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1.
J Neurosurg ; 137(6): 1676-1686, 2022 12 01.
Article in English | MEDLINE | ID: mdl-35426830

ABSTRACT

OBJECTIVE: There is an unmet need for safe and rapidly effective therapies for refractory brain radiation necrosis (RN). The aim of this prospective single-arm phase II trial was to evaluate the safety and efficacy of a single low-dose targeted bevacizumab infusion after blood-brain barrier disruption (BBBD) in adult patients with steroid-refractory brain RN. METHODS: Ten adults with steroid-refractory, imaging-confirmed brain RN were enrolled between November 2016 and January 2018 and followed for 12 months after treatment. Bevacizumab 2.5 mg/kg was administered as a one-time targeted intra-arterial infusion immediately after BBBD. Primary outcomes included safety and > 25% decrease in lesion volume. Images were analyzed by a board-certified neuroradiologist blinded to pretrial diagnosis and treatment status. Secondary outcomes included changes in headache, steroid use, and functional status and absence of neurocognitive sequelae. Comparisons were analyzed using the Fisher exact test, Mann-Whitney U-test, linear mixed models, Wilcoxon signed-rank test, and repeated-measures 1-way ANOVA. RESULTS: Ten adults (mean ± SD [range] age 35 ± 15 [22-62] years) participated in this study. No patients died or exhibited serious adverse effects of systemic bevacizumab. At 3 months, 80% (95% CI 44%-98%) and 90% (95% CI 56%-100%) of patients demonstrated > 25% decrease in RN and vasogenic edema volume, respectively. At 12 months, RN volume decreased by 74% (median [range] 76% [53%-96%], p = 0.012), edema volume decreased by 50% (median [range] 70% [-11% to 83%], p = 0.086), and headache decreased by 84% (median [range] 92% [58%-100%], p = 0.022) among the 8 patients without RN recurrence. Only 1 (10%) patient was steroid dependent at the end of the trial. Scores on 12 of 16 (75%) neurocognitive indices increased, thereby supporting a pattern of cerebral white matter recovery. Two (20%) patients exhibited RN recurrence that required further treatment at 10 and 11 months, respectively, after bevacizumab infusion. CONCLUSIONS: For the first time, to the authors' knowledge, the authors demonstrated that a single low-dose targeted bevacizumab infusion resulted in durable clinical and imaging improvements in 80% of patients at 12 months after treatment without adverse events attributed to bevacizumab alone. These findings highlight that targeted bevacizumab may be an efficient one-time treatment for adults with brain RN. Further confirmation with a randomized controlled trial is needed to compare the intra-arterial approach with the conventional multicycle intravenous regimen. Clinical trial registration no.: NCT02819479 (ClinicalTrials.gov).


Subject(s)
Brain Neoplasms , Radiation Injuries , Radiosurgery , Adult , Humans , Young Adult , Middle Aged , Bevacizumab/therapeutic use , Prospective Studies , Radiation Injuries/etiology , Brain/pathology , Radiosurgery/methods , Brain Neoplasms/drug therapy , Brain Neoplasms/radiotherapy , Brain Neoplasms/pathology , Necrosis/etiology , Edema/drug therapy , Steroids , Headache/etiology
2.
Radiat Oncol ; 8: 101, 2013 Apr 25.
Article in English | MEDLINE | ID: mdl-23618500

