Browse
Submit Data
Databases
API
Help

Dataset Information

114 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evolutionary insights into Trm112-methytransferase holoenzymes involved in translation between archaea and eukaryotes

ABSTRACT: To clarify the function of Trm112 in archaea, we have characterized structurally and functionally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Haloferax Volcanii (halobacterium Volcanii)

SUBMITTER: Leslie MULLER

LAB HEAD: Sarah CIANFERANI

PROVIDER: PXD008466 | Pride | 2018-10-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes.

van Tran Nhan N Muller Leslie L Ross Robert L RL Lestini Roxane R Létoquart Juliette J Ulryck Nathalie N Limbach Patrick A PA de Crécy-Lagard Valérie V Cianférani Sarah S Graille Marc M

Nucleic acids research 20180901 16

Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltran ...[more]

PMID: 30010922

Similar Datasets

Elucidation of the translation initiation factor interaction network of Haloferax volcanii reveals coupling of transcription and translation in haloarchaea

Project description:Translation is an important step in gene expression. Initiation of translation is rate-limiting, and it is 13 phylogenetically more diverse than elongation or termination. Bacteria contain only three initiation 14 factors. In stark contrast, eukaryotes contain more than 10 (subunits of) initiation factors (eIFs). The 15 genomes of archaea contain many genes that are annotated to encode archaeal homologs of 16 eukaryotic initiation factors (aIFs). However, experimental characterization of aIFs is scarce and 17 mostly restricted to very few species. To broaden the view, the protein-protein interaction network of 18 aIFs in the halophilic archaeon Haloferax volcanii has been characterized. To this end, tagged 19 versions of 14 aIFs were overproduced, affinity isolated, and the co-isolated binding partners were 20 identified by peptide mass fingerprinting.

2021-09-29 | PXD028666 | Pride

A small RNA and its involvement in zinc transport

Project description:The function and mode of action of small regulatory RNAs is currently still understudied in archaea. In the halophilic archaeon H. volcanii a plethora of sRNAs have been identified, however, in-depth functional analysis is missing for most of them. We selected a small RNA (s479) from H. volcanii for detailed characterization. The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a distinct cellular function. Proteome comparison of wild type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance.

2021-08-10 | PXD022750 | Pride

Haloferax volcanii Proteome Response to Deletion of a Rhomboid Protease Gene

Project description:Rhomboids are conserved intramembrane serine proteases involved in cell signaling processes. Their role in prokaryotes is scarcely known and remains to be investigated in Archaea. We previously constructed a rhomboid homologue deletion mutant (ΔrhoII) in Haloferax volcanii, which showed reduced motility, increased novobiocin sensitivity, and an Nglycosylation defect. To address the impact of rhoII deletion on H. volcanii physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. A total of 1847 proteins were identified (45.8% of H. volcanii predicted proteome), from which 103 differed in amount. Additionally, the mutant strain evidenced 99 proteins with altered electrophoretic migration, which suggested differential post-translational processing/modification. Integral membrane proteins that evidenced variations in concentration, electrophoretic migration, or semitryptic cleavage in the mutant were considered as potential RhoII targets. These included a PrsW protease homologue (which was less stable in the mutant strain), a predicted halocyanin, and six integral membrane proteins potentially related to the mutant glycosylation (S-layer glycoprotein, Agl15) and cell adhesion/motility (flagellin1, HVO_1153, PilA1, and PibD) defects. This study investigated for the first time the impact of a rhomboid protease on the whole proteome of an organism.

2020-05-14 | PXD011218 | Pride

Accelerated growth in the absence of DNA replication origins

Project description:DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery. Origins differ in number and structure across the three domains of life1 and their properties determine the dynamics of chromosome replication. Bacteria and some archaea replicate from single origins, whilst most archaea and all eukaryotes replicate using multiple origins. Initiation mechanisms that rely on homologous recombination operate in some viruses. Here we show that such mechanisms also operate in archaea. We have used deep sequencing to study replication in Haloferax volcanii. Four chromosomal origins of differing activity were identified. Deletion of individual origins resulted in perturbed replication dynamics and reduced growth. However, a strain lacking all origins has no apparent defects and grows significantly faster than wild-type. Origin-less cells initiate replication at dispersed sites rather than at discrete origins and have an absolute requirement for the recombinase RadA, unlike strains lacking individual origins. Our results demonstrate that homologous recombination alone can efficiently initiate the replication of an entire cellular genome. This raises the question of what purpose replication origins serve and why they have evolved. Measurement of replication dynamics (marker frequency analysis; MFA) for Haloferax volcanii strains, including wild-type, the laboratory strain, individual and combinations of replication origin deletions.

