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Notes: The excitation spectra of the 15V 31 344.9 band of the CS2 V 1B2←X 1Σg+ transition and the changes in these spectra with the application of a magnetic field of up to 12 kG have been measured with sub-Doppler resolution. The radiative lifetimes of rotationally resolved single lines and single Zeeman components were measured under collision-free conditions. All of the fluorescence decays were observed to be of a single exponential. Large Zeeman splittings were observed for many lines. The only symmetry allowed spin–orbit interaction is that of the 3A2(B2) component with the 1B2 state. The 3A2(B2) component has no magnetic moment, but a magnetic moment is induced when it is mixed with the 3A2(A1,B1) components. The mixing of the 3A2(B2) and 3A2(A1,B1) components is facilitated by spin–rotation interaction and the Zeeman interaction. From analysis of the observed Zeeman splittings of the perturbed levels, the 3A2(B2) component was determined to lie 14 cm−1 below the nearly degenerate 3A2(A1) and 3A2(B1) components in the energy region where the 15V band is observed. Irregular energy shifts and splittings of rotational lines were observed, and these were attributed to (a) Coriolis interaction between the V1B2(v′(a1);K=0JM) and V 1B2(v(b2);K=1JM) levels and (b) resonant spin–orbit interaction between the rotational levels V 1B2(v′(a1);KJM) and R 3A2(v(a1);KJM). These interactions become appreciable when two levels lie close in energy. Large Zeeman splittings were observed in case (b). Many vibrational lines with irregular intensity and spacing were observed in each band. These were attributed to (c) Fermi resonance between the vibrational levels in the V 1B2 state and (d) resonant spin–orbit interaction between vibrational levels in the V 1B2 and R 3A2 states. In case (d), large Zeeman splittings were observed for a series of rotational lines in a vibrational band. The background lines were identified from observed Zeeman splittings as the transitions to levels of the R 3A2 state, which are induced by resonant spin–orbit interaction with the levels of the V 1B2 state. The intensity of the excitation spectrum of the V 1B2←X1Σg+ transition was observed to decrease as the magnetic field increases. This was attributed to a mixing of the 3A2 state with the V 1B2 state and the resulting triplet–triplet emission, which was not detected in this experiment. It was possible to evaluate the lifetime of the radiative triplet–triplet emission via deperturbation analysis of the perturbed lines. © 2000 American Institute of Physics.

Notes: SdiA, an Escherichia coli homologue of the quorum-sensing regulator, controls the expression of the ftsQAZ operon for cell division. Transcription of ftsQ is under the control of two promoters, upstream ftsQP2 and downstream ftsQP1, which are separated by 125 bp. SdiA activates transcription from ftsQP2 in vivo. Here, we demonstrate that SdiA facilitates the RNA polymerase binding to ftsQP2 and thereby stimulates transcription from P2. Gel shift and DNase I footprinting assays indicated that SdiA binds to the ftsQP2 promoter region between −51 and −25 with respect to the P2 promoter. Activation of ftsQP2 transcription by SdiA was observed with a mutant RNA polymerase containing a C-terminal domain (CTD)-deleted α-subunit (α235) but not with RNA polymerase containing σS or a CTD-deleted σD (σD529). In good agreement with the transcription assay, no protection of P2 was observed with the RNA polymerase holoenzymes, EσS and EσD529. These observations together indicate that: (i) SdiA supports the RNA polymerase binding to ftsQP2; and (ii) this recruitment of RNA polymerase by SdiA depends on the presence of intact σCTD. This is in contrast to the well-known mechanism of RNA polymerase recruitment by protein–protein contact between class I factors and αCTD. In addition to the P2 activation, SdiA inhibited RNA polymerase binding to the ftsQP1 promoter and thereby repressed transcription from P1. Gel shift assays indicate weak binding of SdiA to the P1 promoter region downstream from −13 (or +112 with respect to P2). Neither αCTD nor σCTD are required for this inhibition. Thus, the transcription repression of P1 by SdiA may result from its competition with the RNA polymerase in binding to this promoter.

Notes: PhoP is a response regulator of the PhoQ-PhoP two-component system controlling a set of the Mg(II)-response genes in Escherichia coli. Here we demonstrate the mode of transcription regulation by phosphorylated PhoP of divergently transcribed mgtA and treR genes, each encoding a putative Mg(II) transporter and a repressor for the trehalose utilization operon respectively. Under Mg(II)-limiting conditions in vivo, two promoters, the upstream constitutive P2 and the downstream inducible P1, were detected for the mgtA gene. Gel-shift analysis in vitro using purified PhoP indicates its binding to a single DNA target, centred between –43 and –24 of the mgtAP1 promoter. This region includes the PhoP box, which consists of a direct repeat of the heptanucleotide sequence (T)G(T)TT(AA). Site-directed mutagenesis studies indicate the critical roles for T (position 3), T (position 4) and A (position 6) for PhoP-dependent transcription from mgtAP1. DNase I footprinting assays reveal weak binding of PhoP to this PhoP box, but the binding becomes stronger in the simultaneous presence of RNA polymerase. Likewise the RNA polymerase binding to the P1 promoter becomes stronger in the presence of PhoP. For the PhoP-assisted formation of open complex at the mgtAP1 promoter, however, the carboxy-terminal domain of α subunit (αCTD) is not needed. For transcription in vivo of the treR gene, four promoters were identified. The most upstream promoter treRP4 divergently overlaps with the mgtAP1 promoter, sharing the same sequence as the respective –10 signal in the opposite direction. In vitro transcription using mutant promoters support this prediction. In the presence of PhoP, transcription from the promoter treRP3 was repressed with concomitant activation of mgtAP1 transcription. The PhoP box is located between −46 and –30 with respect to treRP3, and the αCTD is needed for this repression.

