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R G Martin

Publications and source records attributed to R G Martin.

At least 19 recordsLinked to original sources
PubMed2001

Structure and dynamics of MarA-DNA complexes: an NMR investigation.

An unanswered question regarding gene regulation is how certain proteins are capable of binding to DNA with high affinity at specific but highly degenerate consensus sequences. We have investigated the interactions between the Escherichia coli transcription factor, MarA, and its diverse binding sites using NMR techniques. Complete resonance assignments for the backbone of the MarA protein complexed with DNA oligomers corresponding to its binding sites at the mar, fumC, micF and the fpr promoters were obtained. Secondary structure analysis based on chemical shifts reveals that regions identified as helical in the X-ray structure of the MarA-mar complex are present in the solution structure, although some of the helices are less well defined. The chemical shift differences between the four complexes confirm that helix 3 and helix 6 constitute the major DNA-binding elements. However, in striking contrast with the X-ray data: (i) the protein appears to be present in two or more conformations in each of the complexes; (ii) no slowly exchanging N(zeta)H(2) protons (indicative of hydrogen bonded groups) were observed by NMR for the two arginine residues proposed to form crucial hydrogen bonds in the X-ray structure; and (iii) regions at the N terminus, not observed in the X-ray structure, may be involved in DNA-binding. Taken together, the NMR results indicate that MarA in its complexes with DNA target sites is in a highly dynamic state, allowing for small but significant rearrangements of the side-chains and/or backbone to bind to the different DNA sequences.

Bacterial Proteins↗
PubMed2001

The AraC transcriptional activators.

The AraC family of bacterial transcriptional activators regulate diverse genetic systems. Recent X-ray diffraction studies show that the monomeric MarA and Rob activators bind to their asymmetric degenerate DNA sites via two different helix-turn-helix elements. Activation by MarA, SoxS or Rob requires a particular orientation of the asymmetric binding sequence (and hence the activator), depending on its distance from the -10 RNAP signal. Genetic studies are beginning to clarify how the activators interact with RNAP. Growing evidence suggests that for the sugar metabolism activators, multiple binding sites upstream of the promoter anchor the activator in a repressing or nonactivating configuration. By interaction with the sugar and/or CRP, the activator is allosterically altered so it can bind a new set of sites that enable it to activate the promoter. Surprisingly, the virulence activator, Rns, must bind to both upstream and downstream sites in order to activate the rns promoter.

Binding Sites↗
PubMed2000

Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation.

The MarA transcriptional activator binds to a 20 bp asymmetric degenerate sequence (marbox) located at different positions and orientations within the promoters of the genes of the Escherichia coli mar regulon. Solution of the MarA-marbox X-ray crystallographic structure suggested the presence of base-specific and non-specific interactions between the marbox and two helix-turn-helix (HTH) motifs on the monomeric MarA. Here, we use alanine-scanning mutagenesis and DNA retardation analysis to: (i) evaluate the contacts between MarA and the marboxes of five differently configured mar regulon promoters; (ii) assess the role of conserved hydrophobic amino acid residues for MarA activity; and (iii) identify residues required for RNA polymerase activation. These analyses revealed that the phosphate-backbone contacts and hydrogen bonds with the bases of the marbox are more significant for DNA binding than are the van der Waals interactions. While both N and C-terminal HTH motifs make essential contributions to binding site affinity, MarA is more sensitive to alterations in the N-terminal HTH. In a similar way, the activity of MarA is more sensitive to alterations in the hydrophobic core of this HTH. Solvent-exposed amino acid residues located at many positions on the MarA surface are important for activity. Some of these residues affect activity on all promoters and thus, are implicated in maintaining MarA structure whereas several solvent-exposed amino acids not involved in DNA binding were important for MarA activity on specific promoters. The pattern of activation defects defined a class II promoter-specific activating region. However, a localized class I activating region was not apparent. These results suggest that MarA activates transcription by at least two distinct mechanisms. Furthermore, the important role of phosphate contacts in marbox affinity suggests that indirect readout contributes to binding site recognition by MarA.

Alanine↗
PubMed2000

Promoter discrimination by the related transcriptional activators MarA and SoxS: differential regulation by differential binding.

