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Journal of Bacteriology, April 2004, p. 2366-2375, Vol. 186, No. 8
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.8.2366-2375.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Properties of Bacillus subtilis ^A Factors with Region 1.1 and the Conserved Arg-103 at the N Terminus of Region 1.2 Deleted

Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan, Republic of China

Received 13 October 2003/ Accepted 17 December 2003

factors in the ⁷⁰ family can be classified into the primary and alternative factors according to their physiological functions and amino acid sequence similarities. The primary factors are composed of four conserved regions, with the conserved region 1 being divided into two subregions. Region 1.1, which is absent from the alternative factor, is poor in conservation; however, region 1.2 is well conserved. We investigated the importance of these two subregions to the function of Bacillus subtilis ^A, which belongs to a subgroup of the primary factor lacking a 254-amino-acid spacer between regions 1 and 2. We found that deletion of not more than 100 amino acid residues from the N terminus of ^A, which removed part or all region 1.1, did not affect the overall transcription activity of the truncated ^A-RNA polymerase in vitro, indicating that region 1.1 is not required for the functioning of ^A in RNA polymerase holoenzyme. This finding is consistent with the complementation data obtained in vivo. However, region 1.1 is able to negatively modulate the promoter DNA-binding activity of the ^A-RNA polymerase. Further deletion of the conserved Arg-103 at the N terminus of region 1.2 increased the content of stable secondary structures of the truncated ^A and greatly reduced the transcription activity of the truncated ^A-RNA polymerase by lowering the efficiency of transcription initiation after core binding of ^A. More importantly, the conserved Arg-103 was also demonstrated to be critical for the functioning of the full-length ^A in RNA polymerase.

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