ABSTRACT

BACKGROUND: We investigated the pattern of failure in glioblastoma multiforma (GBM) patients treated with concurrent radiation, bevacizumab (BEV), and temozolomide (TMZ). Previous studies demonstrated a predominantly in-field pattern of failure for GBM patients not treated with concurrent BEV. METHODS: We reviewed the treatment of 23 patients with GBM who received 30 fractions of simultaneous integrated boost IMRT. PTV60 received 2 Gy daily to the tumor bed or residual tumor while PTV54 received 1.8 Gy daily to the surrounding edema. Concurrent TMZ (75 mg/m^2) daily and BEV (10 mg/kg every 2 weeks) were given during radiation therapy. One month after RT completion, adjuvant TMZ (150 mg/m^2 × 5 days) and BEV were delivered monthly until progression or 12 months total. RESULTS: With a median follow-up of 12 months, the median disease-free and overall survival were not reached. Four patients discontinued therapy due to toxicity for the following reasons: bone marrow suppression (2), craniotomy wound infection (1), and pulmonary embolus (1). Five patients had grade 2 or 3 hypertension managed by oral medications. Of the 12 patients with tumor recurrence, 7 suffered distant failure with either subependymal (5/12; 41%) or deep white matter (2/12; 17%) spread detected on T2 FLAIR sequences. Five of 12 patients (41%) with a recurrence demonstrated evidence of GAD enhancement. The patterns of failure did not correlate with extent of resection or number of adjuvant cycles. CONCLUSIONS: Treatment of GBM patients with concurrent radiation, BEV, and TMZ was well tolerated in the current study. The majority of patients experienced an out-of-field pattern of failure with radiation, BEV, and TMZ which has not been previously reported. Further investigation is warranted to determine whether BEV alters the underlying tumor biology to improve survival. These data may indicate that the currently used clinical target volume thought to represent microscopic disease for radiation may not be appropriate in combination with TMZ and BEV.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Brain Neoplasms/pathology , Brain Neoplasms/therapy , Chemoradiotherapy/methods , Glioblastoma/pathology , Glioblastoma/therapy , Neoplasm Recurrence, Local/pathology , Adult , Aged , Antibodies, Monoclonal, Humanized/administration & dosage , Bevacizumab , Dacarbazine/administration & dosage , Dacarbazine/analogs & derivatives , Disease-Free Survival , Female , Humans , Male , Middle Aged , Radiotherapy, Intensity-Modulated , Retrospective Studies , Temozolomide
3.
J Bacteriol ; 189(19): 6882-90, 2007 Oct.
Article in English | MEDLINE | ID: mdl-17675384

ABSTRACT

The coordinate expression of Salmonella enterica invasion genes on Salmonella pathogenicity island 1 is under the control of the complex circuits of regulation that involve the AraC/XylS family transcriptional activators HilD, HilC, and RtsA and nucleoid-associated proteins. Single-copy transcription fusions were used to assess the effects of nucleoid-associated proteins Hha and H-NS on hilD, hilC, and rtsA expression. The data show that all three genes, hilD, hilC, and rtsA, were repressed by H-NS and/or Hha. The repression of rtsA was the highest among tested genes. The level of rtsA-lac was equally elevated in hns and hha mutants and was further enhanced in the hns hha double mutant under low-osmolarity conditions. Electrophoretic mobility shift experiments showed that H-NS and Hha directly bind to the rtsA promoter. In addition to the negative control that was exerted by H-NS/Hha under low-osmolarity conditions, the homologous virulence activators HilD, HilC, and RtsA (Hil activators) induced rtsA-lac expression in a high-salt medium. A DNase footprinting assay of the rtsA promoter revealed one common DNA-binding site for all three Hil activators centered at position -54 relative to the transcriptional start site. In the absence of Hha and H-NS, however, osmoregulation of the rtsA promoter was lost, and Hil activators were not required for rtsA transcription. These results taken together suggest that the HilD, HilC, and RtsA proteins induce the transcription of the rtsA promoter by counteracting H-NS/Hha-mediated repression.


Subject(s)
Bacterial Proteins/physiology , Repressor Proteins/physiology , Salmonella enterica/metabolism , Transcription Factors/physiology , Bacterial Proteins/genetics , Base Sequence , DNA, Intergenic/genetics , Deoxyribonuclease I/metabolism , Electrophoretic Mobility Shift Assay , Gene Deletion , Gene Expression Regulation, Bacterial , Models, Biological , Molecular Sequence Data , Promoter Regions, Genetic/genetics , Protein Binding , Repressor Proteins/genetics , Salmonella enterica/genetics , Salmonella enterica/growth & development , Transcription Factors/genetics , Transcription, Genetic
4.
J Mol Biol ; 357(2): 373-86, 2006 Mar 24.
Article in English | MEDLINE | ID: mdl-16443238

ABSTRACT

The hilA gene on the Salmonella enterica pathogenicity island-1 encodes the key transcriptional regulator of host cell invasion. Transcription of hilA is regulated by numerous physiological signals, including repression under low osmolarity conditions. To investigate the osmotic control of hilA transcription, promoter truncations that remove sequences flanking the hilA promoter were examined. Expression of the minimal hilA core promoter (-55 to +90, relative to the transcription start site) was 57-times higher than the intact promoter (-242 to +505) in the absence of osmotic stress. Both flanking sequences contributed to the strong silencing effect, which was greatly relieved by the simultaneous loss of the two nucleoid-structuring proteins, H-NS and Hha. Mobility-shift assays revealed the presence of binding sites for the H-NS and Hha proteins, both upstream and downstream of the promoter. Either flanking region depressed expression when it was placed downstream of the lacUV5 promoter, and this inhibition was increased when the other flanking sequence was present upstream of the promoter. These results show that the hilA promoter is highly active without other transcription regulators. Its high activity is strongly depressed in low osmolarity conditions by the nucleoid-structuring proteins H-NS and Hha, possibly by formation of a repressive DNA loop. The hilA activators, HilD and HilC appear to overcome effects of downstream silencing region and disrupt repressive DNA loop. Action of activators requires contact with RNA polymerase from their DNA binding site, centered at position -77, relative to the hilA transcription start site.


