A Third Recognition Element in Bacterial Promoters: DNA Binding by the α Subunit of RNA Polymerase

Abstract

A DNA sequence rich in (A+T), located upstream of the -10, -35 region of the Escherichia coli ribosomal RNA promoter rrnB P1 and called the UP element, stimulates transcription by a factor of 30 in vivo, as well as in vitro in the absence of protein factors other than RNA polymerase (RNAP). When fused to other promoters, such as lacUV5, the UP element also stimulates transcription, indicating that it is a separate promoter module. Mutations in the carboxyl-terminal region of the alpha subunit of RNAP prevent stimulation of these promoters by the UP element although the mutant enzymes are effective in transcribing the "core" promoters (those lacking the UP element). Protection of UP element DNA by the mutant RNAPs is severely reduced in footprinting experiments, suggesting that the selective decrease in transcription might result from defective interactions between alpha and the UP element. Purified alpha binds specifically to the UP element, confirming that alpha acts directly in promoter recognition. Transcription of three other promoters was also reduced by the COOH-terminal alpha mutations. These results suggest that UP elements comprise a third promoter recognition region (in addition to the -10, -35 recognition hexamers, which interact with the sigma subunit) and may account for the presence of (A+T)-rich DNA upstream of many prokaryotic promoters. Since the same alpha mutations also block activation by some transcription factors, mechanisms of promoter stimulation by upstream DNA elements and positive control by certain transcription factors may be related.

Deletion analysis of cspA of Escherichia coli: requirement of the AT‐rich UP element for cspA transcription and the downstream box in the coding region for its cold shock induction

“…The present results indicate that this UP element plays an important role in maintaining the high promoter activity of cspA at both 37ЊC and low temperature. Such an AT-rich sequence, called the UP element, located upstream of the ¹35 region has been shown to play an important role in enhancing transcription (Ross et al, 1993).…”

Transcriptional analysis of the divergent cagAB genes encoded by the pathogenicity island of Helicobacter pylori

“…The DNA promoter region shows characteristics of a promoter UP element, which are constituted by AT-rich regions of 20 bp spanning from ¹40 to ¹60 with a possible non-perfect inverted repeat. It has been demonstrated that these UP elements are the target sites of the C-terminal domain ᮊ 1997 Blackwell Science Ltd, Molecular Microbiology, 26, 361-372 of the ␣-subunit of RNA polymerase, thereby enhancing transcription (Ross et al, 1993;Attey et al, 1994;Landini and Volkert, 1995). In the case of the rrnB P 1 promoter of E. coli, interaction of ␣ with the UP element enhances promoter activity by approximately 30-fold (Ross et al, 1993).…”

“…It has been demonstrated that these UP elements are the target sites of the C-terminal domain ᮊ 1997 Blackwell Science Ltd, Molecular Microbiology, 26, 361-372 of the ␣-subunit of RNA polymerase, thereby enhancing transcription (Ross et al, 1993;Attey et al, 1994;Landini and Volkert, 1995). In the case of the rrnB P 1 promoter of E. coli, interaction of ␣ with the UP element enhances promoter activity by approximately 30-fold (Ross et al, 1993). We have shown that the C-terminal region of the ␣-subunit binds the cagA P 1 UP-like element protecting DNA positions ¹14 to ¹70 from DNase I digestion (Fig.…”

A nested set of C‐terminal deletions of the α subunit of Escherichia coli RNA polymerase define regions concerned with assembly, proteolysis, stabilization and transcriptional activation in vivo

“…However, this mutant RNA polymerase or variants possessing certain substitutions in the C-terminal region failed to activate certain transcription factor-dependent promoters subsequently defined as class I activator-dependent promoters (such as lacP1, P uxuAB , P ompC ) and some UP-element-stimulated promoters (such as rrnB P1, P RNA-II , P leuV ) while retaining transcriptional proficiency at promoters independent of class I transcription factors and AT-rich UP-elements (such as galP1 and the pstS promoter) Igarashi et al 1991a;Zou et al 1992;Ross et al 1993;Murakami et al 1996).…”