Predicting post-treatment symptom severity for adults receiving psychological therapy in routine care for generalised anxiety disorder: a machine learning approach

Approximately half of generalised anxiety disorder (GAD) patients do not recover from first-line treatments, and no validated prediction models exist to inform individuals or clinicians of potential treatment benefits. This study aimed to develop and validate an accurate and explainable prediction model of post-treatment GAD symptom severity. Data from adults receiving treatment for GAD in eight Improving Access to Psychological Therapies (IAPT) services (n=15,859) were separated into training, validation and holdout datasets. Thirteen machine learning algorithms were compared using 10-fold cross-validation, against two simple clinically relevant comparison models. The best-performing model was tested on the holdout dataset and model-specific explainability measures identified the most important predictors. A Bayesian Additive Regression Trees model out-performed all comparison models (MSE=16.54 [95 % CI=15.58; 17.51]; MAE=3.19; R²=0.33, including a single predictor linear regression model: MSE=20.70 [95 % CI=19.58; 21.82]; MAE=3.94; R²=0.14). The five most important predictors were: PHQ-9 anhedonia, GAD-7 annoyance/irritability, restlessness and fear items, then the referral-assessment waiting time. The best-performing model accurately predicted post-treatment GAD symptom severity using only pre-treatment data, outperforming comparison models that approximated clinical judgement and remaining within the GAD-7 error of measurement and minimal clinically important differences. This model could inform treatment decision-making and provide desired information to clinicians and patients receiving treatment for GAD.

Prediction of endogenous thrombolytic activity in patients with coronary artery disease

Background

Endogenous thrombolytic activity (ETA) has been suggested as an essential factor related to the acute coronary syndrome. However, there have been little data regarding clinical characteristics of ETA in East Asians.

Method

As an interim study of the entire cohort (n=2,000), we analyzed a total of 278 patients who underwent percutaneous coronary intervention (PCI) due to coronary artery disease (CAD). Informed consent was obtained from all research subjects. Blood samples of patients were brought before the procedure. The Global Thrombosis Test (GTT, Thromboquest, UK), a novel test for examining ETA, was used. Lysis time (LT), which means the time interval between blood flow occlusion and restart, was used as an indicator for ETA. Clinical, laboratory and angiographic characteristics were obtained. LT=3000 seconds was used as a cut-off value to divide patients into two groups. P value<0.05 was regarded as significant.

Results

LT of Korean CAD patients showed bimodal distribution. Median value was 1695 [IQR: 1099, 5932] and it was higher than previous data from Europeans (Figure 1). Patients with impaired ETA (LT>3000) were older and more diabetic. They showed higher creatinine, aPTT, fibrinogen, D-dimer, c-reactive protein, and proBNP values. Moreover, they had lower hemoglobin and platelet levels. Intracoronary thrombus was more frequently observed in LT>3000 group. In the multivariable regression analysis, hemoglobin (per g/dL, odds ratio 0.766, 95% confidence interval (CI) 0.632–0.928) and fibrinogen level(per 10mg/L, odds ratio 1.054, 95% CI 1.015–1.095) could significantly predict impaired ETA.

Conclusion

East Asian patients showed a right-shifted distribution of ETA compared to that of Europeans. Patients with impaired ETA had different clinical, laboratory and angiographic characteristics from those with intact ETA. Hemoglobin and fibrinogen level were significantly associated with impaired ETA. Further studies are warranted to confirm causal relationship among these factors.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Research Foundation, Republic of Korea