Subject(s)
Bacterial Proteins/genetics , Base Sequence , Gene Silencing , Promoter Regions, Genetic , Salmonella typhimurium/genetics , Trans-Activators/genetics , Bacterial Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Escherichia coli Proteins/metabolism , Molecular Sequence Data , Osmolar Concentration , Trans-Activators/metabolism , Transcription, Genetic
6.
Proteins ; 59(2): 240-51, 2005 May 01.
Article in English | MEDLINE | ID: mdl-15739205

ABSTRACT

TonB-dependent outer membrane transporters (TBDTs) transport organometallic substrates across the outer membranes of Gram-negative bacteria. Currently, structures of four different TBDTs have been determined by X-ray crystallography. TBDT structures consist of a 22-stranded beta-barrel enclosing a hatch domain. Structure-based sequence alignment of these four TBDTs indicates the presence of highly conserved motifs in both the hatch and barrel domains. The conserved motifs of the two domains are always in close proximity to each other and interact. We analyzed the very large interfaces between the barrel and hatch domains of TBDTs and compared their properties to those of other protein-protein interfaces. These interfaces are extensively hydrated. Most of the interfacial waters form hydrogen bonds to either the barrel or the hatch domain, with the remainder functioning as bridging waters in the interface. The hatch/barrel interfacial properties most resemble those of obligate transient protein complexes, suggesting that the interface is conducive to conformational change and/or movement of the hatch within the barrel. These results indicate that TBDTs can readily accommodate substantial conformational change and movement of their hatch domains during the active transport cycle. Also, these structural changes may require only modest forces exerted by the energy-coupling TonB protein upon the transporter.


Subject(s)
Bacterial Outer Membrane Proteins/chemistry , Bacterial Outer Membrane Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Membrane Proteins/chemistry , Membrane Proteins/metabolism , Membrane Transport Proteins/chemistry , Membrane Transport Proteins/metabolism , Amino Acid Sequence , Binding Sites , Biological Transport , Conserved Sequence , Kinetics , Models, Molecular , Protein Conformation , Protein Structure, Secondary , Sequence Alignment
7.
J Bacteriol ; 187(5): 1732-9, 2005 Mar.
Article in English | MEDLINE | ID: mdl-15716445

ABSTRACT

The Escherichia coli outer membrane TonB-dependent transporters for iron complexes and cobalamins recognize their multiple and diverse substrates with high specificity and affinity. The X-ray crystallographic structures of several transporters show that the substrate-binding surfaces are comprised of residues from the internal globular domain and multiple extracellular loops. The extracellular loops on the N-terminal half of the transmembrane beta-barrel of the cobalamin transporter BtuB participate in binding of the cofactor calcium atoms and undergo substantial conformation changes upon substrate binding. The functional relevance of the five C-terminal loops was examined by examining the effects of short in-frame deletions. Each loop contributed in different ways to the binding of BtuB substrates. Deletions in loops 7, 8, 9, and 11 strongly decreased cobalamin binding and transport, whereas deletions in loops 8, 9, and 10 affected binding and entry of phage BF23. None of the loops were essential for the action of colicin E1 or E3, which is consistent with the crystallographic observation that the colicin E3 receptor-binding domain can contact almost all of the loops. A deletion in loop 9 or 11 eliminated the ability of cobalamin to inhibit the action of colicin E1. These phenotypes show that there are multiple independent binding elements and point out similarities and differences in binding properties among the TonB-dependent transporters.


Subject(s)
Bacterial Adhesion/physiology , Carrier Proteins/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/physiology , Receptors, Peptide/chemistry , Amino Acid Sequence , Bacterial Outer Membrane Proteins , Biological Transport, Active/physiology , Carrier Proteins/metabolism , Colicins , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Gene Expression , Membrane Transport Proteins , Mutation , Protein Conformation , Receptors, Peptide/metabolism , Siphoviridae , Structure-Activity Relationship , Vitamin B 12/metabolism
8.
J Bacteriol ; 186(10): 3249-53, 2004 May.
Article in English | MEDLINE | ID: mdl-15126488

ABSTRACT

Expression of invasion genes in Salmonella pathogenicity island 1 (SPI-1) is mainly driven by the transcriptional activator HilA. Transcription of hilA is subject to complex control and is stimulated by the SPI-1-encoded HilC and HilD proteins. The C-terminal domain of RpoA contributes to hilA activation by HilC/D under certain inducing conditions.


