Chemical Proteomics Strategies for Analyzing Protein Lipidation Reveal the Bacterial O-Mycoloylome

Protein lipidation dynamically controls protein localization and function within cellular membranes. A unique form of protein O-fatty acylation in Corynebacterium, termed protein O-mycoloylation, involves the attachment of mycolic acids─unusually large and hydrophobic fatty acids─to serine residues of proteins in these organisms' outer mycomembrane. However, as with other forms of protein lipidation, the scope and functional consequences of protein O-mycoloylation are challenging to investigate due to the inherent difficulties of enriching and analyzing lipidated peptides. To facilitate the analysis of protein lipidation and enable the comprehensive profiling and site mapping of protein O-mycoloylation, we developed a chemical proteomics strategy integrating metabolic labeling, click chemistry, cleavable linkers, and a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method employing LC separation and complementary fragmentation methods tailored to the analysis of lipophilic, MS-labile O-acylated peptides. Using these tools in the model organism Corynebacterium glutamicum, we identified approximately 30 candidate O-mycoloylated proteins, including porins, mycoloyltransferases, secreted hydrolases, and other proteins with cell envelope-related functions─consistent with a role for O-mycoloylation in targeting proteins to the mycomembrane. Site mapping revealed that many of the proteins contained multiple spatially proximal modification sites, which occurred predominantly at serine residues surrounded by conformationally flexible peptide motifs. Overall, this study (i) discloses the putative protein O-mycoloylome for the first time, (ii) yields new insights into the undercharacterized proteome of the mycomembrane, which is a hallmark of important pathogens (e.g., Corynebacterium diphtheriae, Mycobacterium tuberculosis), and (iii) provides generally applicable chemical strategies for the proteomic analysis of protein lipidation.

Fine-Tuning of σE Activation Suppresses Multiple Assembly-Defective Mutations in Escherichia coli

The Gram-negative outer membrane (OM) is a selectively permeable asymmetric bilayer that allows vital nutrients to diffuse into the cell but prevents toxins and hydrophobic molecules from entering. Functionally and structurally diverse β-barrel outer membrane proteins (OMPs) build and maintain the permeability barrier, making the assembly of OMPs crucial for cell viability. In this work, we characterize an assembly-defective mutant of the maltoporin LamB, LamBG439D We show that the folding defect of LamBG439D results in an accumulation of unfolded substrate that is toxic to the cell when the periplasmic protease DegP is removed. Selection for suppressors of this toxicity identified the novel mutant degSA323E allele. The mutant DegSA323E protein contains an amino acid substitution at the PDZ/protease domain interface that results in a partially activated conformation of this protein. This activation increases basal levels of downstream σE stress response signaling. Furthermore, the enhanced σE activity of DegSA323E suppresses a number of other assembly-defective conditions without exhibiting the toxicity associated with high levels of σE activity. We propose that the increased basal levels of σE signaling primes the cell to respond to envelope stress before OMP assembly defects threaten cell viability. This finding addresses the importance of envelope stress responses in monitoring the OMP assembly process and underpins the critical balance between envelope defects and stress response activation.IMPORTANCE Gram-negative bacteria, such as Escherichia coli, inhabit a natural environment that is prone to flux. In order to cope with shifting growth conditions and the changing availability of nutrients, cells must be capable of quickly responding to stress. Stress response pathways allow cells to rapidly shift gene expression profiles to ensure survival in this unpredictable environment. Here we describe a mutant that partially activates the σE stress response pathway. The elevated basal level of this stress response allows the cell to quickly respond to overwhelming stress to ensure cell survival.

The Synthetic Phenotype of ΔbamB ΔbamE Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF

The selective permeability of the Gram-negative outer membrane (OM) is maintained by integral β-barrel outer membrane proteins (OMPs). The heteropentomeric β-barrel assembly machine (Bam) folds and inserts OMPs into the OM. Coordination of the essential proteins BamA and BamD is critical for OMP assembly and therefore the viability of the cell. The role of the nonessential lipoproteins BamBCE has yet to be characterized; however, genetic evidence suggests that they have nonoverlapping roles in OMP assembly. In this work, we quantify changes of the proteome in the conditional lethal ΔbamB ΔbamE double mutant. We show that cells lacking BamB and BamE have a global OMP defect that is a result of a lethal obstruction of an assembly-competent Bam complex by the lipoprotein RcsF. RcsF is a stress-sensing lipoprotein that is threaded through the lumen of abundant β-barrel OMPs by the Bam complex to expose the amino terminus on the cell surface. We demonstrate that simply removing this lipoprotein corrects the severe OMP assembly defect of the double mutant nearly as efficiently as a previously isolated suppressor mutation in bamA We propose that BamB and BamE play crucial, nonoverlapping roles to coordinate the activities of BamA and BamD during OMP biogenesis.IMPORTANCE Protein assembly into lipid bilayers is an essential process that ensures the viability of diverse organisms. In Gram-negative bacteria, the heteropentomeric β-barrel assembly machine (Bam) folds and inserts proteins into the outer membrane. Due to its essentiality, outer membrane protein (OMP) assembly by the Bam complex is an attractive target for antibiotic development. Here, we show that the conditional lethal phenotype of a mutant lacking two of the three nonessential lipoproteins, BamB and BamE, is caused by lethal jamming of the stripped-down Bam complex by a normally surface-exposed lipoprotein, RcsF. The heterotrimeric Bam complex (BamA, BamD, BamC) is nearly as efficient as the wild-type complex in OMP assembly if RcsF is removed. Our study highlights the importance of BamB and BamE in regulating the interaction between BamA and BamD and expands our understanding of the role of the Bam complex in outer membrane biogenesis.