Small molecule activator of Nm23/NDPK as an inhibitor of metastasis

Nm23-H1/NDPK-A is a tumor metastasis suppressor having NDP kinase (NDPK) activity. Nm23-H1 is positively associated with prolonged disease-free survival and good prognosis of cancer patients. Approaches to increasing the cellular levels of Nm23-H1 therefore have significance in the therapy of metastatic cancers. We found a small molecule, (±)-trans-3-(3,4-dimethoxyphenyl)-4-[(E)-3,4-dimethoxystyryl]cyclohex-1-ene, that activates Nm23, hereafter called NMac1. NMac1 directly binds to Nm23-H1 and increases its NDPK activity. Employing various NMac1 derivatives and hydrogen/deuterium mass spectrometry (HDX-MS), we identified the pharmacophore and mode of action of NMac1. We found that NMac1 binds to the C-terminal of Nm23-H1 and induces the NDPK activation through its allosteric conformational changes. NMac1-treated MDA-MB-231 breast cancer cells showed dramatic changes in morphology and actin-cytoskeletal organization following inhibition of Rac1 activation. NMac1 also suppressed invasion and migration in vitro, and metastasis in vivo, in a breast cancer mouse model. NMac1 as an activator of NDPK has potential as an anti-metastatic agent.

Enzymatic hydrolysis of ovomucoid and the functional properties of its hydrolysates

Ovomucoid is well known as a "trypsin inhibitor" and is considered to be the main food allergen in egg. However, the negative functions of ovomucoid can be eliminated if the protein is cut into small peptides. The objectives of this study were to hydrolyze ovomucoid using various enzyme combinations, and compare the functional properties of the hydrolysates. Purified ovomucoid was dissolved in distilled water (20 mg/mL) and treated with 1% of pepsin, α-chymotrypsin, papain, and alcalase, singly or in combinations. Sodium sodium dodecyl sulfate-polyacrylamide (SDS-PAGE) results of the hydrolysates indicated that pepsin (OMP), alcalase (OMAl), alcalase+trypsin (OMAlTr), and alcalase+papain (OMAlPa) treatments best hydrolyzed the ovomucoid, and the 4 treatments were selected to determine their functional characteristics. Among the 4 enzyme treatments, hydrolysate from OMAlTr showed the highest iron-chelating and antioxidant activities, while OMP showed higher ACE-inhibitory activity, but lower Fe-chelating activity than the other treatments. However, no difference in the copper-chelating activity among the treatments was found. MS/MS analysis identified numerous peptides from the hydrolysates of OMAlPa and OMAlTr, and majority of the peptides produced were <2 kDa. Pepsin treatment (OMP), however, hydrolyzed ovomucoid almost completely and produced only amino acid monomers, di- and tri-peptides. The ACE-inhibitory, antioxidant and iron-chelating activities of the enzyme hydrolysates were not consistent with the number and size of peptides in the hydrolysates, but we do not have information about the quantity of each peptide present in the hydrolysates at this point.

Streptomyces sp. strain PGPA39 alleviates salt stress and promotes growth of 'Micro Tom' tomato plants

AIMS

To identify an actinobacterial strain that can promote growth and alleviate salinity stress in tomato plants.

METHODS AND RESULTS

Actinobacteria were isolated from agricultural soil and screened for ACC deaminase activity, production of indole acetic acid (IAA), solubilization of tricalcium phosphate and sodium chloride (NaCl) salinity tolerance. Among the several strains tested, one strain designated PGPA39 exhibited higher IAA production, and phosphate solubilization in addition to ACC deaminase activity, and tolerance to 1 mol l(-1) NaCl. Strain PGPA39 was identified as a Streptomyces strain based on 16S rDNA sequence and designated Streptomyces sp. strain PGPA39. It promoted the growth of Arabidopsis seedlings in vitro as evidenced by a significant increase in plant biomass and number of lateral roots. Salinity stress-alleviating activity of PGPA39 was evaluated using 'Micro Tom' tomato plants with 180 mmol l(-1) NaCl stress under gnotobiotic condition. A significant increase in plant biomass and chlorophyll content and a reduction in leaf proline content were observed in PGPA39-inoculated tomato plants under salt stress compared with control and salt-stressed noninoculated plants.

CONCLUSIONS

Streptomyces sp. strain PGPA39 alleviated salt stress and promoted the growth of tomato plants.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows the potential of Streptomyces sp. strain PGPA39 in alleviating salinity stress in tomato plants and could be utilized for stress alleviation in crop plants under field conditions.

