Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Single-stranded DNA and RNA binds to a conserved surface of cold-shock domains

Cold-shock domains occur ubiquitously in proteins from all kingdoms of life. They occur in proteins that function in transcriptional and/or translational control of gene expression. Bacterial cold shock domains are autonomous, small proteins, whereas their eukaryal orthologs usually occur as structural modules in larger proteins. Some, but not all bacterial cold-shock proteins are upregulated under cold-shock conditions and are thought to mediate cold-stress-response functions.

Already the first crystal structure of a bacterial cold-shock protein suggested a possible mode of DNA or RNA single-strand binding to a basic protein surface with conspicuously exposed aromatic side chains (1). It was not until recently, however, that this binding mode was proven by crystal structure analysis of oligothymidine strands bound to the major cold shock proteins Bs-CspB of Bacillus subtilis and Bc-Csp of Bacillus caldolyticus (2, 3). These structures identified 7 subsites for nucleotide binding and, combined with fluorescence-based binding DNA studies, suggested the consensus sequence NTCTTTN for DNA binding to the Bacillus cold-shock domains which was confirmed by DNA microarray studies (4).

The crystal structure of the Bc-Csp:dT7 complex showed a domain-swapped dimeric structure of the cold-shock domain (3). Domain swapping has never been observed before in a series of crystal structures of bacterial cold-shock proteins (5-9).

Recently, we have extended the structural characterization of cold-shock domains by studying the binding of ribooligonucleotides to bacterial cold-shock proteins and cold-shock domains from human Y-box factors. We find a conservation of the general binding mode observed before, but there is significant variation in subsite interactions which may be functionally relevant.

References and Footnotes
  1. Schindelin, H. et al. Nature 364, 164-168 (1993).
  2. Max, K.E.A. et al. J. Mol. Biol. 360, 702-714 (2006).
  3. Max, K.E.A. et al. FEBS J. 274, 1265-1279 (2007).
  4. Morgan, H.P. et al. Nucleic Acids Res. 35, e75 (2007).
  5. Schindelin, H. et al. Proteins: Struct. Funct. Genet. 14, 120-124 (1992).
  6. Schindelin, H. et al. Proc. Natl. Acad. Sci. USA 91, 5119-5123 (1994).
  7. Mueller, U. et al. J. Mol. Biol. 297, 975-988 (2000).
  8. Perl, D. et al. Nature Struct. Biol. 7, 380-383 (2000).
  9. Delbrück, H. et al. J. Mol. Biol. 313, 359-369 (2001).

Klaas E.A. Max
Udo Heinemann*

Macromolecular Structure and Interactions
Max-Delbrück Center for Molecular Medicine
Robert-Rössle-Str. 10
13125 Berlin, Germany

Phone: +49 30 9406 3420
Fax: +49 30 9406 2548
email Udo Heinemann