MarA and SoxS are closely related proteins ( approximately 45% identical) that transcriptionally activate a common set of unlinked genes, resulting in multiple antibiotic and superoxide resistance in Escherichia coli. Both proteins bind as monomers to a 20 bp degenerate asymmetric recognition sequence, the 'marbox', located upstream of the promoter. However, the proteins differ widely in the extents to which they activate particular promoters, with the consequence that overexpression of SoxS leads to greater superoxide resistance than does overexpression of MarA. This 'discrimination' between activators by promoters was demonstrated in vivo, using promoters fused to lacZ, and in vitro, using purified RNA polymerase, promoter DNA and MarA or SoxS. The marbox was found to be a critical element in discrimination by in vivo and in vitro assays of hybrid promoters containing the marbox from one gene and the core promoter from another. Furthermore, by sequential mutation of its marbox, a promoter that discriminated 35-fold in favour of SoxS was converted into one that did not discriminate. The relative activation of a promoter by MarA or SoxS was paralleled by the relative binding of the two activators to the promoter's marbox as assayed by band shift experiments. Thus, differential recognition of closely related marbox sequences by the closely related activators is the primary basis for promoter discrimination. Discrimination enables the cell to customize its response to the stresses that trigger synthesis of the activators.

Anti-Bacterial Agents↗
PubMed1999

Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter.

The promoters of the mar/sox/rob regulon of Escherichia coli contain a binding site (marbox) for the homologous transcriptional activators MarA, SoxS and Rob. In spite of data from footprinting studies, the marbox has not been precisely defined because of its degeneracy and asymmetry and seemingly variable location with respect to the -10 and -35 hexamers for RNA polymerase (RNP) binding. Here, we use DNA retardation studies and hybrid promoters to identify optimally binding 20 bp minimal marboxes from a number of promoters. This has yielded a more defined marbox consensus sequence (AYnGCACnnWnnRYYAAAYn) and has led to the demonstration that some marboxes are inverted relative to others. Using transcriptional fusions to lacZ, we have found that only one marbox orientation is functional at a given location. Moreover, the functional orientation is determined by marbox location: marboxes that are 15 or more basepairs upstream of the -35 hexamer are oriented opposite those closer to the -35 hexamer. Marbox orientation and the spacing between marbox and signals for RNP binding are critical for transcriptional activation, presumably to align MarA with RNP.

Bacterial Proteins↗
PubMed1998

A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator.

A crystal structure for a member of the AraC prokaryotic transcriptional activator family, MarA, in complex with its cognate DNA-binding site is described. MarA consists of two similar subdomains, each containing a helix-turn-helix DNA-binding motif. The two recognition helices of the motifs are inserted into adjacent major groove segments on the same face of the DNA but are separated by only 27 A thereby bending the DNA by approximately 35 degrees. Extensive interactions between the recognition helices and the DNA major groove provide the sequence specificity.

Amino Acid Sequence↗
PubMed1998

Preparation of uniformly isotope-labeled DNA oligonucleotides for NMR spectroscopy.

Two methods for the large scale preparation of uniformly isotope-labeled DNA for NMR studies have been developed. The first method comprises the growth of a suitable plasmid harboring multiple copies of the desired oligonucleotide in a medium based on 15N and 13C nutrients. The second method uses a polymerase chain reaction (PCR)-based approach with 15N- and/or 13C-labeled deoxynucleoside triphosphates. The novelty of our PCR strategy over existing ones is that the primer and template are the identical molecule, resulting in an exponential growth in the length of the double strand that contains tandem repeats of the target DNA sequence. This novel PCR approach, which we have termed ESRA for endonuclease-sensitive repeat amplification, is easy to use, results in high yields, and can be accomplished at low costs. The utility of both methods is demonstrated for the preparation of a double-stranded 21-mer uniformly labeled with 15N and a double-stranded 17-mer DNA uniformly labeled with 15N and 13C.

Base Sequence↗
PubMed1998

Hodgkin's disease: correlation of clinical characteristics with probabilities for negative lymphangiogram vs. negative laparotomy findings in patients with Stage I supradiaphragmatic presentations vs. those in patients with Stage II.

