Effects of a Single Base-pair Deletion in the Bacteriophage λ PRM Promoter

Structure of open promoter complexes withEscherichia coliRNA polymerase as revealed by the DNase I footprinting technique: compilation analysis

“…Designations: *, base pairs partially resistant to nuclease without any protein (indicated if at least three consecutive bases are resistant); black line, phosphodiester bonds protected against DNase digestion by RNA polymerase; gaps, unprotected base pairs; dashed line, regions protected by activator molecule; filled triangles, hypereactive base pairs (V, base pairs whose hyperreactivity was estimated by FUTPR and is not discussed in the original papers); *, promoter complexes that were not analyzed by FUJTPR. References to original papers and discrepancies: pap (24); tyrT (25); merPR (26); galPl(9A16C) and 9A16C(-1) (27); galPl(19T) (28, agrees with 19); galPl(19T, constructs d and g) (8); gaIP3 (29);fdPVIll (30); D108Pe (31); rmBPl (+ATP and CTP) (18, agrees with 32); rmBPl (UAR deleted) (+ATP and CTP) (32); T7D (33); Tn3 bla (34, agrees with 35), but hyperreactivity at -27 is not registered); lacPl(L8UV5) (36), additional hyperreactivity at-48 was registered in (37); lacPl(UV5) (38, agrees with 39-41), additional hyperreactivity at +18 registered in (42), hyperreactivity at -49 was not registered in (43); tac/pT T7 (44); aroG (45); XPR(PRM 1 16) (46, agrees with 47 for (PR); XPRMA34(PRX3) (46); tetR (48); lacP2 (36); T7A3 (43); lacPrl 15 (37); deoPl (49); gaIP2 (28, agrees with 50); crp (51); groE, dnaKP2 and rpoDpHS (52); lacPl (UV5)+CRP-cAMP (40); mll+CRP-cAMP (53); D108Pe+IHF (31); galPl+CRP-cAMP (50); galPl(9A16C)+CRP-cAMP (27); katG+OxyR (54), merPT+MerR-Hg (26); malP+MalT (55); P22Pa23+P22 Cl (56);…”

Sequence-Dependent Upstream DNA–RNA Polymerase Interactions in the Open Complex with λPR and λPRM Promoters and Implications for the Mechanism of Promoter Interference

“…Previous work has shown that in the case of phage λ, an RNAP can bind to P RM also in the context of a P R –bound RNAP but it is unable to form a transcriptionally competent complex 8,9,10,11 . The data presented herein, indicate that simultaneous binding to P R and P RM is rare in the wild-type case, and it increases whenever DNA wrapping at P R is impaired.…”

“…Open complex (RPo) formation at P R is much faster than open complex formation at P RM , thus, binding of a RNA polymerase (RNAP) to P RM only takes place in the context of an RNAP bound to P R 6,7 . It has been shown that P RM activity is increased by mutations designed to inactivate P R 8,9,10,11 and conversely, an RNAP bound to P RM interferes with the utilization of a weakened P R promoter 12 . Interestingly, it has been shown that P R and P RM promoters can be occupied simultaneously by an RNAP and this has led to the conclusion that formation of an open complex at P R does not prevent binding of an RNAP to P RM but rather impairs the isomerization from closed complex to open complex 8,9,10,11 .…”

“…It has been shown that P RM activity is increased by mutations designed to inactivate P R 8,9,10,11 and conversely, an RNAP bound to P RM interferes with the utilization of a weakened P R promoter 12 . Interestingly, it has been shown that P R and P RM promoters can be occupied simultaneously by an RNAP and this has led to the conclusion that formation of an open complex at P R does not prevent binding of an RNAP to P RM but rather impairs the isomerization from closed complex to open complex 8,9,10,11 . Contrary to the expectation, a ten bp deletion between the −35 elements of the two promoters, which should reduce the space available for two polymerases without affecting promoter sequences, resulted in a relief of interference 13,14 .…”

Antagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2

“…In these interactions, modularity is a recurring theme to regulate diverse functions of proteins 2 . While the specific sequence and position of DNA cis -regulatory elements have been intensively studied to elucidate their roles in regulating gene expression 3-5 , the basic principles underlying how protein modules are designed and arranged to govern their conformations and functions remain largely elusive. X-ray crystallography, NMR spectroscopy, and single-molecule spectroscopic methods can pro­vide details of molecular conformations in vitro , but have limited capability in live cells, particularly for proteins containing multiple interacting domains and capable of adopting diverse conformations 6 .…”