Abstract:
:Abortive transcription initiation can be rate-limiting for promoter escape and therefore represents a barrier to productive gene expression. The mechanism for abortive initiation is unknown, but the amount of abortive transcript is known to vary with the composition of the initial transcribed sequence (ITS). Here, we used a thermodynamic model of translocation combined with experimental validation to investigate the relationship between ITS and promoter escape on a set of phage T5 N25 promoters. We found a strong, negative correlation between RNAP's propensity to occupy the pretranslocated state during initial transcription and the efficiency of promoter escape (r = -0.67; p < 10(-6)). This correlation was almost entirely caused by free energy changes due to variation in the RNA 3' dinucleotide sequence at each step, implying that this sequence element controls the disposition of initial transcribing complexes. We tested our model experimentally by constructing a set of novel N25-ITS promoter variants; quantitative transcription analysis again showed a strong correlation (r = -0.81; p < 10(-6)). Our results support a model in which sequence-directed bias for the pretranslocated state during scrunching results in increased backtracking, which limits the efficiency of promoter escape. This provides an answer to the long-standing issue of how sequence composition of the ITS affects promoter escape efficiency.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Skancke J,Bar N,Kuiper M,Hsu LMdoi
10.1021/acs.biochem.5b00272subject
Has Abstractpub_date
2015-07-21 00:00:00pages
4267-75issue
28eissn
0006-2960issn
1520-4995journal_volume
54pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by Sphingomonas chlorophenolica. The sequence of the active site region of tetrachlorohydroquinone dehalogenase is ver...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9923813
更新日期:2000-05-09 00:00:00
abstract::The effect of ionic strength, temperature, and divalent cations on the association of myosin with actin was determined in the ultracentrifuge using scanning absorption optics. The association constant (Ka) for the binding of heavy meromyosin (HmM) to F-actin was 1 X 10(7) M-1 at 20 degrees C, in 0.10 M KCl, 0.01 M imi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00618a017
更新日期:1978-12-12 00:00:00
abstract::In a previously determined minimal kinetic scheme for DNA polymerization catalyzed by the Klenow fragment (KF) of Escherichia coli DNA polymerase I, a nonchemical step that interconverted the KF'.DNAn+1.PPi and KF.DNAn+1PPi complexes was not observed in correct incorporation [Kuchta, R. D., Mizrahi, V., Benkovic, P.A....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00234a002
更新日期:1991-05-21 00:00:00
abstract::We have examined the reduction of cyanide by using the purified component proteins of nitrogenase (Av1 and Av2). The previously reported self-inhibition phenomenon was found to be an artifact. One of the two species present in cyanide solutions, CN-, was shown to be a potent reversible inhibitor (Ki = 27 microM) of to...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00261a031
更新日期:1982-08-31 00:00:00
abstract::Intrastrand cross-links represent the majority of modifications in DNA resulting from interaction with the cancer chemotherapeutic drug cis-diamminedichloroplatinum(II) (cis-DDP). These adducts were recently characterized although several discrepancies remained to be resolved. In these studies, [3H]-cis-dichloro(ethyl...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00361a026
更新日期:1986-07-01 00:00:00
abstract::Class A beta-lactamases hydrolyze penicillins and other beta-lactams via an acyl-enzyme catalytic mechanism. Ser70 is the active site nucleophile. By constructing the S70A mutant, which is unable to form the acyl-enzyme intermediate, it was possible to make stable ES complexes with various substrates. The stability of...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9928041
更新日期:2000-05-30 00:00:00
abstract::In the nacre or aragonite layer of the mollusk shell, proteomes that regulate both the early stages of nucleation and nano-to-mesoscale assembly of nacre tablets from mineral nanoparticle precursors exist. Several approaches have been developed to understand protein-associated mechanisms of nacre formation, yet we sti...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00163
更新日期:2016-04-26 00:00:00
abstract::Epigallocatechin-3-gallate (EGCG) is a catechin found in green tea that can inhibit the amyloid formation of a wide variety of proteins. EGCG's ability to prevent or redirect the amyloid formation of so many proteins may reflect a common mechanism of action, and thus, greater molecular-level insight into how it exerts...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.0c00043