PURPOSE: At a time both when late complications and second malignancies have become a growing concern and when staging laparotomy has been largely abandoned and comparative studies for staging Hodgkin's disease by state of the art computed tomography (CT) vs. lymphangiography have revealed minimal differences in results for these procedures, our purpose for undertaking this study was twofold. Our initial reason was to determine and compare probabilities for negative abdominal findings for patients with Stage I presentations with those for patients with Stage II as determined by lymphangiography and subsequently by laparotomy for those patients who had negative lymphangiograms. Our second reason, being an extension of the first, was to create a resource that can be used in conjunction with other information for arriving at appropriate treatment decisions including giving either more or particularly less than standard institutional therapy and especially with respect to the abdomen. METHODS AND MATERIALS: Data on 714 patients with prelymphangiogram Stage I-II upper torso presentations of Hodgkin's disease were entered prospectively in our database between 1968 and 1987. Twenty-eight with lymphocyte predominant disease, who had both negative lymphangiogram and negative laparotomy findings and 17 with questionable diagnoses of lymphocyte-depleted or unclassified disease were excluded from subsequent analyses of 669 patients with nodular sclerosis (NS) and mixed cellularity (MC) diagnoses. RESULTS: Stage I: in final logistic models, negative lymphangiogram findings were associated strongly with a combination of no constitutional symptoms and nodular sclerosis histology, whereas negative laparotomy findings correlated strongly with a combination of no constitutional symptoms and female sex. Predicted probabilities depended on the ratios of favorable to unfavorable characteristics. Stage II: in final logistic models, negative lymphangiogram findings were associated strongly with a combination of no constitutional symptoms, nodular sclerosis histology, age <40 years, and <4 involved sites, whereas negative laparotomy findings correlated strongly with a combination of <4 involved sites and mediastinal disease. Predicted probabilities again depended on the ratios of favorable to unfavorable characteristics. CONCLUSION: This study demonstrated that probabilities for negative abdominal findings for patients with supradiaphragmatic presentations of NS and MC Hodgkin's disease depended on: 1) whether the disease presented as Stage I or as Stage II; 2) whether staging was limited to a lymphangiogram or whether it included a laparotomy; and 3) or whether the clinical features associated with the presenting stage and methods of staging were favorable or unfavorable.

Abdomen↗
PubMed1998

Safety and efficacy of intracameral injections of unpreserved lidocaine to reduce intraocular sensation.

PURPOSE: To determine the safety and efficacy of intracameral injections of unpreserved lidocaine to reduce intraocular sensation. SETTING: Carolina Eye Associates, Southern Pines, North Carolina, USA. METHODS: In this prospective study, 100 patients having phacoemulsification under topical anesthesia were randomly assigned to receive an intracameral injection of unpreserved lidocaine (0.5 cc of a 1% unpreserved solution) or balanced salt solution. RESULTS: Ninety-three patients completed the study. There were no significant between-group differences in cell density parameters or Kowa laser flare-cell meter measurements. Seventy-eight percent of lidocaine patients and 56% of controls reported no sensation (P = .048, Fisher's exact test). CONCLUSION: Intracameral injections of unpreserved lidocaine safely and effectively reduced intraocular sensation during phacoemulsification.

Anesthesia, Local↗
PubMed1998

Staar Collamer intraocular lens: clinical results from the phase I FDA core study.

PURPOSE: To assess the early postoperative efficacy and safety of the Staar Collamer intraocular lens (IOL) in small incision cataract surgery. SETTING: Six private ophthalmology practices geographically distributed throughout the United States. METHODS: One hundred twenty-five patients with a mean age of 72.1 years were enrolled in the U.S. Food and Drug Administration (FDA) Phase 1 clinical study of the Staar Collamer IOL after having cataract removal by phacoemulsification. Of these, 107 completed 4 to 6 months of follow-up. RESULTS: At 4 to 6 months postoperatively, 97.1% of patients achieved 20/40 or better corrected visual acuity; 100% of patients without pre-existing pathology (best case) achieved the same result; both results were better than FDA grid values. No persistent sight-threatening complications were reported. Through 6 months, 4.7% of patients required a neodymium:YAG capsulotomy. No IOL dislocations or removals were reported. CONCLUSION: Results indicate that the Collamer material is safe and effective for platehaptic IOLs used in small incision cataract surgery.

