Bacillus subtilis delta Factor Functions as a Transcriptional Regulator by Facilitating the Open Complex Formation

: Prajapati RK, Sengupta S, Rudra P, Mukhopadhyay J

Publisher: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

: 2016

Journal of Biological Chemistry

: JOURNAL OF BIOLOGICAL CHEMISTRY

: J BIOL CHEM

: 291

: 3

: 1064

: 1075

: 12

DOI: https://doi.org/10.1074/jbc.M115.686170

Most bacterial RNA polymerases (RNAP) contain five conserved subunits, viz. 2 alpha , beta, beta ', and omega. However, in many Grampositive bacteria, especially in fermicutes, RNAP is associated with an additional factor, called delta. For over three decades since its identification, it had been thought that delta functioned as a subunit of RNAP to enhance the level of transcripts by recycling RNAP. In support of the previous observations, we also find that delta is involved in recycling of RNAP by releasing the RNA from the ternary complex. We further show that delta binds to RNA and is able to recycle RNAP when the length of the nascent RNA reaches a critical length. However, in this work we decipher a new function of delta. Performing biochemical and mutational analysis, we show that Bacillus subtilis delta binds to DNA immediately upstream of the promoter element at A-rich sequences on the abrB and rrnB1 promoters and facilitates open complex formation. As a result, delta facilitates RNAP to initiate transcription in the second scale, compared with minute scale in the absence of delta. Using transcription assay, we show that delta-mediated recycling of RNAP cannot be the sole reason for the enhancement of transcript yield. Our observation that delta does not bind to RNAP holo enzyme but is required to bind to DNA upstream of the -35 promoter element for transcription activation suggests that delta functions as a transcriptional regulator.