2013-11-03 | E-GEOD-41961 | biostudies-arrayexpress

Haloferax volcanii lysine acetylation

Project description:Oxidative stress adaptation strategies are important to cell function and are linked to cardiac, neurodegenerative disease and cancer. Representatives of the domain Archaea are used as model organisms based on their extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. Study of the halophilic archaeon Haloferax volcanii reveals lysine acetylation to be associated with oxidative stress responses. The strong oxidant hypochlorite: i) stimulates an increase in lysine acetyltransferase HvPat2 to HvPat1 abundance ratios and ii) selects for lysine deacetylase sir2 mutants. Here we report the dynamic occupancy of the lysine acetylome of glycerol-grown H. volcanii as it shifts in profile in response to hypochlorite. These findings are revealed by the: 1) quantitative multiplex LC-MS/MS analysis of the SILAC-compatible parent and Δsir2 mutant strains and 2) label free LC-MS/MS analysis of H26 ‘wild type’ cells. The results show that lysine acetylation is associated with key biological processes including DNA topology, central metabolism, cobalamin biosynthesis and translation. Lysine acetylation targets are found conserved across species. Moreover, lysine residues modified by acetylation and ubiquitin-like sampylation are identified suggesting post-translational modification (PTM) crosstalk. Overall, the results of this study expand the current knowledge of lysine acetylation in Archaea, with the long-term goal to provide a balanced evolutionary perspective of PTM systems in living organisms.

2023-07-20 | PXD041799 | Pride

The small protein CdrS is involved in cell division regulation

Project description:Recently the function and cellular importance of small proteins became more and more visible. Whereas many examples of small protein functions have been described in eukarya and bacteria, less is known about small protein functions in archaea. A previous determination of the proteome in the halophilic archaeon Haloferax volcanii by mass spectrometry confirmed the expression of several annotated genes for small proteins. One such protein is encoded by HVO_0582. To identify the biological function of the encoded small protein we attempted to generate a deletion strain. Since we were not successful in generating the deletion we repressed HVO_0582 using CRISPRi. The repression strain showed a severe growth defect as well as strong changes in morphology. ChIPSeq experiments revealed several binding sites for this putative transcription factor. Transcriptome and proteome analyses show a clear effect on RNA and protein expression in the CRISPRi strain. Based on our findings we conclude that the small protein CdrS is involved in regulation of cell division / cell morphology.

2021-08-09 | PXD017903 | Pride

Characterization of two mutually orthogonal pyrrolysyl-tRNA synthetase/tRNAPyl pairs residing in the same organism

Project description:Site-specific incorporation of distinct non-canonical amino acids (ncAAs) into proteins via genetic code expansion requires mutually orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs. Pyrrolysyl–tRNA synthetase (PylRS)/tRNAPyl pairs are ideal for genetic code expansion and have been extensively engineered for developing mutually orthogonal pairs. Here, we identify two novel PylRS/tRNAPyl pairs from extremely halophilic methyl-reducing euryarchaeal HMET1. In order to demonstrate that HMET1 PylRS/tRNAPyl pairs are functional and orthogonal in H. volcanii, we transformed plasmids encoding HMET1 PylRS/tRNAPyl pair and reporter protein SAMP1(G24amb), and cultured the cells in the presence and absence of 1 mM ncAA. Amber suppression ability of HMET1 PylRS/tRNAPyl pairs were assayed by monitoring the production of the full-length SAMP1(G24amb) and the SAMP1(G24amb)-MoaE conjugate via anti-Flag immunoblotting. LC-MS/MS confirmed that BocK (ncAA) was incorporated into the reporter protein at site-directed position. Thus, these two distinct PylRS/tRNAPyl pairs are functional in Haloferax volcanii, a model halophilic archaeon. Furthermore, by swapping these two PylRS/tRNAPyl pairs in the expression vector followed by anti-Flag immunoblotting, we found these two PylRS/tRNAPyl pairs are mutually orthogonal. Finally, we demonstrate HMET1 PylRS/tRNAPyl-derived pairs can decode two stop codons and incorporate distinct ncAAs. LC-MS/MS analysis of the purified reporter protein confirmed that BocK and 3-I-phe were incorporated at the TAA and TAG-directed positions respectively.

2022-05-12 | PXD027053 | Pride

The response of Haloferax volcanii to salt and temperature stress: a proteome study by label-free mass spectrometry

Project description:We performed an in-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii under standard, low and high salt and low and high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high pH/reversed phase fractionated samples indicated 61.1% proteome coverage (2,509 proteins), which is close to the maximum recorded values in archaea. Identified proteins matched to the predicted proteome in their physicochemical protein properties, with only a small bias against low molecular wright and membrane-associated proteins. Cells grown under low and high salt stress as well as low and high temperature stress were quantitatively compared to standard cultures by SWATH mass spectrometry. 2,244 proteins, or 54.7% of the predicted proteome, were quantified across all conditions at high reproducibility which allowed for global analysis of protein expression changes under these stresses. Pathway enrichment analysis by KEGG annotation showed that most major cellular pathways are part of H. volcanii’s universal stress response. In addition, specific pathways were found to be selectively affected by either salt or temperature stress.

2019-09-04 | PXD011056 | Pride

Quantitative (Glyco-)Proteomics of Haloferax volcanii Biofilm Formation

Project description:A quantitative proteomics analysis comparing planktonic and sessile cells at different stages of biofilm development, using iTRAQ labeling, has been performed for Haloferax volcanii. Samples were taken from liquid, shaking cultures were compared to samples from static cultures, separated into sessile (biofilm) and planktonic cells. This dataset resulted in the identification of more than 50% of the H. volcanii proteome. Most importantly, expression as well as N-glycosylation of various surface filaments (pili, flagella and SLG) has been quantified, strongly supporting the hypothesis, that differential N-glycosylation plays important roles in the biofilm formation of H. volcanii.

2020-05-11 | PXD011012 | Pride

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

Project description:We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

2019-03-11 | GSE127727 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data