiRe_1142) and three HerA helicases involved in DNA double break repair (encoded by SiRe_0064 and SiRe_0095 of nurA-herA operons, and SiRe_1857) were significantly up-regulated. Our data indicated that the Csa3a regulator couples transcriptional activation of spacer acquisition genes, CRISPR RNA transcription, DNA repair and genome stability genes.

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Thermal proteomics of Sulfolobus Islandicus

Project description:Quantitative proteomics of Sulfolobus islandicus after treatment at different temperatures

2021-12-06 | PXD030196 |

Continuous CRISPR spacer acquisition in STSV2-infected crenarchaeon Sulfolobus islandicus REY15A over a 6-day period

Project description:A whole transcriptome study was performed on Sulfolobus islandicus REY15A actively undergoing CRISPR spacer acquisition from the crenarchaeal monocaudavirus STSV2 in rich (TYS) and basal (SCV) media over a 6 day period. Spacer acquisition preceded strong host growth retardation, and changes in viral transcript abundance and virus copy numbers showed significant differences between the two media. Results showed that rich medium favoured CRISPR-Cas immunity generation.

2015-12-06 | E-MTAB-4027 | biostudies-arrayexpress

Project description:Sulfolobus islandicus transcriptome

| PRJNA608153 | ENA

Functional insights into protein acetylation in the hyperthermophilic archaeon Sulfolobus islandicus

Project description:Proteins undergo acetylation at the Nε-amino group of lysine residues and the Nα-amino group of the N-terminus in Archaea as in Bacteria and Eukarya. However, the extent, pattern and roles of the modifications in Archaea remain poorly understood. Here we report the proteomic analyses of a wild-type Sulfolobus islandicus strain and its mutant derivative strains lacking either a homologue of the protein acetyltransferase Pat (SisPat) or a homologue of the Nt-acetyltransferase Ard1 (ΔSisArd1). A total of 1,708 Nε-acetylated lysine residues in 684 proteins (26% of the total proteins), and 158 Nt-acetylated proteins (44% of the identified proteins) were found in S. islandicus. ΔSisArd1 grew more slowly than the parental strain, whereas ΔSisPat showed no significant growth defects. Only 24 out of the 1,503 quantifiable Nε-acetylated lysine residues were differentially acetylated, and all but one of the 24 residues were less acetylated, by >1.3 fold in ΔSisPat than in the parental strain, indicating the narrow substrate specificity of the enzyme. Six acyl-CoA synthetases were the preferred substrates of SisPat in vivo, suggesting that Nε-acetylation by the acetyltransferase is involved in maintaining metabolic balance in the cell. Acetylation of acyl-CoA synthetases by SisPat occurred at a sequence motif conserved among all three domains of life. On the other hand, 92% of the identified N-termini were acetylated by SisArd1 in the cell. The enzyme exhibited broad substrate specificity and was capable of modifying nearly all types of the target N-termini of human NatA-NatF. The deletion of the SisArd1 gene altered the cellular levels of 18% of the quantifiable proteins (1,518) by >1.5 fold. Consistent with the growth phenotype of ΔSisArd1, the cellular levels of proteins involved in cell division and cell cycle control, DNA replication, and purine synthesis were significantly lowered in the mutant than those in the parental strain.

2019-06-12 | PXD012246 | Pride

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