Subject(s)
Bacterial Proteins/physiology , DNA-Directed RNA Polymerases/chemistry , Promoter Regions, Genetic , Salmonella enterica/genetics , Trans-Activators/genetics , Transcription Factors/physiology , Binding Sites , DNA-Directed RNA Polymerases/physiology , Gene Expression Regulation, Bacterial , Transcription, Genetic
9.
Proc Natl Acad Sci U S A ; 100(20): 11382-7, 2003 Sep 30.
Article in English | MEDLINE | ID: mdl-13679579

ABSTRACT

BtuB is a TonB-dependent outer-membrane transporter for vitamin B12 (or cyanocobalamin, CN-Cbl) in Escherichia coli. The binding of CN-Cbl is believed to promote an unfolding or undocking of the Ton box, the conserved N-terminal energy coupling motif at the periplasmic surface of the transporter. This structural change may facilitate the interaction of BtuB with the inner membrane protein TonB. In this work, the effect of the receptor binding fragment of colicin E3 (E3R) on the conformation of the Ton box was examined with site-directed spin labeling. Addition of E3R reverses the undocking of the Ton box that is promoted by CN-Cbl, consistent with a competitive binding between the substrate and the colicin fragment. EPR spectroscopy indicates that the Ton box is in a two-state equilibrium between docked and undocked conformations. In the absence of substrate, the docked conformation is the predominant state; however, the equilibrium can be shifted to the undocked state by the addition of detergents or site-specific proline substitutions. Even when the undocking is induced by detergents or by certain proline mutations, E3R binding shifts the equilibrium to the docked conformation. Thus, two competitive extracellular ligands, CN-Cbl and ER3, transduce opposite conformations of the N-terminal Ton box. Substrate binding stabilizes an undocked conformation, whereas E3R binding stabilizes a docked conformation of the Ton box.


Subject(s)
Bacterial Proteins/physiology , Escherichia coli Proteins , Membrane Proteins/physiology , Biological Transport , Electron Spin Resonance Spectroscopy , Ligands , Protein Conformation
10.
J Mol Biol ; 332(5): 999-1014, 2003 Oct 03.
Article in English | MEDLINE | ID: mdl-14499604

ABSTRACT

Gram-negative bacteria possess specialized active transport systems that function to transport organometallic cofactors or carriers, such as cobalamins, siderophores, and porphyrins, across their outer membranes. The primary components of each transport system are an outer membrane transporter and the energy-coupling protein TonB. In Escherichiacoli, the TonB-dependent outer membrane transporter BtuB carries out active transport of cobalamin (Cbl) substrates across its outer membrane. Cobalamins bind to BtuB with nanomolar affinity. Previous studies implicated calcium in high-affinity binding of cyanocobalamin (CN-Cbl) to BtuB. We previously solved four structures of BtuB or BtuB complexes: an apo-structure of a methionine-substitution mutant (used to obtain experimental phases by selenomethionine single-wavelength anomalous diffraction studies); an apo-structure of wild-type BtuB; a binary complex of calcium and wild-type BtuB; and a ternary complex of calcium, CN-Cbl and wild-type BtuB. We present an analysis of the binding of calcium in the binary and ternary complexes, and show that calcium coordination changes upon substrate binding. High-affinity CN-Cbl binding and calcium coordination are coupled. We also analyze the binding mode of CN-Cbl to BtuB, and compare and contrast this binding to that observed in other proteins that bind Cbl. BtuB binds CN-Cbl in a manner very different from Cbl-utilizing enzymes and the periplasmic Cbl binding protein BtuF. Homology searches of bacterial genomes, structural annotation based on the presence of conserved Cbl-binding residues identified by analysis of our BtuB structure, and detection of homologs of the periplasmic Cbl-binding binding protein BtuF enable identification of putative BtuB orthologs in enteric and non-enteric bacterial species.


