Probing Contacts of Phosphate Groups of Oligonucleotides from the Non-Template Strand of lac UV5 Promoter with E. coli RNA Polymerase Using Regioselective Cross-Linking

E. A. Rudakova^1*, M. G. Ivanovskaya¹, M. V. Kozlov¹, M. V. Khoretonenko¹, T. S. Oretskaya¹, and V. G. Nikiforov²

¹Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119899 Russia; fax: (7-095) 939-3181; E-mail: erudakova@bioorg.chem.msu.ru

²Institute of Molecular Genetics, Russian Academy of Sciences, pl. Kurchatova, Moscow, 123182 Russia; fax: (7-095) 196-0221; E-mail: vnikifor@img.ras.ru

^* To whom correspondence should be addressed.

Received January 14, 2000; Revision received March 10, 2000

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Contacts of phosphate groups at positions -12, -15, and -18 in relation to the transcription initiation site in the non-template strand of lac UV5 promoter with lysines or histidines of E. coli RNA polymerase in the open complex model were studied. A number of synthetic oligonucleotides from the -10-area of the non-template strand containing activated 5´-terminal phosphate group were cross-linked with holo- or core-enzyme of RNA polymerase. 5´-N-Hydroxybenzotriazole phosphodiesters of oligonucleotides were used as phosphate activated derivatives. They are capable of phosphorylating amino groups of lysines and histidines in the enzyme molecule that are brought into proximity with activated phosphate in the complex, resulting in the formation of a covalent bond between the oligonucleotide and the protein. The analysis of the products of cross-linking allowed the protein subunit and the amino acid residue taking part in the formation of the covalent bond for each oligonucleotide to be identified. It was found that all oligonucleotides from the non-template strand of promoter in the complex with the holo-enzyme are bound with the sigma⁷⁰-subunit. When analyzing the products of partial cleavage of the complexes cross-linked at cysteines and methionines using SDS-PAGE, it was shown that phosphate at position -12 made contacts with His180 or His242 of the sigma⁷⁰-subunit, the reactive amino acid residue being located between the first and second conservative regions. Phosphate at position -15 is located near lysines from two different areas--between Met413 and Met456 (regions 2.3 and 2.4) and between Met470 and Met507 (region 3.1). Phosphate at position -18 makes preferential contacts with a lysine situated between Met470 and Met507 (region 3.1). Based on the analysis of contacts of phosphate groups and the structure of the isolated sigma⁷⁰-subunit established previously, a scheme of the mutual arrangement of the oligonucleotide and the sigma⁷⁰-subunit possessed by the holo-enzyme has been proposed.

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KEY WORDS: RNA polymerase from E. coli, oligonucleotide, cross-linking, activated phosphate group, lac UV5 promoter

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