Sigma factor is not released during transcription in Bacillus subtilis

Mechanism of δ Mediated Transcription Activation in Bacillus subtilis: Interaction with α CTD of RNA Polymerase Stabilizes δ and Successively Facilitates the Open Complex Formation

The α CTD (C-terminal domain of the α subunit) of RNA polymerase (RNAP) is a target for transcriptional regulators. In the transcription activation at Class I, Class II, and Class III promoters of bacteria, the transcriptional regulator, binds to DNA at different sites and interacts with the α CTD to stabilize the RNAP at the promoter or it binds to the α CTD to form a prerecruitment complex that searches for its cognate binding site. This 'simple recruitment mechanism' of the transcriptional machinery at the promoter is responsible for the activation of transcription. Strikingly, in B. subtilis the binding of RNAP at the promoter stabilizes the transcriptional regulator, δ at the -41 site of the promoter DNA through an interaction with its α CTD and successively facilitates the open complex formation. Two residues R293 and K294 of α CTD (equivalent to K297 and K298 of E. coli) are involved in the interactions with δ and essential for the activation of transcription. R293 is responsible for the stabilization of δ, while K294 is responsible for facilitating the open complex formation. Based on our data we propose a new model of transcription activation by δ of B. subtilis that is similar to (its binding location and interaction with α CTD), but distinct from (the recruitment of transcription factor by RNAP at the DNA, and enhancement of the open complex formation) the model Class II promoters in bacteria.

A Novel Function of δ Factor from Bacillus subtilis as a Transcriptional Repressor

δ, a small protein found in most Gram-positive bacteria was, for a long time, thought to be a subunit of RNA polymerase (RNAP) and was shown to be involved in recycling of RNAP at the end of each round of transcription. However, how δ participates in both up-regulation and down-regulation of genes in vivo remains unclear. We have recently shown, in addition to the recycling of RNAP, δ functions as a transcriptional activator by binding to an A-rich sequence located immediately upstream of the -35 element, consequently facilitating the open complex formation. The result had explained the mechanism of up-regulation of the genes by δ. Here, we show that Bacillus subtilis δ could also function as a transcriptional repressor. Our results demonstrate that δ binds to an A-rich sequence located near the -35 element of the spo0B promoter, the gene involved in the regulatory cascade of bacterial sporulation and inhibits the open complex formation due to steric clash with σ region 4.2. We observed a significant increase in the mRNA level of the spo0B gene in a δ-knock-out strain of B. subtilis compared with the wild-type. Thus, the results report a novel function of δ, and suggest the mechanism of down-regulation of genes in vivo by the protein.

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

Most bacterial RNA polymerases (RNAP) contain five conserved subunits, viz. 2α, β, β', and ω. However, in many Gram-positive bacteria, especially in fermicutes, RNAP is associated with an additional factor, called δ. For over three decades since its identification, it had been thought that δ 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 δ is involved in recycling of RNAP by releasing the RNA from the ternary complex. We further show that δ 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 δ. Performing biochemical and mutational analysis, we show that Bacillus subtilis δ 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, δ facilitates RNAP to initiate transcription in the second scale, compared with minute scale in the absence of δ. Using transcription assay, we show that δ-mediated recycling of RNAP cannot be the sole reason for the enhancement of transcript yield. Our observation that δ 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 δ functions as a transcriptional regulator.

Visualization of intermediary transcription states in the complex between Escherichia coli DNA-dependent RNA polymerases and a promoter-carrying DNA fragment using the gel retardation method

DNA-dependent RNA polymerase in complex with a DNA fragment was analyzed by electrophoresis in non-denaturing gels as core enzyme, holoenzyme, during initiation and elongation. The DNA fragment carried the promoter A1 of the phage T7. The stoichiometry between holoenzyme and promoter and between sigma and core enzyme in complex with DNA was determined. Holoenzyme bound as a monomer to the DNA, whereas core enzyme formed aggregates before binding to the DNA. If the molar ratio of holoenzyme to DNA exceeded 0.5:1 a second holoenzyme molecule interacted with the DNA fragment with diminished affinity. A large difference in the frictional coefficient of the holoenzyme-promoter and the core enzyme-DNA complex indicated a drastic conformational difference between the two types of complexes. The stability of the holoenzyme-promoter complex decreased with decreasing temperature, accompanied by at least partial dissociation of holoenzyme into core enzyme and sigma factor. Addition of nucleoside triphosphates did not change the electrophoretic mobility of the complex if abortive transcription only was allowed, but increased it after addition of all four nucleoside triphosphates owing to release of the sigma factor.