Subject(s)
Bacterial Physiological Phenomena , Bacterial Proteins/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/metabolism , Receptors, Peptide/chemistry , Vitamin B 12/chemistry , Amino Acid Motifs , Amino Acid Sequence , Bacterial Outer Membrane Proteins , Biological Transport , Calcium/chemistry , Databases as Topic , Escherichia coli Proteins/metabolism , Hydrogen Bonding , Membrane Transport Proteins , Models, Molecular , Molecular Sequence Data , Protein Binding , Protein Structure, Secondary , Protein Transport , Receptors, Peptide/metabolism , Sequence Homology, Amino Acid , Substrate Specificity
11.
Proc Natl Acad Sci U S A ; 100(19): 10688-93, 2003 Sep 16.
Article in English | MEDLINE | ID: mdl-12958215

ABSTRACT

The BtuB transporter mediates high-affinity binding and TonB-dependent active transport of vitamin B12 [cyanocobalamin (CNCbl)] across the outer membrane of Escherichia coli. A characteristic feature of TonB-dependent transporters is the Ton box, a conserved sequence near the N terminus and exposed to the periplasm. Crosslinking to TonB and site-directed spin labeling indicated that the Ton box of BtuB undergoes a substantial conformational transition in response to CNCbl binding, but only slight movement was seen in crystal structures. An in vivo method of detecting substrate-induced changes in the Ton box environment measured reaction of a biotin maleimide derivative with cysteine substitutions through the N-terminal region of BtuB between positions 1 and 31. The degree of maleimide labeling of different residues correlated with their accessibility in the crystal structure. Labeling of many positions was increased strongly when CNCbl was present, consistent with the undocking of this region proposed from spin-labeling analyses. The receptor-binding domain of colicin E3, which binds to BtuB competitively with CNCbl, resulted in decreased labeling. Both substrate-induced transitions occur in and beyond the Ton box and were affected by transport-uncoupling substitutions. Thus, two transport substrates that bind competitively to the extracellular face of BtuB stabilize opposite transitions of the Ton box.


Subject(s)
Bacterial Proteins/metabolism , Escherichia coli Proteins/metabolism , Membrane Proteins/metabolism , Receptors, Peptide/metabolism , Signal Transduction , Arabidopsis Proteins , Bacterial Outer Membrane Proteins , Membrane Transport Proteins , Microscopy, Fluorescence , Mutagenesis, Site-Directed , Phosphoprotein Phosphatases , Substrate Specificity
12.
Mol Microbiol ; 49(4): 869-82, 2003 Aug.
Article in English | MEDLINE | ID: mdl-12890014

ABSTRACT

The TonB system of Gram-negative bacteria appears to exist for the purpose of transducing the protonmotive force energy from the cytoplasmic membrane, where it is generated, to the outer membrane, where it is needed for active transport of iron siderophores, vitamin B12 and, in pathogens, iron from host-binding proteins. In this review, we bring the reader up to date on the developments in the field since the authors each wrote reviews in this journal in 1990.


Subject(s)
Bacterial Proteins/metabolism , Cell Membrane/metabolism , Energy Transfer/physiology , Gram-Negative Bacteria/metabolism , Membrane Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Binding Sites , Biological Transport , Escherichia coli Proteins/metabolism , Iron/metabolism , Macromolecular Substances , Membrane Proteins/chemistry , Membrane Proteins/genetics , Models, Molecular , Protein Conformation
13.
Nat Struct Biol ; 10(5): 394-401, 2003 May.
Article in English | MEDLINE | ID: mdl-12652322

ABSTRACT

The outer membranes of Gram-negative bacteria possess transport proteins essential for uptake of scarce nutrients. In TonB-dependent transporters, a conserved sequence of seven residues, the Ton box, faces the periplasm and interacts with the inner membrane TonB protein to energize an active transport cycle. A critical mechanistic step is the structural change in the Ton box of the transporter upon substrate binding; this essential transmembrane signaling event increases the affinity of the transporter for TonB and enables active transport to proceed. We have solved crystal structures of BtuB, the outer membrane cobalamin transporter from Escherichia coli, in the absence and presence of cyanocobalamin (vitamin B(12)). In these structures, the Ton box is ordered and undergoes a conformational change in the presence of bound substrate. Calcium has been implicated as a necessary factor for the high-affinity binding (K(d) approximately 0.3 nM) of cyanocobalamin to BtuB. We observe two bound calcium ions that order three extracellular loops of BtuB, thus providing a direct (and unusual) structural role for calcium.