更新日期:2020-03-17 00:00:00
abstract::A three-component soluble methane monooxygenase (sMMO) enzyme system catalyzes the hydroxylation of methane to methanol at a carboxylate-bridged diiron center housed in the alpha-subunit of the hydroxylase (MMOH). Catalysis is facilitated by the presence of a regulatory protein (MMOB) and inhibited by MMOD, a protein ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi048140z
更新日期:2004-12-28 00:00:00
abstract::Genetic knockout of the BtR4 gene encoding the Heliothis virescens cadherin-like protein (HevCaLP) is linked to resistance against Cry1Ac toxin from Bacillus thuringiensis. However, the functional Cry1Ac receptor role of this protein has not been established. We previously proposed HevCaLP as a shared binding site for...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0606703
更新日期:2006-08-15 00:00:00
abstract::Interleukin-8 (IL-8), a member of the chemokine superfamily, exists as both monomers and dimers, and mediates its function by binding to neutrophil CXCR1 and CXCR2 receptors that belong to the G protein-coupled receptor class. It is now well established that the monomer functions as a high-affinity ligand, but the bin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0605944
更新日期:2006-06-27 00:00:00
abstract::To investigate the possible role of viral glycoprotein mobility in membrane fusion, fluorescence photobleaching recovery was employed to study the effects of exposure to mildly acidic pH (required to convert many viral fusion proteins to the fusion-active form) on the lateral mobility of influenza hemagglutinin (HA) p...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00052a014
更新日期:1993-01-12 00:00:00
abstract::Guanidine hydrochloride (GdnHCl) and thermally induced unfolding measurements on the oxidized form of Escherichia coli thioredoxin at pH 7 were combined for the purpose of assessing the functional dependence of unfolding free energy changes on denaturant concentration over an extended GdnHCl concentration range. Conve...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00135a022
更新日期:1992-05-26 00:00:00
abstract::Cibacron Blue F3GA, the polycyclic blue chromophore of Blue Dextran 2000, inhibits the catalytic subunit of bovine brain protein kinase. The rate of inactivation exhibits a hyperbolic dependence on the dye concentration. This suggests that an enzyme-dye complex forms prior to inactivation. Protein and peptide substrat...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00542a022
更新日期:1980-01-08 00:00:00
abstract::We have previously shown that introduction of an engineered Met160 residue in ascorbate peroxidase (S160M variant) leads to the formation of a covalent link between Met160 and the heme vinyl group [Metcalfe, C. L., et al. (2004) J. Am. Chem. Soc. 126, 16242-16248]. In this work, we have used electronic spectroscopy, H...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi7015316
更新日期:2007-11-20 00:00:00
abstract::The thermotropic phase behavior of 10 mixed-chain phosphatidylcholines, in excess water, has been examined and compared with that of identical-chain C(16):C(16)PC by using high-resolution differential scanning calorimetry (DSC). The molecular weights (MW) of these 11 molecular species are the same, but their delta C/C...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00243a022
更新日期:1991-07-23 00:00:00
abstract::A combination of mutagenesis, calorimetry, kinetics, and small-angle X-ray scattering (SAXS) has been used to study the mechanism of ligand binding energy propagation through human cytochrome P450 reductase (CPR). Remarkably, the energetics of 2',5'-ADP binding to R597 at the FAD-binding domain are affected by mutatio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700596s
更新日期:2007-07-17 00:00:00
abstract::The ErbB family of tyrosine kinase receptors is a key element in preserving cell growth homeostasis. This family is comprised of four single-transmembrane domain proteins designated ErbB-1-4. Ligand binding initiates dimerization followed by tyrosine phosphorylation and signaling, which when uncontrolled lead to cance...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00450
更新日期:2016-10-04 00:00:00
abstract::The immunophilin FKBP52 interacts with nuclear steroid hormone receptors. Studying the crystal structure of human estrogen receptor α (hERα) and using nuclear magnetic resonance, we show here that the short V(364)PGF(367) sequence, which is located within its ligand-binding domain and adopts a type II β-turn conformat...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00506