Aged↗
PubMed1998

Implantable contact lens for moderate to high myopia: phase 1 FDA clinical study with 6 month follow-up.

PURPOSE: To assess the short-term safety and efficacy of the implantable contact lens (ICL) to treat moderate to high myopia. SETTING: Phase 1 U.S. Food and Drug Administration clinical study of the ICL conducted at four sites in the United States. METHODS: Ten patients with myopia of 7.00 diopters (D) or greater had implantation of a Staar Surgical ICL and were examined preoperatively (baseline) and 1 day, 1 week, and 1, 3, and 6 months postoperatively. Mean preoperative myopia was 7.75 D (range 7.25 to 9.37 D). RESULTS: Six months postoperatively, 5 of 10 eyes (50%) had an uncorrected visual acuity (UCVA) of 20/20 or better, and all eyes had a UCVA of 20/30 or better. All eyes had a best spectacle-corrected visual acuity (BSCVA) of 20/20 or better and 6 eyes (60%), of 20/15 or better. Six eyes (60%) had an improvement of one or more lines of BSCVA. Mean postoperative spherical equivalent was -0.025 D +/- 0.47 (SD). Eight eyes (80%) were within +/- 0.250 D of emmetropia, and all were within +/- 1.125 D. No intraoperative or postoperative complications or adverse reactions were observed. CONCLUSIONS: The results support the short-term safety, efficacy, and predictability of ICL implantation to treat moderate to high myopia.

Adult↗
PubMed1997

Fis, an accessorial factor for transcriptional activation of the mar (multiple antibiotic resistance) promoter of Escherichia coli in the presence of the activator MarA, SoxS, or Rob.

Transcription of the multiple antibiotic resistance marRAB operon increases when one of the sequence-related activators, MarA, SoxS, or Rob, binds to the "marbox" centered at -61.5 relative to the transcriptional start site. Previous deletion analyses showed that an adjacent upstream "accessory region" was needed to augment the marbox-dependent activation. To analyze the roles of the marbox and accessory regions on mar transcription, thirteen promoters, each with a different 5-bp transversion of the -96 to -32 sequence, were synthesized, fused to lacZ, and assayed for beta-galactosidase production in single-copy lysogens with appropriate genotypes. The accessory region is shown here to be a binding site for Fis centered at -81 and to bind Fis, a small DNA-binding and -bending protein, with a Kd of approximately 5 nM. The binding of MarA to the marbox and that of Fis to its site were independent of each other. MarA, SoxS, and Rob each activated the mar promoter 1.5-to 2-fold when it had a wild-type marbox but Fis was absent. In the presence of MarA, SoxS, or Rob, Fis further enhanced the activity of the promoter twofold provided the promoter was also capable of binding Fis. However, in the absence of MarA, SoxS, or Rob or in the absence of a wild-type marbox, Fis nonspecifically lowered the activity of the mar promoter about 25% whether or not a wild-type Fis site was present. Thus, Fis acts as an accessory transcriptional activator at the mar promoter.

Bacterial Proteins↗
PubMed1996

Utilization of endogenous and dietary urea in the large intestine of the mature horse.

The dynamics of N metabolism in mature horses were investigated when they were fed on a low-N diet or the same diet supplemented with sufficient urea or soybean meal to meet their theoretical N requirements. There were no differences in DM, organic matter or neutral-detergent-fibre digestibilities for the three diets. N digestibilities and digestible-N intakes were similar for the urea- and soyabean-supplemented diets and very low for the low-N diet. For all three diets plasma urea was degraded in the digestive tract to NH3 which was utilized by the bacterial population as a N source. NH3 was absorbed from the large intestine into the blood and converted to urea. NH3 was also incorporated into plasma proteins. The horses fed on the low-N diet degraded a greater proportion of endogenous urea in the digestive tract than did horses fed on the urea-or soyabean-supplemented diets. However, the horses fed on the urea diet had the highest degradation rate of urea. The quantity of urea degraded in the digestive tract of horses fed on the urea-supplemented and the low-N diets could not compensate for a lack of dietary crude protein in these diets. The horses were in a negative N balance when fed on the low-N and urea-supplemented diets and a positive N balance when fed on the soyabean-supplemented diet. Dietary urea supplementation did not benefit the horses.