WHOLE BODY NONRIGID CT-PET REGISTRATION USING WEIGHTED DEMONS

We present a new registration method for whole-body rat computed tomography (CT) image and positron emission tomography (PET) images using a weighted demons algorithm. The CT and PET images are acquired in separate scanners at different times and the inherent differences in the imaging protocols produced significant nonrigid changes between the two acquisitions in addition to heterogeneous image characteristics. In this situation, we utilized both the transmission-PET and the emission-PET images in the deformable registration process emphasizing particular regions of the moving transmission-PET image using the emission-PET image. We validated our results with nine rat image sets using M-Hausdorff distance similarity measure. We demonstrate improved performance compared to standard methods such as Demons and normalized mutual information-based non-rigid FFD registration.

SERIAL NONRIGID VASCULAR REGISTRATION USING WEIGHTED NORMALIZED MUTUAL INFORMATION

Vascular registration is a challenging problem with many potential applications. However, registering vessels accurately is difficult as they often occupy a small portion of the image and their relative motion/deformation is swamped by the displacements seen in large organs such as the heart and the liver. Our registration method uses a vessel detection algorithm to generate a vesselness image (probability of having a vessel at any given voxel) which is used to construct a weighting factor that is used to modify the intensity metric to give preference to vascular structures while maintaining the larger context. Therefore, our proposing method uses fully data-driven calculated weights and needs no prior knowledge for the weight calculation. We applied our method to the registration of serial MRI lamb images obtained from studies on tissue engineered vascular grafts and demonstrate encouraging performance as compared to non-weighted registration methods.

Biological control agent of common scab disease by antagonistic strain Bacillus sp. sunhua

AIMS

To identify an antagonistic strain against Streptomyces scabiei and to characterize the antibiotic agent. The efficacy of the isolated strain in controlling common scab disease was also evaluated.

METHODS AND RESULTS

A bacterial strain antagonistic against S. scabiei was isolated from the soil of a potato-cultivating area. This bacterium was identified as a Bacillus species by 16S rRNA gene sequence analysis and was designated Bacillus sp. sunhua. Antibiotics produced by this strain were proven to be stable within a broad pH range and at high temperatures. The culture broth was extracted with ethyl acetate, and then the crude extract was applied to HPLC. Two compounds were isolated and identified as iturin A and macrolactin A by 1H-NMR, 13C-NMR, HMBC, HMQC and mass spectrometer. The culture broth of Bacillus sp. sunhua had a suppressive effect on common scab disease in a pot assay, decreasing the infection rate from 75 to 35%. This strain also suppressed Fusarium oxysporum, the pathogen of potato dry rot disease.

CONCLUSIONS

Bacillus sp. sunhua was shown to inhibit S. scabiei effectively.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report demonstrating that macrolactin A and iturin A inhibit S. scabiei. This study demonstrated the possibility of controlling potato scab disease using Bacillus sp. sunhua.

Phylogenetic diversity of thermophilic actinomycetes and Thermoactinomyces spp. isolated from mushroom composts in Korea based on 16S rRNA gene sequence analysis

Forty one strains isolated from 21 samples of various mushroom composts in Korea were analyzed by 16S rRNA gene sequencing to investigate the phylogenetic diversity of thermophilic actinomycetes. The 25 strains of thermophilic actinomycete isolates were related to the five genera, Pseudonocardia, Saccharomonospora, Saccharopolyspora, Streptomyces, and Thermobifida, within the order Actinomycetales, and 16 strains were classified into the genus Thermoactinomyces within the family Bacillaceae. Most of 41 isolates were encompassed by two genera, Streptomyces and Thermoactinomyces, that were isolated mainly in composts prepared from waste cotton and hay, respectively. Among them, M104 and M109 were placed in distinct taxonomic positions although these strains formed phylogenetic lineages related to the genus Streptomyces and to the family Streptosporangiaceae, respectively. Therefore, a phenetic and genetic characterization of these strains will be needed to pinpoint their taxonomic position.