Subject(s)
Cell Membrane/physiology , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Receptors, Peptide/chemistry , Receptors, Peptide/metabolism , Signal Transduction/physiology , Vitamin B 12/metabolism , Amino Acid Substitution , Bacterial Outer Membrane Proteins/chemistry , Bacterial Outer Membrane Proteins/metabolism , Crystallography, X-Ray , Membrane Transport Proteins , Models, Molecular , Mutagenesis, Site-Directed , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism
14.
Biochemistry ; 42(6): 1391-400, 2003 Feb 18.
Article in English | MEDLINE | ID: mdl-12578351

ABSTRACT

The structure and dynamics of the N-terminal and core regions of BtuB, an outer membrane vitamin B(12) transporter from Escherichia coli, were investigated by site-directed spin labeling. Cysteine mutants were generated by site-directed mutagenesis to place spin labels in the N-terminal region (residues 1-17), the core region (residues 25-30), and double labels into the Ton box (residues 6-12). BtuB mutants were expressed, spin labeled, purified, and reconstituted into phosphatidylcholine. In the presence of substrate (vitamin B(12)), EPR spectroscopy demonstrates that there is a conformational change in the Ton box similar to that seen previously for BtuB in intact outer membranes. The Ton box is positioned within the beta-barrel of BtuB in the absence of substrate (docked configuration) but becomes unfolded and increases its aqueous exposure upon substrate binding (undocked configuration). This conformational change and the similarity in the EPR spectra between reconstituted and native membranes indicate that BtuB is correctly folded and functional in the reconstituted system. The protein segment on the N-terminal side of the Ton box is highly mobile, and it becomes more mobile in the presence of substrate. Side chains in the region C-terminal to the Ton box also show increases in mobility with substrate addition, but position 16 appears to define a hinge point for this conformation change. EPR line shapes and relaxation data indicate that residues 25-30 form a beta-strand structure, which is analogous to the first beta-strand in the cores of the homologous iron transporters. When substrate binds to BtuB, this first beta-strand remains folded. The EPR spectra of double-nitroxide labels within the Ton box are broadened because of dipolar and collisional exchange interactions. The broadening pattern indicates that the Ton box is not helical but is in an extended or beta-strand structure.


Subject(s)
Bacterial Outer Membrane Proteins/chemistry , Escherichia coli Proteins/chemistry , Mutagenesis, Site-Directed , Peptide Fragments/chemistry , Periplasmic Proteins/chemistry , Receptors, Peptide/chemistry , Spin Labels , Bacterial Outer Membrane Proteins/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Biological Transport/genetics , Electron Spin Resonance Spectroscopy/methods , Escherichia coli Proteins/genetics , Membrane Proteins/chemistry , Membrane Proteins/genetics , Membrane Transport Proteins , Peptide Fragments/genetics , Periplasmic Proteins/genetics , Protein Conformation , Protein Structure, Secondary/genetics , Receptors, Peptide/genetics , Substrate Specificity/genetics , Thermodynamics , Vitamin B 12/chemistry
15.
Acta Crystallogr D Biol Crystallogr ; 59(Pt 3): 509-11, 2003 Mar.
Article in English | MEDLINE | ID: mdl-12595710

ABSTRACT

BtuB, the cobalamin transporter from Escherichia coli, has been overexpressed, purified and crystallized. The purified protein was solubilized in n-octyl tetraoxyethylene (C(8)E(4)) and was crystallized using sitting-drop vapor diffusion with PEG 3350 and magnesium acetate as precipitants (pH 6.5). Two crystal forms have been obtained. Crystal type I belongs to space group P3(1)21, with unit-cell parameters a = b = 81.6, c = 210.0 A, alpha = beta = 90, gamma = 120 degrees. Crystal type II belongs to space group P3(1)21, with unit-cell parameters a = b = 81.6, c = 226.0 A, alpha = beta = 90, gamma = 120 degrees. Each crystal form contains a monomer in the asymmetric unit. Diffraction for crystal type I extends to 2.0 A and diffraction for crystal type II extends to 2.7 A. Both crystal forms are suitable for structure determination.


Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli/chemistry , Receptors, Peptide/chemistry , Bacterial Outer Membrane Proteins , Cloning, Molecular , Crystallization , Electrophoresis, Polyacrylamide Gel , Escherichia coli Proteins/biosynthesis , Membrane Transport Proteins , Receptors, Peptide/biosynthesis , Vitamin B 12/metabolism , X-Ray Diffraction
16.
Biochemistry ; 41(39): 11543-51, 2002 Oct 01.
Article in English | MEDLINE | ID: mdl-12269798