RNA polymerase: interaction of RNA and rifampicin with the subassembly alpha 2 beta

We studied the inhibition of tryptic digestion of the subassembly alpha 2 beta of Escherichia coli DNA-dependent RNA polymerase to investigate its interaction with RNA and rifampicin. Both agents decreased distinctly the cleavage of subunit beta in the subassembly as well as the degradation of the transiently formed polypeptides (Mr greater than 80000). Short RNAs with a chain length of approximately 35 nucleotides were most protective at a concentration of 1 mg/ml while long RNAs were less effective at the same concentration. DNA did not exert any observable protective effects. The association of RNA with alpha 2 beta was shown by chromatography on phosphocellulose, which separates alpha 2 beta bound to RNA from free alpha 2 beta. The association of alpha 2 beta with RNA was inhibited by rifampicin.

The role of the components sigma and y of the DNA-dependent RNA polymerase of Lactobacillus curvatus in promotor selection

An average of 0.44 molecule each of the initiation factor sigma and the RNA polymerase binding protein y and 0.54 molecule of the subunit gamma per molecule of Lactobacillus curvatus DNA-dependent RNA polymerase have been found in the cell. Free factor y displaces sigma from free holo enzyme, E sigma. The formation of a binary complex from Ey, free sigma, and poly[d(A-T)], leads to immediate release of factor y. The release of the sigma factor occurs upon the transition of the binary to a ternary complex. A mixture of E and sigma forms binary complexes with all T7 DNA HpaII restriction fragments. In contrast a mixture of Ey and sigma binds selectively to promoter-containing DNA fragments, indicating that the stimulatory effect of y on transcription is due to an increase in the rate of promoter selection. The same RNA products are synthesised by E sigma and by Ey plus sigma with T7 DNA as template. Thus the nonspecific complexes formed by E sigma and T7 DNA are nonproductive. On the basis of these findings we propose a model for the transcription cycle in Lactobacillus curvatus.

Effects of the positively regulating product of gene 28 of the B. subtilis phage SPO1 on in vitro transcription

Some of the properties of the RNA polymerase purified from SPO1-infected Bacillus subtilis have been compared with the properties of RNA polymerase from uninfected cells (core + sigma). The two enzymes synthetize RNA from nonoverlapping regions on SPO1 DNA, and they lead to the retention of different restriction fragments of SPO1 DNA on cellulose-nitrate filters. The action of the positively regulating product of gene 28 of SPO1 (gp 28) has been analyzed. The isolated gp 28 has been shown to be unable to increase the dissociation rate of core + sigma from SPP1 DNA, while it efficiently blocks the initiation of RNA synthesis if it is added to performed complexes between core + sigma and SPP1 DNA in 0.2 M NaCl.

Free sigma subunit of Bacillus subtilis RNA polymerase binds to DNA

The affinity of Bacillus subtilis RNA polymerase sigma and delta subunits to DNA was examined by a non-denaturing polyacrylamide slab gel electrophoresis method which made it possible to resolve DNA-bound and free subunits. The results revealed that sigma subunit, but not delta subunit had a relatively high affinity for double stranded DNA. The sigma subunit was bound maximally to super-coiled pGR1-3 plasmid DNA at a mass ratio of sigma/DNA of 0.7. With B. subtilis double stranded linear DNA one sigma subunit was bound per approximately 1,000 base pairs. The sigma-DNA complex was sufficiently stable for isolation by a molecular gel filtration column. The sigma subunit had much higher affinity for super-coiled than for linear pGR1-3 DNA or for linear double stranded or denatured DNA from B. subtilis, E. coli, and calf thymus. These results indicate that the free B. subtilis sigma subunit, in contrast to the E. coli sigma subunit, can bind by itself to DNA.