Uncorrected total anomalous pulmonary venous drainage in pregnancy

Total anomalous pulmonary venous drainage is a rare form of congenital heart disease. It usually presents in the neonatal period, although later presentation, including in adulthood, is known to occur. We could not find any accounts of adult survivors with the undiagnosed disease becoming pregnant. We describe the case of a 19-year-old Bengali primiparous woman who arrived in the UK at 27 weeks' gestation and needed an urgent caesarean section for intrauterine growth restriction at 34 weeks' gestation. Uncorrected congenital heart disease was diagnosed at this time although the exact nature of the pathology was not clear. She underwent an uncomplicated caesarean section using a combined spinal-epidural technique with invasive monitoring. Intrathecal 0.5% hyperbaric bupivacaine 0.7 mL and fentanyl 25 microg were sufficient for surgery. She remained cardiovascularly stable throughout the procedure and a female infant was successfully delivered. She underwent corrective cardiac surgery 14 months after delivery. To our knowledge, this is the first report of caesarean section in a patient with uncorrected total anomalous pulmonary venous drainage. In this case, regional anaesthesia was successfully used.

Impact study of the introduction of low-dose epidural (bupivacaine 0.1%/fentanyl 2μg.mL−1) compared with bupivacaine 0.25% for labour analgesia

We conducted a retrospective analysis of the obstetric effects of introducing a low-dose epidural regimen for epidural analgesia in labour. Before this, all women in our unit requesting epidural analgesia for labour received intermittent boluses (10 mL) of 0.25% bupivacaine. After the introduction of the low-dose service in March 2000, intermittent boluses (10 mL) of 0.1% bupivacaine with fentanyl 2 microg . mL(-1) were given. The records of 300 women were examined, 150 who had received the standard regimen before the introduction of the new service and 150 women afterwards. The groups were compared for outcome of labour, quality of analgesia and any adverse events related to the epidural analgesia. There was a significant reduction in the low-dose group in the number of women requiring instrumental delivery (41% vs. 29%, P = 0.04). The need for indwelling bladder catheters was also reduced in the patients receiving the low-dose regimen (21.3% vs. 4.7%, P < 0.001). Duration of analgesia was longer in patients receiving bupivacaine 0.25% (mean minimum time between boluses 42.25 +/- 33.8 vs. 24.37 +/- 19.8 min, P < 0.001). The need for further anaesthetic intervention was higher with the low-dose regimen (24% vs. 34%, P = 0.037). Maternal satisfaction was high in both groups (95 and 97%, respectively). We conclude that the introduction of a low-dose regimen of epidural analgesia for labour reduces the incidence of instrumental deliveries. It also decreases the incidence of bladder catheterisation during labour, but the need for anaesthetic intervention may be greater.

A pattern classification approach to characterizing solitary pulmonary nodules imaged on high resolution CT: preliminary results

The purpose of this research is to characterize solitary pulmonary nodules as benign or malignant based on quantitative measures extracted from high resolution CT (HRCT) images. High resolution CT images of 31 patients with solitary pulmonary nodules and definitive diagnoses were obtained. The diagnoses of these 31 cases (14 benign and 17 malignant) were determined from either radiologic follow-up or pathological specimens. Software tools were developed to perform the classification task. On the HRCT images, solitary nodules were identified using semiautomated contouring techniques. From the resulting contours, several quantitative measures were extracted related to each nodule's size, shape, attenuation, distribution of attenuation, and texture. A stepwise discriminant analysis was performed to determine which combination of measures were best able to discriminate between the benign and malignant nodules. A linear discriminant analysis was then performed using selected features to evaluate the ability of these features to predict the classification for each nodule. A jackknifed procedure was performed to provide a less biased estimate of the linear discriminator's performance. The preliminary discriminant analysis identified two different texture measures--correlation and difference entropy--as the top features in discriminating between benign and malignant nodules. The linear discriminant analysis using these features correctly classified 28/31 cases (90.3%) of the training set. A less biased estimate, using jackknifed training and testing, yielded the same results (90.3% correct). The preliminary results of this approach are very promising in characterizing solitary nodules using quantitative measures extracted from HRCT images. Future work involves including contrast enhancement and three-dimensional measures extracted from volumetric CT scans, as well as the use of several pattern classifiers.

