Proteomic Characterization of Archaeal Ribosomes Reveals the Presence of Novel Archaeal-Specific Ribosomal Proteins

Márquez, Viter; Fröhlich, Thomas; Armache, Jean-Paul; Sohmen, Daniel; Dönhöfer, Alexandra; Mikolajka, Aleksandra; Berninghausen, Otto; Thomm, Michael; Beckmann, Roland; Arnold, Georg J.; Wilson, Daniel N.

doi:10.1016/j.jmb.2010.11.055

Cited by 30 publications

(45 citation statements)

References 77 publications

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“…MkTIP49 neither forms stable complexes with mkTBP nor with the cognate TATA-TBP or with TATA-TBP-TFB transcription initiation complexes (F.W., unpublished data), which does not support a role in the regulation of transcription similar to its eukaryotic homologs. However, the archaeal TIP49 gene is induced under heat-shock conditions; the protein is stable at elevated temperatures (Iqbal and Qureshi, 2010; Kanai et al., 2010); and it has been found to associate with ribosomes in a mass spectrometry approach (Marquez et al., 2011). These observations are congruent with a role of TIP49 as a protein chaperone and/or ATP-dependent remodeling factor of higher-order complexes.…”

Section: Discussionmentioning

confidence: 99%

Lytic Water Dynamics Reveal Evolutionarily Conserved Mechanisms of ATP Hydrolysis by TIP49 AAA+ ATPases

et al. 2014

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SummaryEukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis.

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Section: Discussionmentioning

confidence: 99%

Lytic Water Dynamics Reveal Evolutionarily Conserved Mechanisms of ATP Hydrolysis by TIP49 AAA+ ATPases

et al. 2014

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“…Ribosomes and ribosomal subunits from Thermococcus kodakarensis were prepared as described (9). In a total reaction volume of 150 μl, 50 pmoles of 30S, 50S or 70S T. kodakarensis ribosomal subunits or ribosomes were incubated with 400 pmoles of His 6 -tagged pfu ThermoDBP-RP1 or ape ThermoDBP-RP2 in a buffer containing 10 mM Tris–HCl, pH 7.5, 10 mM MgCl 2 , 1 mM DTT, 45 mM NH 4 Cl and the varying concentrations of NaCl.…”

Section: Methodsmentioning

confidence: 99%

“…However, tte ThermoDBP-RP1 was not recovered from cell lysates via a biotinylated oligodeoxynucleotide used for isolation of tte ThermoDBP (7). Furthermore, Sulfolobus solfataricus ( sso ) ThermoDBP-RP1 was reported to associate with box C/D small (s) RNAs and with the 30S ribosomal subunit (8), but the protein was not detected in a subsequent proteomic characterization of sso ribosomes (9). We therefore set out to further characterize the structures and functions of ThermoDBP-RPs.…”

Section: Introductionmentioning

confidence: 99%

Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein

Ghalei

Moeller

Eppers

et al. 2014

Nucleic Acids Research

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Instead of a classical single-stranded deoxyribonuleic acid (DNA)-binding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP-related proteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro. A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.

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“…Among these, 34 r-proteins are universally conserved in the three domains of cellular life (bacteria, archaea and eukaryotes); 33 r-proteins are shared between archaea and eukaryotes to the exclusion of bacteria; 23 r-proteins are bacteria-specific, 1 r-protein is archaea-specific and 11 r-proteins are eukaryotes-specific [6]. In addition, we included in our analysis three recently discovered ribosomal proteins that appear to be specific for the Sulfolobales/Desulfurococcales branch of archaea [7]. In bacteria and archaea, genes encoding r-proteins are organized in genomic clusters that include several partially conserved operons and are often called ribosomal superoperons [8], [9].…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics of Prokaryotic Ribosomal Proteins

et al. 2012

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Archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. We developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. As a result of this analysis, we performed a census of prokaryotic r-protein complements, enumerated missing and paralogous r-proteins, and analyzed the distributions of ribosomal protein genes among chromosomal partitions. Phyletic patterns of bacterial and archaeal r-protein genes were mapped to phylogenetic trees reconstructed from concatenated alignments of r-proteins to reveal the history of likely multiple independent gains and losses. These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies.

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Proteomic Characterization of Archaeal Ribosomes Reveals the Presence of Novel Archaeal-Specific Ribosomal Proteins

Cited by 30 publications

References 77 publications

Lytic Water Dynamics Reveal Evolutionarily Conserved Mechanisms of ATP Hydrolysis by TIP49 AAA+ ATPases

Lytic Water Dynamics Reveal Evolutionarily Conserved Mechanisms of ATP Hydrolysis by TIP49 AAA+ ATPases

Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein

Phylogenomics of Prokaryotic Ribosomal Proteins

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