Structures and function of the amino acid polymerase cyanophycin synthetase

Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide bonds. Cyanophycin is synthesized from ATP, aspartic acid and arginine by a homooligomeric enzyme called cyanophycin synthetase (CphA1). CphA1 has domains that are homologous to glutathione synthetases and muramyl ligases, but no other structural information has been available. Here, we present cryo-electron microscopy and X-ray crystallography structures of cyanophycin synthetases from three different bacteria, including cocomplex structures of CphA1 with ATP and cyanophycin polymer analogs at 2.6 Å resolution. These structures reveal two distinct tetrameric architectures, show the configuration of active sites and polymer-binding regions, indicate dynamic conformational changes and afford insight into catalytic mechanism. Accompanying biochemical interrogation of substrate binding sites, catalytic centers and oligomerization interfaces combine with the structures to provide a holistic understanding of cyanophycin biosynthesis.

A mutation in an exoglucanase of Xanthomonas oryzae pv. oryzae, which confers an endo mode of activity, affects bacterial virulence, but not the induction of immune responses, in rice

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, a serious disease of rice. Xoo secretes a repertoire of cell wall-degrading enzymes, including cellulases, xylanases and pectinases, to degrade various polysaccharide components of the rice cell wall. A secreted Xoo cellulase, CbsA, is not only a key virulence factor of Xoo, but is also a potent inducer of innate immune responses of rice. In this study, we solved the crystal structure of the catalytic domain of the CbsA protein to a resolution of 1.86 Å. The core structure of CbsA shows a central distorted TIM barrel made up of eight β strands with N- and C-terminal loops enclosing the active site, which is a characteristic structural feature of an exoglucanase. The aspartic acid at the 131st position of CbsA was predicted to be important for catalysis and was therefore mutated to alanine to study its role in the catalysis and biological functions of CbsA. Intriguingly, the D131A CbsA mutant protein displayed the enzymatic activity of a typical endoglucanase. D131A CbsA was as proficient as wild-type (Wt) CbsA in inducing rice immune responses, but was deficient in virulence-promoting activity. This indicates that the specific exoglucanase activity of the Wt CbsA protein is required for this protein to promote the growth of Xoo in rice.

X-Ray Crystallography and Electron Microscopy of Cross- and Multi-Module Nonribosomal Peptide Synthetase Proteins Reveal a Flexible Architecture

Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP). The action of the inhibitor and the role of the MLP were investigated using adenylation reactions and isothermal titration calorimetry. In the structure, the PCP and A domains adopt a novel conformation, and noncovalent, cross-module interactions are limited. We calculated envelopes of dimodular DhbF using negative-stain electron microscopy. The data show large conformational variability between modules. Together, our results suggest that NRPSs lack a uniform, rigid supermodular architecture.

Reasons for failure to quit: a cross-sectional survey of tobacco use in major cities in Pakistan

BACKGROUND

Tobacco dependence has been defined as a chronic relapsing disease. Around 5 million annual tobacco-related deaths have been reported worldwide. The majority of smokers want to quit but are not successful.

OBJECTIVES

To screen our population for tobacco use, gauge the baseline demographics of tobacco users and assess factors associated with failed attempts to quit.

METHODS

Free health camps supervised by a physician were held across two major cities of Pakistan. All consenting participants were administered a questionnaire and had their exhaled carbon monoxide (CO) levels measured.

RESULTS

Of 12 969 participants successfully enrolled, the mean age was 31.4 ± 10.0 years. More than three quarters were aged 20-40 years (n = 10 168, 78.4%). The overall average CO level was 12.0 ± 8.0 ppm. The majority of the participants wanted to quit, and nearly everyone had received advice about quitting. The majority had tried smoking cessation pharmacotherapy. Friends/peer pressure (n = 1554, 12%), anxiety (n = 681, 5.3%), tobacco dependence (n = 1965, 15.2%) and stress/mood changes (n = 390, 3.0%) were the most widely observed reasons for failure to quit in study participants.

CONCLUSION

The information provided by this study can guide the development of more targeted intervention programmes for smokers who wish to quit.

A pilot study to assess relationship between total IgE and 95% predictive decision points of food specific IgE concentration

BACKGROUND

False positive test results in children who are tested for food allergies may lead to inappropriate dietary restrictions.

OBJECTIVE

The aim of this study was to report our experience with a 3 year-old boy, who presented with "multiple food allergies" and, however, passed the food challenges, and to review our experience regarding management of children with high specific food IgEs with high total IgE.

METHODS

Medical records of 16 children with food challenges were reviewed. Median age of subjects was 39 months, with a history of adverse clinical reaction to a food, a specific IgE greater than the decision point, and an elevated total serum IgE level of 500 IU, underwent challenges to the offending food.

RESULTS

13 out of 16 subjects were successfully re-exposed to the suspected foods and continued to tolerate these foods well.

