Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic Archaeon<i>Pyrococcus horikoshii</i>OT3

Hada, Koji; Nakashima, Takashi; Osawa, Takuo; Shimada, Hiroaki; Kakuta, Yoshimitsu; Kimura, Makoto

doi:10.1271/bbb.70639

Cited by 19 publications

(18 citation statements)

References 39 publications

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“…Based on the structural similarities between Sac10b and prokaryotic and eukaryotic RNA-binding proteins, Aravind et al [43] had predicted that the Sac10b family probably originated as RNA-binding proteins, which would have been realistic in a primordial RNA world, and that at least some of the family members may play a role in RNA metabolism. However, the latter does not seem to be the case for the RNA-binding Sac10b proteins [34,41,58]. PhoAlba, for example, interacted with the RNA of RNase P but was not essential for the catalytic activity of this ribozyme [34].…”

Section: Functional Divergence -Rna-binding Proteinsmentioning

confidence: 95%

“…The Sac10b protein family shows significant structural similarity to several bacterial and eukaryotic proteins including the C-terminal domain of bacterial initiation factor IF3, Escherichia coli protein Yhhp implicated in cell division, Arabidopsis protein At2g34160, the N-terminal DNAbinding domain of DNase I [34], and bacterial stage V sporolation protein S (SpoVS) [45]. These similarities indicate that an ancestral protein was retained by bacteria, archaea, and eukarya and evolved in all three domains of life into different protein families involved in the structural and functional regulation of DNA and RNA.…”

Section: Structures Of Sac10b Family Proteinsmentioning

confidence: 99%

“…More recently, Hada et al [34] determined the crystal structure of PhoAlba, a Sac10b homologue of the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Not unexpectedly, this structure was similar to that of archaeal homologues and RNA-binding proteins including B. stearothermophilus IF3-C and E. coli YhhP.…”

Section: Functional Divergence -Rna-binding Proteinsmentioning

confidence: 99%

“…Alba was the first Sac10b family protein whose highresolution structure was determined by X-ray crystallography and for which a model of its interaction with DNA was proposed [27]. Meanwhile the structures of further hyperthermophilic archaeal proteins of the Sac10b family were solved by X-ray crystallography and/or NMR spectroscopy [28][29][30][31][32][33][34][35]. Another member of the Sac10b protein family, the hyperthermophilic Ssh10b, served as a model to explain the folding and the extreme stability of hyperthermophilic proteins [33,[36][37][38][39][40] and was found to bind not only to doublestranded and single-stranded DNA but also to RNA in a sequence-independent manner [41].…”

Section: Introductionmentioning

confidence: 99%

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The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

Xuan¹,

Feng²

2012

CPPS

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Abstract:Here we review the present state of structural and functional studies of the Sac10b protein family, a class of highly conserved 10 kDa nucleic acid-binding proteins in archaea. Based on biochemical and structural studies, these proteins were originally assigned a role in the structural organization of chromatin; Sac10b proteins of hyperthermophilic archaea, for example, showed tight, unspecific DNA binding. More recently, however, Sac10b proteins of mesophilic archaea were found to interact preferentially with specific DNA sequences thereby affecting the expression of distinct genes. Furthermore, Sac10b proteins of hyperthermophilic, thermophilic and mesophilic archaea were also shown to bind to RNA with distinct affinities and specificities but functional consequences of RNA binding of these proteins, besides perhaps RNA stabilization, have not yet been observed. To better understand the physiological meaning of the various interactions of Sac10b proteins with nucleic acids, future work should concentrate on elucidating the molecular structures of complexes of Sac10b proteins of hyperthermophilic and mesophilic archaea with DNA and RNA. In addition, existing and new X-ray and NMR structures of individual hyperthermophilic Sac10b proteins may represent very good models for introducing thermostability especially in enzymes for industrial use.

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Section: Functional Divergence -Rna-binding Proteinsmentioning

confidence: 95%

Section: Structures Of Sac10b Family Proteinsmentioning

confidence: 99%

Section: Functional Divergence -Rna-binding Proteinsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

Xuan¹,

Feng²

2012

CPPS

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“…The first candidate is Alba, an archaeal chromatin protein, whose family members include human RPP20 and RPP25 (17)(18)(19). However, despite weak binding of the Pyrococcus horikoshii (Pho) Alba to its cognate RPR, it neither affects the cleavage rate nor the temperature optimum of the in vitro reconstituted Pho RNase P activity (19).…”

mentioning

confidence: 99%

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Cho

Lai

Susanti

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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To the mounting evidence of nonribosomal functions for ribosomal proteins, we now add L7Ae as a subunit of archaeal RNase P, a ribonucleoprotein (RNP) that catalyzes 5′-maturation of precursor tRNAs (pre-tRNAs). We first demonstrate that L7Ae coelutes with partially purified Methanococcus maripaludis (Mma) RNase P activity. After establishing in vitro reconstitution of the single RNA with four previously known protein subunits (POP5, RPP21, RPP29, and RPP30), we show that addition of L7Ae to this RNase P complex increases the optimal reaction temperature and k cat ∕K m (by ∼360-fold) for pre-tRNA cleavage to those observed with partially purified native Mma RNase P. We identify in the Mma RNase P RNA a putative kink-turn (K-turn), the structural motif recognized by L7Ae. The large stimulatory effect of Mma L7Ae on RNase P activity decreases to ≤4% of wild type upon mutating either the conserved nucleotides in this K-turn or amino acids in L7Ae shown to be essential for K-turn binding. The critical, multifunctional role of archaeal L7Ae in RNPs acting in tRNA processing (RNase P), RNA modification (H/ACA, C/D snoRNPs), and translation (ribosomes), especially by employing the same RNA-recognition surface, suggests coevolution of various translation-related functions, presumably to facilitate their coordinate regulation.pre-tRNA processing | RPP38 | protein-aided RNA catalysis R Nase P is a Mg 2þ -dependent endoribonuclease that is primarily responsible for catalyzing the removal of the 5′ leaders of precursor-tRNAs (pre-tRNAs) (1-3). Except for some unique organellar variants, RNase P functions in all three domains of life as a ribonucleoprotein (RNP) (1, 2). Although catalysis rests with the essential RNase P RNA (RPR) in all three domains of life (4-6), the RNase P protein (RPP) cofactors play essential roles. In the simple one RPR-one RPP bacterial RNase P, the RPP aids RPR catalysis by enhancing cleavage efficiency and affinity for substrate and Mg 2þ (7-9). The bacterial RPP has not been found in any archaeal or eukaryal genome (10). Eukaryal (nuclear) RNase P, which comprises an RPR and 9 or 10 RPPs (11, 12), has not been reconstituted from recombinant subunits, thus thwarting efforts to uncover the individual functions of eukaryal RPPs. Archaeal RNase P, with an RPR and four RPPs (all homologous to eukaryal RPPs), has therefore been explored as an experimental surrogate for its so-far-intractable eukaryal cousin (13-16). Although native archaeal RNase P has not been characterized, Western analysis and immunoprecipitation validated these four RPPs (POP5, RPP21, RPP29, and RPP30) as being associated with partially purified Methanothermobacter thermautotrophicus (Mth) RNase P activity (14). Subsequent structural and biochemical reconstitution studies using recombinant subunits have proven the utility of archaeal RNase P as a model system to dissect the role of multiple protein cofactors in facilitating RNA catalysis (16).Besides POP5, RPP21, RPP29, and RPP30, weak homologies are evident in the archaeal genomes...

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