Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshiiOT3

Usui, Kengo; Katayama, Shintaro; Kanamori-Katayama, Mutsumi; Ogawa, Chihiro; Cui, Kai; Okada, Makiko; Kawai, Jun; Arakawa, Takahiro; Carninci, Piero; Itoh, Masayoshi; Takio, Koji; Miyano, Masashi; Kidoaki, Satoru; Matsuda, Takehisa; Hayashizaki, Yoshihide; Suzuki, Harukazu

doi:10.1186/gb-2005-6-12-r98

Cited by 12 publications

(11 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The high conservation of CheD among chemotactic bacteria and archaea [3] and the severe phenotype of a CheD deletion (almost complete loss of tactic capabilities; our unpublished results) support the hypothesis that this protein has a central role in the taxis signaling network. Of the interactions detected here, only CheC-CheD has been described before [29,66]. In B.subtilis an interaction of CheD with the MCPs was identified through Y2H analysis [113].…”

Section: Resultsmentioning

confidence: 93%

“…However, the comparability of the datasets is rather low because the only other protein-protein interaction (PPI) study in an archaeal organism ( P.horikoshii , [66]) reported just one interaction between Che proteins (CheC-CheD). The large-scale studies in bacteria ( Escherichia coli [67,68], Helicobacter pylori [69], Campylobacter jejuni [70], Treponema pallidum [71]) as well as a dedicated PPI study of the E.coli taxis signaling system [72] were performed in organisms with quite different taxis signaling systems compared to that of Hbt.salinarum .…”

Section: Resultsmentioning

confidence: 99%

“…An interaction between CheC and CheD has been demonstrated in B.subtilis , P.horikoshii and T.maritima [29,32,66]. The genome of Hbt.salinarum codes for three CheC proteins [5,6].…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

The protein interaction network of a taxis signal transduction system in a Halophilic Archaeon

et al. 2012

View full text Add to dashboard Cite

BackgroundThe taxis signaling system of the extreme halophilic archaeon Halobacterium (Hbt.) salinarum differs in several aspects from its model bacterial counterparts Escherichia coli and Bacillus subtilis. We studied the protein interactions in the Hbt. salinarum taxis signaling system to gain an understanding of its structure, to gain knowledge about its known components and to search for new members.ResultsThe interaction analysis revealed that the core signaling proteins are involved in different protein complexes and our data provide evidence for dynamic interchanges between them. Fifteen of the eighteen taxis receptors (halobacterial transducers, Htrs) can be assigned to four different groups depending on their interactions with the core signaling proteins. Only one of these groups, which contains six of the eight Htrs with known signals, shows the composition expected for signaling complexes (receptor, kinase CheA, adaptor CheW, response regulator CheY). From the two Hbt. salinarum CheW proteins, only CheW1 is engaged in signaling complexes with Htrs and CheA, whereas CheW2 interacts with Htrs but not with CheA. CheY connects the core signaling structure to a subnetwork consisting of the two CheF proteins (which build a link to the flagellar apparatus), CheD (the hub of the subnetwork), two CheC complexes and the receptor methylesterase CheB.ConclusionsBased on our findings, we propose two hypotheses. First, Hbt. salinarum might have the capability to dynamically adjust the impact of certain Htrs or Htr clusters depending on its current needs or environmental conditions. Secondly, we propose a hypothetical feedback loop from the response regulator to Htr methylation made from the CheC proteins, CheD and CheB, which might contribute to adaptation analogous to the CheC/CheD system of B. subtilis.

show abstract

Section: Resultsmentioning

confidence: 93%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

The protein interaction network of a taxis signal transduction system in a Halophilic Archaeon

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Such differential binding is generally ascribed to involvement of co-regulators, other transcription factors or nucleoid-associated proteins, which may enhance binding affinity and/or stability at sites with a low intrinsic affinity for the regulator. In a proteome-wide study of protein–protein interactions in Pyrococcus horikoshii OT3, hetero-interactions have been identified for two Lrp-like proteins (49). Additionally, FL9 and DM1 from Pyrococcus OT3, a full-length and truncated Lrp protein, respectively, have been shown to form hetero-octamers (44).…”

Section: Discussionmentioning

confidence: 99%

Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus

Song

Duc

Oeffelen

et al. 2013

Nucleic Acids Research

View full text Add to dashboard Cite

Previously, Lrp-like transcriptional regulator LysM from the hyperthermoacidophilic crenarchaeon Sulfolobus solfataricus was proposed to have a single target, the lysWXJK operon of lysine biosynthesis, and a single effector molecule, l-lysine. Here we identify ∼70 novel binding sites for LysM in the S. solfataricus genome with a LysM-specific nanobody-based chromatin immunoprecipitation assay coupled to microarray hybridization (ChIP-chip) and in silico target site prediction using an energy-based position weight matrix, and validate these findings with in vitro binding. LysM binds to intergenic and coding regions, including promoters of various amino acid biosynthesis and transport genes. We confirm that l-lysine is the most potent effector molecule that reduces, but does not completely abolish, LysM binding, and show that several other amino acids and derivatives, including d-lysine, l-arginine, l-homoarginine, l-glutamine and l-methionine and branched-chain amino acids l-leucine, l-isoleucine and l-valine, significantly affect DNA-binding properties of LysM. Therefore, it appears from this study that LysM is a much more versatile regulator than previously thought, and that it uses a variety of amino acids to sense nutritional quality of the environment and to modulate expression of the metabolic machinery of Sulfolobus accordingly.

show abstract

“…Thus, analyzing genome-wide gene functions in Pyrococcus could lead to new insights into the fundamental knowledge of life. For example, the results of DNA microarray analysis of Pyrococcus furiosus (Schut et al 2001;Schut et al 2003) and of a genome-wide protein-protein interaction study in Pyrococcus horikoshii OT3 (Usui et al 2005) have contributed to our general understanding of archaeal biology, in addition to pointing to features unique to these species. We have been studying RNA metabolism in P. furiosus Sato et al 2003;Fujishima et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus

Kanai

Sato²,

Fukuda³

et al. 2009

RNA

View full text Add to dashboard Cite

Using an expression protein library of a hyperthermophilic archaeon, Pyrococcus furiosus, we identified a gene (PF0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase (CPDase) activity. The PF0027 gene encoded a 21-kDa protein and an amino acid sequence that showed ;27% identity to that of the 29-59 tRNA ligase protein, ligT (20 kDa), from Escherichia coli. We found that the purified PF0027 protein possessed GTP-dependent RNA ligase activity and that synthetic tRNA halves bearing 29,39-cyclic phosphate and 59-OH termini were substrates for the ligation reaction in vitro. GTP hydrolysis was not required for the reaction, and GTPgS enhanced the tRNA ligation activity of PF0027 protein, suggesting that the ligation step is regulated by a novel mechanism. In comparison to the strong CPDase activity of the PF0027 protein, the RNA ligase activity itself was quite weak, and the ligation product was unstable during in vitro reaction. Finally, we used NMR to determine the solution structure of the PF0027 protein and discuss the implications of our results in understanding the role of the PF0027 protein.

show abstract

Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshiiOT3

Abstract: Protein-protein interactions among 960 Pyrococcus soluble proteins have been analysed by mammalian two-hybrid analysis and thirteen interactions between annotated and unannotated proteins detected.

Cited by 12 publications

References 44 publications

The protein interaction network of a taxis signal transduction system in a Halophilic Archaeon

The protein interaction network of a taxis signal transduction system in a Halophilic Archaeon

Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus

Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus

Contact Info

Product

Resources

About