ABSTRACT

Site-directed spin labeling and EPR spectroscopy were used to map two consecutive beta-strands of the putative transmembrane beta-barrel of BtuB. For these studies, a series of 29 consecutive single cysteine mutants of BtuB were produced covering residues 148-176. The proteins were then expressed, reacted with a sulfhydryl-specific spin label, purified in octyl glucoside (OG), and reconstituted into palmitoyloleoylphosphatidylcholine (POPC) bilayers. The labeled residues spanned from the extracellular region (position 148) to the small periplasmic loop (positions 160-163) and back up to the extracellular side (position 176) of BtuB. Continuous wave power saturation in the presence of oxygen or NiAA yielded an i, i + 2 periodicity for the collision frequencies at these sites and demonstrated the presence of a beta-strand structural motif. For both strands studied, the even-numbered residues were found to be exposed to the hydrophobic phase of the bilayer, whereas the odd-numbered residues pointed toward the interior of the barrel and the core of the protein. In addition, the collision parameters yielded the position of the protein within the bilayer. The phase relationship between the oxygen and metal collision frequencies along with the corresponding membrane depth parameters, Phi, indicates that segments 151-159 and 164-172 are within the bilayer. In POPC bilayers, there is a mobility gradient for spin labels along the barrel indicating enhanced backbone flexibility toward the periplasmic surface of the barrel. In POPC/OG mixed micelles, the even-numbered residues facing the hydrocarbon show an increased mobility compared with the bilayer environment whereas the inward-facing side chains show little change in motion. The data indicate that the protein core remains folded in POPC/OG mixed micelles but that this environment increases the backbone fluctuations of the strands. A model for the beta-barrel of BtuB is presented in part on the basis of these EPR data.


Subject(s)
Bacterial Outer Membrane Proteins/chemistry , Escherichia coli Proteins/chemistry , Membrane Transport Proteins/chemistry , Mutagenesis, Site-Directed , Receptors, Peptide/chemistry , Spin Labels , Vitamin B 12/chemistry , Amino Acid Sequence , Bacterial Outer Membrane Proteins/genetics , Electron Spin Resonance Spectroscopy/methods , Escherichia coli Proteins/genetics , Membrane Transport Proteins/genetics , Micelles , Models, Molecular , Molecular Sequence Data , Protein Structure, Secondary , Receptors, Peptide/genetics , Surface Properties , Thermodynamics
17.
J Bacteriol ; 184(15): 4148-60, 2002 Aug.
Article in English | MEDLINE | ID: mdl-12107132

ABSTRACT

The HilC and HilD proteins of Salmonella enterica serovar Typhimurium are members of the AraC/XylS family of transcription regulators. They are encoded on Salmonella pathogenicity island 1 (SPI1) and control expression of the hilA gene, which encodes the major transcriptional activator for many genes encoded on SPI1 and elsewhere that contribute to invasion of host cells. Gel electrophoretic shift and DNase footprinting assays revealed that purified HilC and HilD proteins can bind to multiple regions in the hilA and hilC promoters and to a single region in the hilD promoter. Although both HilC and -D proteins can bind to the same DNA regions, they showed different dependencies on the sequence and lengths of their DNA targets. To identify the binding-sequence specificity of HilC and HilD, a series of single base substitutions changing each position in a DNA fragment corresponding to positions -92 to -52 of the hilC promoter was tested for binding to HilC and HilD in a gel shift DNA-binding assay. This mutational analysis in combination with sequence alignments allowed deduction of consensus sequences for binding of both proteins. The consensus sequences overlap but differ so that HilC can bind to both types of sites but HilD only to one. The hilA and hilC promoters contain multiple binding sites of each type, whereas the hilD promoter contains a site that binds HilC but not HilD without additional binding elements. The HilC and HilD proteins had no major effect on transcription from the hilA or hilD promoters using purified proteins in vitro but changed the choice of promoter at hilC. These results are consistent with a model derived from analysis of lacZ fusions stating that HilC and HilD enhance hilA expression by counteracting a repressing activity.


Subject(s)
Bacterial Proteins/metabolism , Salmonella typhimurium/metabolism , Transcription Factors/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Base Sequence , Binding Sites , DNA Mutational Analysis , Electrophoretic Mobility Shift Assay , Escherichia coli/genetics , Gene Expression Regulation, Bacterial , Promoter Regions, Genetic , Salmonella typhimurium/pathogenicity , Sequence Alignment , Trans-Activators/genetics , Trans-Activators/metabolism , Transcription Factors/genetics , Transcription Factors/isolation & purification , Transcription, Genetic , Transformation, Bacterial , Virulence
18.
J Bacteriol ; 184(10): 2682-91, 2002 May.
Article in English | MEDLINE | ID: mdl-11976297