Ammonia↗
PubMed1996

Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli.

Transcriptional activation of the promoters of the mar/soxRS regulons by the sequence-related but independently inducible MarA and SoxS proteins renders Escherichia coli resistant to a broad spectrum of antibiotics and superoxide generators. Here, the effects of MarA and SoxS on transcription of the marRAB promoter itself were assayed in vitro by using a minimal transcription system and in vivo by assaying beta-galactosidase synthesized from marR::lacZ fusions. Purified MarA and MalE-SoxS proteins stimulated mar transcription about 6- and 15-fold, respectively, when the RNA polymerase/DNA ratio was 1. Purified MarA bound as a monomer to a 16-bp "marbox" located 69 to 54 nucleotides upstream of a putative RNA initiation site. Deletion of the marbox reduced MarA-mar binding 100-fold, abolished the stimulatory effects of MarA and SoxS on transcription in vitro, and reduced marR::lacZ synthesis about 4-fold in vivo. Deletion of upstream DNA adjoining the marbox reduced MarA binding efficiency 30-fold and transcriptional activation 2- to 3-fold, providing evidence for an accessory marbox. Although MarA and the mar operon repressor, MarR, bound to independent sites, they competed for promoter DNA in band shift experiments. Assays of marR::lacZ transcriptional fusions in marRAB deletion or soxRS deletion strains showed that the superoxide generator paraquat stimulates mar transcription via soxRS and that salicylate stimulates mar transcription both by antagonizing MarR and by a MarR-independent mechanism. Thus, transcription of the marRAB operon is autorepressed by MarR and autoactivated by MarA at a site that also can be activated by SoxS.

Bacterial Proteins↗
PubMed1995

Binding of purified multiple antibiotic-resistance repressor protein (MarR) to mar operator sequences.

Elevated expression of the marORAB multiple antibiotic-resistance operon enhances the resistance of Escherichia coli to various medically significant antibiotics. Transcription of the operon is repressed in vivo by the marR-encoded protein, MarR, and derepressed by salicylate and certain antibiotics. The possibility that repression results from MarR interacting with the marO operator-promoter region was studied in vitro using purified MarR and a DNA fragment containing marO. MarR formed at least two complexes with marO DNA, bound > 30-fold more tightly to it than to salmon sperm DNA, and protected two separate 21-bp sites within marO from digestion by DNase I. Site I abuts the downstream side of the putative -35 transcription-start signal and includes 4 bp of the -10 signal. Site II begins 13 bp downstream of site I, ending immediately before the first base pair of marR. Site II, approximately 80% homologous to site I, is not required for repression since a site II-deleted mutant (marO133) was repressed in trans by wild-type MarR. The absence of site II did not prevent MarR from complexing with the site I of marO133. Salicylate bound to MarR (Kd approximately 0.5 mM) and weakened the interaction of MarR with sites I and II. Thus, repression of the mar operon, which curbs the antibiotic resistance of E. coli, correlates with the formation of MarR-site I complexes. Salicylate appears to induce the mar operon by binding to MarR and inhibiting complex formation, whereas tetracycline and chloramphenicol, which neither bind MarR nor inhibit complex formation, must induce by an indirect mechanism.

Bacterial Proteins↗
PubMed1995

Wedge resection in the cone after failed refractive surgery in a patient with keratoconus.

A 30-year-old man with keratoconus in the right eye had radial keratotomy in the left eye. Two pairs of corneal relaxing incisions (CRIs) were made in the right eye to flatten the central cornea and reduce high astigmatism. The right eye required an enhancement, and two additional arcuate CRIs were made. A corneal ulcer developed in the right eye, with infiltrates in the incision and corneal thinning. Although the second set of CRIs resulted in more regular astigmatism, the corneal thinning and ulcer caused regression at two months postoperatively. A wedge resection was performed to even the irregular astigmatism. The results are presented.

Adult↗