CT of pulmonary thromboembolism

Conventional incremental CT has for many years been useful in the fortuitous diagnosis of pulmonary thromboembolic disease, allowing for visualization of both the central occluding thrombus and the pleuroparenchymal sequelae. Unfortunately, the slow data acquisition times precluded the inclusion of conventional CT in diagnostic algorithms for the diagnosis of this disease. The development and increasing availability of fast scanning techniques, namely helical (spiral) CT and electron-beam CT, now provide a noninvasive means of consistently and accurately demonstrating acute and chronic pulmonary arterial thrombus to the segmental level. CT has the added advantage over ventilation-perfusion scanning and pulmonary angiography of depicting unsuspected intrathoracic disease that may account for the patient's presenting illness.

Risk factors for higher cost in congenital heart operations

BACKGROUND

For many congenital heart defects, hospital mortality is no longer a sensitive parameter by which to measure outcome. Although hospital survival rates are now excellent for a wide variety of lesions, many patients require expensive and extensive hospital-based services during the perioperative period to enable their convalescence. These services can substantially increase the cost of care delivery. In today's managed care environment, it would be useful if risk factors for higher cost could be identified preoperatively so that appropriate resources could be made available for the care of these patients. The focus of this retrospective investigation is to determine if risk factors for high cost for repair of congenital heart defects can be identified.

METHODS

We assessed financial risk by tracking actual hospital costs (not charges) for 144 patients undergoing repair of atrial septal defect (58 patients), ventricular septal defect (48 patients), atrioventricular canals (14 patients), or tetralogy of Fallot (24 patients) at Duke University Medical Center between July 1, 1992, and September 15, 1995. Furthermore, we were able to identify where the costs occurred within the hospital. Financial risk was defined as a large (> 60% of mean costs) standard deviation, which indicated unpredictability and variability in the treatment for a group of patients.

RESULTS

Cost for atrial septal defect repair was predictably consistent (low standard deviation) and was related to hospital length of stay. There were factors, however, for ventricular septal defect, atrioventricular canal, and tetralogy of Fallot repair that are identifiable preoperatively that predict low- and high-risk groups using cost as an outcome parameter. Patients undergoing ventricular septal defect repair who were younger than 6 months of age at the time of repair, who required preoperative hospital stays of longer than 7 days before surgical repair, or who had Down's syndrome had a less predictable cost picture than patients undergoing ventricular septal defect repair who were older than 2 years, who had short (< 4 days) preoperative hospitalization, or who did not have Down's syndrome ($48,252 +/- $42,539 versus $15,819 +/- $7,219; p = 0.008). Patients with atrioventricular canals who had long preoperative hospitalization (> 7 days), usually due to pneumonia (respiratory syncytial virus) with preoperative mechanical ventilation had significantly higher cost than patients with atrioventricular canals who underwent elective repair with short preoperative hospitalization ($83,324 +/- $60,138 versus $26,904 +/- $5,384; p = 0.05). Patients with tetralogy of Fallot had higher costs if they had multiple congenital anomalies, previous palliation (combining costs of both surgical procedures and hospital stays), or severe "tet" spells at the time of presentation for operation compared with patients without these risk factors ($114,202 +/- $88,524 versus $22,241 +/- $7,071; p = 0.0005). One patient (with tetralogy of Fallot) with multiple congenital anomalies died 42 days after tetralogy of Fallot repair of sepsis after a gastrointestinal operation. Otherwise, hospital mortality was 0% for all groups.

CONCLUSIONS

Low mortality and good long-term outcome for surgical correction of congenital heart defects is now commonplace, but can be expensive as some patients with complex problems receive the care necessary to survive. This study demonstrates that it is possible to identify factors preoperatively that predict financial risk. This knowledge may facilitate implementation of risk adjustments for managed care contracting and for strategic resource allocation.

Detection of simulated lung nodules with computed radiography: effects of nodule size, local optical density, global object thickness, and exposure

RATIONALE AND OBJECTIVES

We quantified differences in the detection of simulated lung nodules on computed radiographs on the basis of variations in nodule size, local contrast, body habitus (global contrast), and exposure.

