The hyperthermophile chromosomal protein Sac7d sharply kinks DNA

Robinson, Howard; Gao, Yu; McCrary, Bradford S.; Edmondson, Stephen P.; Shriver, John W.; Wang, Andrew H.‐J.

doi:10.1038/32455

Cited by 206 publications

(219 citation statements)

References 27 publications

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“…The data were processed using software HKL2000. 16 The structure was solved by molecular replacement of the software PHASER 17 using the NMR structure of Cren7 (PDB: 2JTM) 10 and the DNA molecules in Sac7d-dsDNA complex (PDB: 1AZP) 12 as searching templates. The structural model was further constructed in Coot 18 and refined in Refmac5 19 and PHENIX 20 with TLS refinement.…”

Section: Methodsmentioning

confidence: 99%

“…These hydrogen bonds were considered to determine the sequence location of Sul7d on the dsDNA. 12 It seems the different conformations of R51 and R42 might also contribute to the 1-bp shift. Second, the orientations of dsDNA relative to proteins in both complexes are different, although Cren7 and Sul7d have similar overall fold and binding region.…”

Section: Structure Of the Cren7àdsdna Complexmentioning

confidence: 99%

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Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double‐stranded DNA complex

2010

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Cren7 is a crenarchaeal conserved chromatin protein discovered recently. To explore the mechanism of the DNA packaging in Crenarchaeota, the crystal structure of Cren7ÀGCGATCGC complex has been determined and refined at 1.6 Å resolution. Cren7 kinks the dsDNA sharply similar to Sul7d, another chromatin protein existing only in Sulfolobales, which reveals that the ''bending and unwinding'' compacting mechanism is conserved in Crenarchaeota. Significant structural differences are revealed by comparing both proteinÀdsDNA complexes. The kinked sites on the same dsDNA in the complexes with Sul7d and Cren7 show one base pair shift. For Cren7, fewer charged residues in the b-barrel structural region bind to DNA, and additionally, the flexible loop L b3b4 is also involved in the binding. Electrophoretic mobility shift assays indicate that loop L b3b4 is essential for DNA-binding of Cren7. These differences provide insight into the functional difference of both chromatin proteins, suggesting that Cren7 may be more regulative than Sul7d in the DNA-binding affinity by the methylation in the flexible loop L b3b4 in vivo.

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Section: Methodsmentioning

confidence: 99%

Section: Structure Of the Cren7àdsdna Complexmentioning

confidence: 99%

Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double‐stranded DNA complex

2010

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“…Secondary structure prediction using the JPRED server (8) suggested the presence of four ␤-sheets and no ␣-helices. This compares to five ␤-sheets followed by one ␣-helix in the larger Sac7d protein, which adopts a fold reminiscent of the OB fold found in the SSBs, with a triple-stranded ␤-sheet forming the DNA binding interface (18). There is no clear conservation in CC1 of the Sul7 residues involved in the interface with DNA (Fig.…”

Section: Fig 2 Purification Of Novel Dna Binding Proteins From T Tmentioning

confidence: 99%

CC1, a Novel Crenarchaeal DNA Binding Protein

et al. 2007

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The genomes of the related crenarchaea Pyrobaculum aerophilum and Thermoproteus tenax lack any obvious gene encoding a single-stranded DNA binding protein (SSB). SSBs are essential for DNA replication, recombination, and repair and are found in all other genomes across the three domains of life. These two archaeal genomes also have only one identifiable gene encoding a chromatin protein (the Alba protein), while most other archaea have at least two different abundant chromatin proteins. We performed a biochemical screen for novel nucleic acid binding proteins present in cell extracts of T. tenax. An assay for proteins capable of binding to a single-stranded DNA oligonucleotide resulted in identification of three proteins. The first protein, Alba, has been shown previously to bind single-stranded DNA as well as duplex DNA. The two other proteins, which we designated CC1 (for crenarchaeal chromatin protein 1), are very closely related to one another, and homologs are restricted to the P. aerophilum and Aeropyrum pernix genomes. CC1 is a 6-kDa, monomeric, basic protein that is expressed at a high level in T. tenax. This protein binds single-and double-stranded DNAs with similar affinities. These properties are consistent with a role for CC1 as a crenarchaeal chromatin protein.

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“…Hyperthermophilic crenarchaeotes are even more extreme hyperthermophiles than euryarchaeote hyperthermophiles. Since the psychrophilic or mesophilic crenarchaeotes (Cenarchaeales) are phylogenetically derived (DeLong et al, 1998), the ancestral crenarchaeote probably adapted to a hotter habitat than did any previous bacteria ; I suggest that this caused the loss of histones and replacement of their function by other proteins, for example the 66 amino acid Sac7d DNA-binding protein of Sulfolobus, which is exceedingly heat-and acid-stable and sharply kinks and stabilizes DNA by intercalation (Robinson et al, 1998). Although core histones probably evolved in a stem neomuran, H1 linker histones did so much earlier, in the eubacterial ancestors of neomura (Kasinsky et al, 2001).…”

Section: Derived Neomuran Protein-secretion and -Glycosylation Mechanmentioning

confidence: 99%

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Cavalier‐Smith¹

2002

International Journal of Systematic and Evolutionary Microbiology

417

590

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Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms : Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translationarrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids ; flagellar shaft of glycoprotein, not flagellin ; DNA-binding protein 10b ; specially modified tRNA ; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles ; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of T. Cavalier-Smith quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution : the fact that, during major evolutionary transformations, some org...

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The hyperthermophile chromosomal protein Sac7d sharply kinks DNA

Cited by 206 publications

References 27 publications

Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double‐stranded DNA complex

Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double‐stranded DNA complex

CC1, a Novel Crenarchaeal DNA Binding Protein

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

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