CONCLUSION

Our finding suggests a much lower clinical risk with previously defined specific IgE decision points in children with very high levels of total IgE (> 6000 IU/ml).

Telemedicine for multidisciplinary lung cancer meetings

According to recent UK guidelines on the management of lung cancer, all cases should be reviewed prospectively by a lung cancer multidisciplinary team (MDT) and a thoracic surgeon should be readily available to liaise with the MDT. However, there is a shortage of thoracic surgeons in the UK. Over a one-year period, 28 MDT meetings were held at a district general hospital in Southend, at which 62 patients were presented to a tertiary cardiothoracic centre in London, 80 km away, via ISDN videoconferencing at 384 kbit/s. The annual resection rate increased by 30% following the introduction of the telemedicine MDT meetings, and the mean time from first being seen in the clinic to surgery was reduced from 69 to 54 days. We estimate that the telemedicine meetings saved over three working weeks of thoracic surgical time during the year.

Mutations in the Predicted Active Site of Xanthomonas oryzae pv. oryzae XopQ Differentially Affect Virulence, Suppression of Host Innate Immunity, and Induction of the HR in a Nonhost Plant

Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, secretes a number of effectors through a type 3 secretion system. One of these effectors, called XopQ, is required for virulence and suppression of rice innate immune responses induced by the plant cell-wall-degrading enzyme lipase/esterase A (LipA). Bioinformatic analysis suggested that XopQ is homologous to inosine-uridine nucleoside hydrolases (NH). A structural model of XopQ with the protozoan Crithidia fasciculata purine NH suggested that D116 and Y279 are potential active site residues. X. oryzae pv. oryzae xopQ mutants (xopQ-/pHM1::xopQD116A and xopQ-/pHM1::xopQY279A) show reduced virulence on rice compared with xopQ-/pHM1::xopQ. The two predicted XopQ active site mutants (xopQ-/pHM1::xopQD116A and xopQ-/pHM1::xopQY279A) exhibit a reduced hypersensitive response (HR) on Nicotiana benthamiana, a nonhost. However, Arabidopsis lines expressing either xopQ or xopQY279A are equally proficient at suppression of LipA-induced callose deposition. Purified XopQ does not show NH activity on standard nucleoside substrates but exhibits ribose hydrolase activity on the nucleoside substrate analogue 4-nitrophenyl β-D-ribofuranoside. The D116A and Y279A mutations cause a reduction in biochemical activity. These results indicate that mutations in the predicted active site of XopQ affect virulence and induction of the HR but do not affect suppression of innate immunity.

Delineating the reaction mechanism of reductase domains of Nonribosomal Peptide Synthetases from mycobacteria

Substrate binding to enzymes often follows a precise order where catalysis is accomplished through programmed conformational changes. Short-chain dehydrogenase/reductase (SDR) enzymes follow sequential order 'bi-bi' reaction kinetics. The mechanistic study of a SDR homolog, reductase (R) domain, from multifunctional enzymes, e.g. Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) has revealed that it reductively releases 4'-phosphopantetheinyl arm-tethered peptidyl product. We report that the R-domains of NRPSs from Mycobacterium tuberculosis (RNRP) and Mycobacterium smegmatis (RGPL) do not strictly adhere to the obligatory mode of catalysis performed by SDRs, but instead can carry out reductive catalysis of substrate following random bi-bi reaction mechanism as deciphered by NMR and SAXS studies. The crucial conformational change associated with NADPH binding necessary to achieve catalytically competent conformation is also delineated by SAXS studies. Using ITC, we have demonstrated that mutation of catalytic tyrosine to phenylalanine in R-domains results in 3-4-fold decrease in affinity for NADPH and attribute this phenomenon to loss of the noncovalent cation-π interactions present between the tyrosine and nicotinamide ring. We propose that the adaptation to an alternative theme of bi-bi catalytic mechanism enables the R-domains to process the substrates transferred by upstream domains and maintain assembly-line enzymology.

Crystallization and preliminary crystallographic studies of CbsA, a secretory exoglucanase from Xanthomonas oryzae pv. oryzae

The bacterial pathogen Xanthomonas oryzae pv. oryzae causes bacterial leaf blight, a serious disease of rice. The secreted exoglucanase CbsA is an important virulence factor of this pathogen. It belongs to the glycosyl hydrolase 6 family of proteins based on the carbohydrate-active enzyme (CAZY) classification. In this study, CbsA has been overexpressed, purified and crystallized. The crystal diffracted to a resolution of 1.86 Å and belonged to space group P2(1)2(1)2(1). It contained one monomer per asymmetric unit, with a solvent content of 45.8%.

Cigarette smoking among adolescent females in Pakistan

SETTING

Tobacco use among adolescent females is gaining importance as they take up smoking in increasing numbers. Recent studies show that sex differences in tobacco use are disappearing and that tobacco companies are agressively targeting females in developing countries.