更新日期:2016-09-27 00:00:00
abstract::Phosphotriesterase, as isolated from Pseudomonas diminuta, is capable of detoxifying widely used pesticides such as paraoxon and parathion and various mammalian acetylcholinesterase inhibitors. The enzyme requires a binuclear metal center for activity. Recently, the three-dimensional structure of the apoenzyme was sol...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00025a002
更新日期:1995-06-27 00:00:00
abstract::Dihydroorotates deuteriated at both C5 and C6 have been prepared and used to probe the mechanism of the bovine liver mitochondrial dihydroorotate dehydrogenase. Primary deuterium isotope effects on kcat are observed with both (6RS)-[5(S)-2H]- and (6RS)-[6-2H] dihydroorotates (3 and 6, respectively); these effects are ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00429a041
更新日期:1989-02-07 00:00:00
abstract::A single amino acid substitution from methionine-184 to valine (M184V) of HIV-1 reverse transcriptase (RT) evokes the 1000-fold 3TC (Lamivudine) resistance by the HIV-1 virus observed in the clinic. The M184V mutant HIV-1 RT was studied to assess its catalytic efficiency during single nucleotide incorporation using a ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990709m
更新日期:1999-07-20 00:00:00
abstract::Fourier transform infrared (FTIR) spectroscopy was employed to examine the thermal denaturation of the Fe(III), Fe(II), and Fe(II)-CO forms of cytochrome c peroxidase and horseradish peroxidase in phosphate buffer at pD 7.0. The amide I' regions of the deconvolved spectra are consistent with predominantly alpha-helica...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi952233m
更新日期:1996-04-30 00:00:00
abstract::X-ray solution scattering data from skeletal muscle troponin C and from calmodulin have been measured. Modeling studies based on the crystal structure coordinates for these proteins show discrepancies between the solution data and the crystal structure that indicate that if the size and shape of the globular domains a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00403a011
更新日期:1988-02-09 00:00:00
abstract::Aromatic amino acid aminotransferase (ArAT) from Escherichia coli was overexpressed in E. coli cells, purified, and characterized. The enzyme was similar to aspartate aminotransferase (AspAT) of E. coli in many aspects, such as gross protein structure and spectroscopic properties. The reactions of pyridoxal 5'-phospha...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00096a036
更新日期:1993-11-16 00:00:00
abstract::31P NMR measurements were made (at 121.5 MHz and 5 degrees C) on enzyme-bound substrate complexes of 3-phosphoglycerate kinase in order to address three questions pertaining to (i) the integrity of the enzyme-substrate complexes with Mg(II) in the presence of sulfate concentrations typical of those used for crystalliz...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00415a027
更新日期:1988-07-26 00:00:00
abstract::NADPH-cytochrome P450 oxidoreductase (P450 reductase, EC 1.6.2.4) is an essential component of the P450 monooxygenase complex and binds FMN, FAD, and NADPH cofactors. Residues Tyr140 and Tyr178 are known to be involved in FMN binding. A third aromatic side chain, Phe181, is also located in the proximity of the FMN rin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi011147l
更新日期:2001-11-13 00:00:00
abstract::Apo horse spleen ferritin (apo HoSF) was reconstituted to various core sizes (100-3500 Fe3+/HoSF) by depositing Fe(OH)3 within the hollow HoSF interior by air oxidation of Fe2+. Fe2+ and phosphate (Pi) were then added anaerobically at a 1:4 ratio, and both Fe2+ and Pi were incorporated into the HoSF cores. The resulti...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi982727u
更新日期:1999-05-18 00:00:00
abstract::Binding of the coupling ion (Na+ or Li+) and sugars to the purified melibiose permease of Escherichia coli, reconstituted in proteoliposomes, produces selective and cooperative changes of the transporter tryptophan fluorescence. To assess the individual contribution of N- or C-terminal domains of the permease to these...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi961372g
更新日期:1996-09-17 00:00:00
abstract::The natural product hypericin is a photosensitive polycyclic aromatic dione compound, which has been widely investigated because of its virucidal and antitumor properties. Although it has been suggested that singlet oxygen or a radical species might be responsible for its biological action, its mechanism of action rem...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi991147+
更新日期:1999-08-31 00:00:00