Document Detail


Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes.
MedLine Citation:
PMID:  12670964     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Short regularly spaced repeats (SRSRs) occur in multiple large clusters in archaeal chromosomes and as smaller clusters in some archaeal conjugative plasmids and bacterial chromosomes. The sequence, size, and spacing of the repeats are generally constant within a cluster but vary between clusters. For the crenarchaeon Sulfolobus solfataricus P2, the repeats in the genome fall mainly into two closely related sequence families that are arranged in seven clusters containing a total of 441 repeats which constitute ca. 1% of the genome. The Sulfolobus conjugative plasmid pNOB8 contains a small cluster of six repeats that are identical in sequence to one of the repeat variants in the S. solfataricus chromosome. Repeats from the pNOB8 cluster were amplified and tested for protein binding with cell extracts from S. solfataricus. A 17.5-kDa SRSR-binding protein was purified from the cell extracts and sequenced. The protein is N terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also recognizes both main families of repeat sequences in S. solfataricus. The recombinant protein, expressed in Escherichia coli, showed the same binding properties to the SRSR repeat as the native one. The SSO454 protein exhibits a tripartite internal repeat structure which yields a good sequence match with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure at the center of each DNA repeat and thereby produces a binding site for another protein, possibly a more conserved one, in a process that may be essential for higher-order stucturing of the SRSR clusters.
Authors:
Xu Peng; Kim Brügger; Biao Shen; Lanming Chen; Qunxin She; Roger A Garrett
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of bacteriology     Volume:  185     ISSN:  0021-9193     ISO Abbreviation:  J. Bacteriol.     Publication Date:  2003 Apr 
Date Detail:
Created Date:  2003-04-02     Completed Date:  2003-05-09     Revised Date:  2013-04-18    
Medline Journal Info:
Nlm Unique ID:  2985120R     Medline TA:  J Bacteriol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  2410-7     Citation Subset:  IM    
Affiliation:
Danish Archaea Centre, Institute of Molecular Biology, University of Copenhagen, Sølvgade 83H, DK-1307 Copenhagen, Denmark.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Archaeal Proteins / genetics,  isolation & purification,  metabolism*
DNA Footprinting
DNA, Archaeal / genetics,  metabolism*
DNA-Binding Proteins / genetics,  isolation & purification,  metabolism*
Molecular Sequence Data
Molecular Weight
Multigene Family
Protein Binding / genetics
Repetitive Sequences, Nucleic Acid
Sequence Alignment
Species Specificity
Sulfolobus / genetics,  metabolism*
Chemical
Reg. No./Substance:
0/Archaeal Proteins; 0/DNA, Archaeal; 0/DNA-Binding Proteins
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