OBJECTIVE

To determine the factors influencing the use of cigarettes among female high-school students in Karachi, Pakistan, and hence to identify areas for future intervention.

METHOD

A two-stage cluster sample of 644 females was drawn from government and private schools in a locality in Karachi. A self-administered questionnaire was used for data collection.

RESULTS

The mean age was 15.29 years. The prevalence of ever-smokers was found to be 16.3%. Univariate analysis indicated that private school attendance, underage sale of tobacco at shops, tobacco use by family members and exposure to cigarette advertisements predicted smoking among girls. Knowledge assessment of the subjects showed that most girls had good knowledge about the hazards of smoking.

CONCLUSION

Our study has identified several risk factors for smoking among young girls. Appropriate interventions are needed in the form of public education programmes, effective anti-tobacco laws and stricter enforcement of existing laws to restrict the number of young female smokers.

Asthma knowledge and approach among Pakistani family physicians and the impact of an educational programme

OBJECTIVES

To assess asthma knowledge and approach among Pakistani family physicians and the impact of an educational programme.

DESIGN

A total of 89 family physicians attending a continuing medical education programme were evaluated using a 17-item questionnaire before and after a lecture and seminar-based educational programme. Three scores -- total score (TSc), knowledge subscore (KSc) and approach subscore (ASc) -- were calculated before and after the course.

RESULTS

A total of 82 (92%) family physicians completed the questionnaire. A minimum TSc of > or =9 was achieved by 57% physicians before the course; this increased to 78% after the course. Physicians with < or =10 years since graduation achieved a higher baseline TSc than those who had graduated > or =20 years previously. The latter group showed a larger post-course improvement. Analysis of individual questions disclosed that 79% of family physicians were unable to assess the empirical risk of asthma in an unborn child, 61% were unable to correctly classify/treat Stage 2 asthma and a similar number peak expiratory flow rate (PEFR) (l/min) based acute asthma exacerbation. Reassuringly, 97% correctly identified clinical signs and 87% life-threatening features of asthma.

CONCLUSION

Of all family physicians who responded to the questionnaire, 57% achieved acceptable baseline standards. Deficiencies regarding areas such as genetic counselling and disease severity assessment were observed. Strengths in identifying clinical signs and life-threatening features were evident. Continuing medical education resulted in a significant improvement in the post-course assessment, regardless of the years since graduation.

Foreign body aspiration in adults

Foreign body aspiration is not an uncommon problem, particularly in children, the elderly, and those with predisposing factors like neurological impairment. In adults, regional differences exist in the type of foreign body aspirated. We report four cases of foreign body aspiration in South Asian adults, three of which were related to the widespread habit of chewing stimulant seeds such as betel nuts (two) and tamarind seed (one). It is important for clinicians to maintain a high index of suspicion for the diagnosis of foreign body inhalation in the appropriate clinical setting. Bronchoscopy is necessary not only for the diagnosis but also for the removal of foreign body from the bronchial tree. Once the foreign body is removed, the improvement in symptoms is usually dramatic, making it rewarding for any physician to manage.

Increasing social and psychological information conveyed to General Practitioners after bad news consultations by use of separate letters from the Lung Cancer Nurse Specialist

Multidisciplinary teams (MDT) now review all cases of lung cancer. These teams include a Lung Cancer Nurse Specialist (LCNS). These Nurses help support the patient and should facilitate communication and liaise with other services. The LCNS is present when the diagnosis is given to the patient but also usually spends time afterwards with the patient and their family. We postulated that a separate letter from the LCNS to the General Practitioner (GP) after the consultations would convey extra information to the GP. In 58 new lung cancer patients reviewed in the clinic, the LCNS and Physician independently wrote separate letters after the consultation in which the diagnosis of lung cancer was given. The GPs were asked by questionnaire about the usefulness of the letter from the LCNS. This letter was considered by the GP to provide extra information in: (i) 69% concerning the patients reaction to the diagnosis; (ii) 85% concerning who attended the clinic with the patient; (iii) 85% about what referrals were made to community services; (iv) 86% about who the patient was living with; (v) 81% about who the patients carers were; (vi) 81% information on the patients condition; (vii) 70% concerning the information given to patients about benefits. Ninety-seven percent of the GPs found the LCNS letter useful or very useful and 92% of the GPs thought that the information in the letter would be useful or very useful when they next saw the patient. Separate and independent letters from the LCNS after "bad news" consultation in lung cancer provides added useful information for GPs. Ninety-one percent of the GPs wanted the letters from the LCNS to continue.

Documenting clinicopathologic consultations

The role of the clinical pathologist as a provider of services reimbursable under Medicare Part B is increasingly being challenged. This article reports how a group of pathologists is successfully providing consultations that meet the guidelines of Medicare and the Joint Commission on Accreditation of Hospitals.