Notes: The role of the α subunit of Escherichia coli RNA polymerase in transcription activation by the OxyR protein was investigated using in-vitro-reconstituted RNA polymerase containing α subunits carrying C-terminal truncations or an amino acid substitution. Mutant RNA polymerases failed to respond to transcription activation of the E. coli OxyR-dependent promoters. DNase I footprinting analysis indicates that the OxyR protein exerts a co-operative effect on the binding of wild-type RNA polymerase, but not the mutant RNA polymerases, to the katG promoter. Together, these results suggest that direct protein-protein contact between the OxyR protein and the C-terminal contact site I region of the RNA polymerase α subunit plays an essential role in transcription activation at the OxyR-dependent promoters.

Notes: The C-terminal region (amino acid residues 236–329) of the Escherichia coli RNA polymerase α subunit carries the contact site I for positive transcription factors. For detailed mapping of the contact site for the cAMP receptor protein (CRP), we made a library of mutant rpoA by polymerase chain reaction (PCR) mutagenesis, such that each should carry a single mutation on average and exclusively in the C-terminal half of the rpoA gene, and then screened this library for mutants with decreased expression of the lacZ gene. Reconstituted holoenzyme containing the mutant a subunits transcribed galP1 but not lacP1 in vitro in the presence of cAMP–CRP. DNA sequence determination of several ‘Lac-’ mutant rpoA genes revealed that all had mutations clustered within a short segment near the C-terminus of α between amino acid residues 265 and 270. A cluster of contact sites appear to exist within the contact site I region, each comprising of about five amino acids and responding in molecular communication with a different transcription factor(s).

Notes: In Pseudomonas putida, benzoate and 3-chlorobenzoate are converted to catechol and 3-chlorocatechol, respectively, which are then catabolized to tricarboxylic acid cycle intermediates via the catBCA and clcABD pathways. The catBCA and clcABD operons are regulated by homologous transcriptional activators CatR and ClcR. Previous studies have demonstrated that in addition to sequence similarities, CatR and ClcR share functional similarities which allow catR to complement clcR. In this study, we demonstrate that CatR activates the clcABD promoter in vitro without inducer, but more transcript is produced when inducer is added. DNase I footprinting and DNA-bending analyses demonstrate that CatR binds to and bends the clcABD promoter to the same angle as does ClcR plus its inducer, 2-chloromuconate. This implies that CatR binds to the clc promoter in its active conformation. Transcription of the clcABD promoter by the α-subunit truncation mutant (α-235) of RNA polymerase was sharply reduced, indicating that the α-subunit C-terminal domain is important. However, a small amount of transcript was produced under these conditions, indicating that other contact sites on the RNA polymerase may play a role in activation.

Notes: The effects of a number of mutations in crp have been measured at different cyclic AMP receptor protein (CRP)-dependent Class II promoters, where the CRP-binding site is centred around 411/2 base pairs upstream from the transcription start point. The amino acid substitutions HL159 and TA158 result in reduced CRP-dependent activation, but the reduction varies from one Class II promoter to another. Deletions in the C-terminus of the RNA polymerase alpha subunit suppress the effects of HL159 and TA158. The role of the C-terminus of alpha at these promoters is assessed. Other changes at E58, K52 and E96 affect CRP activity specifically at Class II promoters and their role is discussed.

Notes: Purified MalE–SoxS fusion protein specifically stimulated in vitro transcription of the Escherichia colizwffprfumCmicFnfo, and sodA genes, indicating that activation of the superoxide regulon requires only SoxS. As in vivo, a 21 bp sequence adjacent to the zwf promoter was able to activate transcription of an heterologous promoter in vitro. Activation of zwf and fpr transcription required the C-terminal domain (CTD) of the RNA polymerase alpha subunit, while stimulation of fumCmicFnfo, and sodA transcription was independent of CTD truncation. Thus, like the catabolite gene activator protein (CAP), SoxS is an ‘ambidextrous’ activator, activation only requiring the α CTD in a subset of regulated promoters. Indeed, the −35 hexamers of the zwf and fpr promoters lie downstream of the respective MalE–SoxS binding sites, while the binding sites of fumCmicFnfo, and sodA overlap their −35 promoter hexamers.

Notes: To test whether OmpR is involved in regulation of the bolA1p, we investigated possible effects of ompR mutation on transcription from bolA1p. In vivo, bolA1p was found to be repressed by OmpR. Furthermore in vitro, the phospho-OmpR was found to bind to the OmpR binding region of bolA1p and repress the transcription by EσS or EσD. These results suggest that the phosphorylated form of OmpR is a negative regulator for the transcription of the bolA1p promoter.