ABSTRACT

UhpA, a member of the NarL family of response regulators, activates transcription of the Escherichia coli uhpT gene for the sugar phosphate transporter UhpT in response to extracellular glucose-6-phosphate. UhpA binds with different affinities to adjacent regions in the uhpT promoter, termed the strong-binding (S) region from -80 to -50 and the weak-binding (W) region from -50 to -32. Transcription activation by UhpA is stimulated by the catabolite gene activator protein (CAP)-cyclic AMP complex and depends on the C-terminal domains of the RNA polymerase RpoA and RpoD subunits. Because single-base substitutions in the UhpA-binding region had little effect on promoter activity, nucleotide substitutions in successive 4-bp blocks throughout this region were examined for their effects on promoter activation and UhpA binding. Changes in three of four blocks within the W region substantially impaired the ability of UhpA to bind to this region, to drive expression of a uhpT-lacZ reporter, and to support UhpA-dependent in vitro transcription. These W region variant promoters were strongly stimulated by CAP. Changes in several parts of the S region impaired UhpA binding to both the S and W regions and decreased promoter activity in vivo and in vitro. Thus, binding of UhpA to the W region is crucial for UhpA-dependent activation and depends on occupancy of the S region. None of these substitutions eliminated promoter function. The orientation of UhpA-binding sites was assessed by the affinity cleavage method. The iron chelate FeBABE [iron (S)-1-(p-bromoacetamidobenzyl) EDTA] was covalently attached to engineered cysteine residues near the DNA-binding region in UhpA. Hydroxyl radicals generated by the iron chelate attached at position 187 resulted in DNA strand cleavages in two clusters of sites located in the middle of the S and W regions. These results are consistent with the binding of two dimers of UhpA. Each dimer binds to an inverted repeat of monomer-binding sites with the consensus sequence CCTGRR, where R is A or G, and each is separated by 6 bp. It is likely that members of the NarL family bind to dyad targets, in contrast to the binding of OmpR family response regulators to direct-repeat targets.


Subject(s)
Bacterial Proteins/metabolism , DNA-Binding Proteins/metabolism , Escherichia coli Proteins/genetics , Escherichia coli/genetics , Monosaccharide Transport Proteins/genetics , Promoter Regions, Genetic , Base Sequence , Binding Sites , DNA/metabolism , Molecular Sequence Data , Mutation , Transcription, Genetic
19.
J Bacteriol ; 184(3): 706-17, 2002 Feb.
Article in English | MEDLINE | ID: mdl-11790740

ABSTRACT

Cells of Escherichia coli take up vitamin B(12) (cyano-cobalamin [CN-Cbl]) and iron chelates by use of sequential active transport processes. Transport of CN-Cbl across the outer membrane and its accumulation in the periplasm is mediated by the TonB-dependent transporter BtuB. Transport across the cytoplasmic membrane (CM) requires the BtuC and BtuD proteins, which are most related in sequence to the transmembrane and ATP-binding cassette proteins of periplasmic permeases for iron-siderophore transport. Unlike the genetic organization of most periplasmic permeases, a candidate gene for a periplasmic Cbl-binding protein is not linked to the btuCED operon. The open reading frame termed yadT in the E. coli genomic sequence is related in sequence to the periplasmic binding proteins for iron-siderophore complexes and was previously implicated in CN-Cbl uptake in Salmonella. The E. coli yadT product, renamed BtuF, is shown here to participate in CN-Cbl uptake. BtuF protein, expressed with a C-terminal His(6) tag, was shown to be translocated to the periplasm concomitant with removal of a signal sequence. CN-Cbl-binding assays using radiolabeled substrate or isothermal titration calorimetry showed that purified BtuF binds CN-Cbl with a binding constant of around 15 nM. A null mutation in btuF, but not in the flanking genes pfs and yadS, strongly decreased CN-Cbl utilization and transport into the cytoplasm. The growth response to CN-Cbl of the btuF mutant was much stronger than the slight impairment previously described for btuC, btuD, or btuF mutants. Hence, null mutations in btuC and btuD were constructed and revealed that the btuC mutant had a strong impairment similar to that of the btuF mutant, whereas the btuD defect was less pronounced. All mutants with defective transport across the CM gave rise to frequent suppressor variants which were able to respond at lower levels of CN-Cbl but were still defective in transport across the CM. These results finally establish the identity of the periplasmic binding protein for Cbl uptake, which is one of few cases where the components of a periplasmic permease are genetically separated.


Subject(s)
5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase , ATP-Binding Cassette Transporters , Carrier Proteins/metabolism , Escherichia coli/metabolism , Periplasm/metabolism , Periplasmic Binding Proteins , Vitamin B 12/metabolism , Bacterial Proteins , Biological Transport , Carrier Proteins/genetics , Cell Division , Cloning, Molecular , Escherichia coli/genetics , Escherichia coli Proteins , Methyltransferases , Mutation , N-Glycosyl Hydrolases/genetics , Phenotype , Recombinant Proteins/metabolism , Suppression, Genetic
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