METHODS

A step-wedge phantom was developed to simulate the attenuation ranges of the lung, retrocardiac, and subdiaphragmatic regions of the adult human chest. Additional Lucite wedges were used to simulate two different body thicknesses and to provide variable structural noise. Soft-tissue-equivalent nodules of 3-mm and 5-mm diameter that resulted in 10% differences in attenuation from lung equivalence were embedded in lung-equivalent material. By superimposing the sheets in various positions, 84 unique nodule configurations containing eight nodules per image were exposed on a computed radiography system. Computed radiographs were acquired at two different exposures approximating standard exposure and underexposure. For each resulting phantom image, seven observers scored the presence or absence of a nodule within individual cells of a 5 x 5 grid matrix.

RESULTS

True-positive fractions for 3-mm-diameter nodules were very low across all conditions. True-positive fractions for 5-mm-diameter nodules varied from 0.23 to 0.98. Significant differences in the conspicuity of 5-mm nodules depended on differences in phantom thickness and differences in the locations of nodules within lung-, retrocardiac-, or subdiaphragmatic-equivalent regions. Accuracy in detecting nodules was significantly lower at lower exposures when nodules were located in the subdiaphragmatic-equivalent region.

CONCLUSION

On computed radiographs, small nodules (5-mm diameter) can be reliably detected when they are located in areas of high or moderate surrounding local contrast, such as the lung or mediastinal regions. Detection of nodules decreases in regions of lower optical density corresponding to the subdiaphragmatic regions of the chest. The decrease in nodule detectability is greatest under conditions that simulate large body thickness and underexposure.

Pulmonary thromboembolism: spectrum of findings on CT

CT has emerged as a potentially important diagnostic technique in pulmonary thromboembolism that can provide direct visualization of the obstructing embolus and its associated vascular and pleuroparenchymal sequelae. Although the role of contrast-enhanced CT in the diagnostic algorithm of pulmonary embolism has not been defined, patients at risk for pulmonary embolism frequently undergo thoracic CT as part of the assessment for other cardiopulmonary conditions. As such, CT may provide the first indication of clinically significant pulmonary embolic disease. This essay reviews the vascular, pleural, and parenchymal features of pulmonary thromboembolism observed on CT scans, describes the limitations of CT, and discusses the imaging features of pulmonary embolism that overlap other clinical conditions.

Effects of reduced exposure on computed radiography: comparison of nodule detection accuracy with conventional and asymmetric screen-film radiographs of a chest phantom

OBJECTIVE

Radiographic exposure has been thought to have little impact on the diagnostic quality of chest computed radiography because of automatic digital control of global optical density. The objectives of this study were to compare images obtained with two different exposures in computed radiography with conventional and asymmetric screen-film images of the chest for the detection of simulated lung nodules by use of receiver operating characteristic analysis and to relate differences in observer performance to parameters of image noise measured for each receptor condition.

MATERIALS AND METHODS

At 110 kVp (fixed), exposures for the two screen-film systems were those necessary to achieve adequate optical densities over the lung and mediastinal regions of an anthropomorphic phantom. The two exposures used for the computed radiographs corresponded to the exposure used for the conventional chest screen-film system and an exposure 22% lower. An anthropomorphic phantom constructed of materials matched to the muscle, lung, and bone attenuation of a muscular adult man was used. Soft-tissue-equivalent plastic nodules of various sizes were secured at multiple sites on the phantom to simulate lung nodules. The chest phantom was imaged in 50 configurations with a total of 70 superimposed nodules. The perceptual performances of five radiologists were compared by use of receiver operating characteristic analysis. The signal-to-noise ratio in the mediastinum and the coefficient of variation of noise were measured for all four image conditions by use of a step wedge technique to provide an explanation for differences in diagnostic accuracy.

RESULTS

We found no significant differences in the detection of lung nodules between the two screen-film systems or between the conventional screen-film images and the standard-exposure computed radiographs. However, there was a significant decrease in nodule detection on computed radiographs obtained at a reduced exposure; this result was associated with a 21% decrease in the signal-to-noise ratio.

CONCLUSION

Our results show that underexposure of computed radiographs decreases the detection of low-contrast objects such as lung nodules. Although consistent global optical density on computed radiographs is achieved over a wide range of exposures, the alterations in signal-to-noise ratio that result from underexposure can reduce the diagnostic quality of computed radiographs.

Psychosocial concerns of adults with congenital heart disease. Employability and insurability

Addressing the psychosocial concerns of the growing population of adults with congenital heart disease presents a unique challenge to health care providers. These patients frequently need information about their disease with emphasis on how it may affect their sexuality, childbearing, and risk of having children with congenital heart disease. These patients also face problems in securing employment that will provide health insurance coverage for their cardiac conditions.