Alteration of substrate specificity of valine dehydrogenase from Streptomyces albus

The catabolism of branched chain amino acids, especially valine, appears to play an important role in furnishing building blocks for macrolide and polyether antibiotic biosyntheses. To determine the active site residues of ValDH, we previously cloned, partially characterized, and identified the active site (lysine) of Streptomyces albus ValDH. Here we report further characterization of S. albus ValDH. The molecular weight of S. albus ValDH was determined to be 38 kDa by SDS-PAGE and 67 kDa by gel filtration chromatography indicating that the enzyme is composed of two identical subunits. Optimal pHs were 10.5 and 8.0 for dehydrogenase activity with valine and for reductive amination activity with alpha-ketoisovaleric acid, respectively. Several chemical reagents, which modify amino-acid side chains, inhibited the enzyme activity. To examine the role played by the residue for enzyme specificity, we constructed mutant ValDH by substituting alanine for glycine at position 124 by site-directed mutagenesis. This residue was chosen because it has been considered to be important for substrate discrimination by phenylalanine dehydrogenase (PheDH) and leucine dehydrogenase (LeuDH). The Ala-124-Gly mutant enzyme displayed lower activities toward aliphatic amino acids, but higher activities toward L-phenylalanine, L-tyrosine, and L-methionine compared to the wild type enzyme suggesting that Ala-124 is involved in substrate binding in S. albus ValDH.

Valine dehydrogenase from Streptomyces albus: gene cloning, heterologous expression and identification of active site by site-directed mutagenesis

A gene encoding valine dehydrogenase (Vdh) has been cloned from Streptomyces albus, a salinomycin producer, and expressed in Escherichia coli. The S. albus Vdh is composed of 364 amino acids that showed high homology with several other amino acid dehydrogenases as well as Vdhs from Streptomyces spp. and leucine and phenylalanine dehydrogenases (Ldh and Pdh) from Bacillus spp. A protein of 38 kDa, corresponding to the approximate mass of the predicted S. albus Vdh product (38.4 kDa) exhibiting specific Vdh activity, was observed when the S. albus vdh gene was overexpressed in E. coli under the controlled T7 promoter and was subsequently purified to homogeneity. Among branched- and straight-chain amino acids, L-valine and L-alpha-aminobutyrate were the preferred substrates for the enzyme. Lys-79 and Lys-91 of S. albus Vdh were highly conserved in the corresponding region of NAD(P)(+)-dependent amino acid dehydrogenase sequences. To elucidate the functional roles of the lysyl residues, the Lys residues have individually been replaced with Ala by site-directed mutagenesis. Kinetic analyses of the Lys-79 and Lys-91-mutated enzymes revealed that they are involved in the substrate binding site and catalysis, respectively, analogous to the corresponding residues in the homologous Ldh and Pdh.

Nitrofen-induced congenital malformations of the heart and great vessels in rats: an animal model

BACKGROUND

Nitrofen (2,4-dichloro-4'-nitrodiphenyl ether), a diapheny ether herbicide, is known to induce in rat fetuses a variety of congenital cardiovascular anomalies, together with diaphragmatic hernia and hydronephrosis. The purpose of the current study was to produce congenital cardiovascular anomalies in rat fetuses by oral nitrofen administration at the indicated doses and days of gestation, and to determine the characteristics of resulting nitrofen-induced cardiovascular anomalies.

METHODS

All the observed fetuses were removed from pregnant Sprague-Dawley rats killed on the 21st day of gestation. They were preserved in 10% formalin, and dissection for examination was carried out under a dissecting microscope.

RESULTS

The following results were based on dissecting microscopic findings of 482 offspring: (1) The 11th day of gestation was the most sensitive for nitrofen induction of congenital cardiovascular anomalies. The incidence of these was dose related. (2) Ventricular septal defect was the most common single cardiovascular anomaly, representing more than half of all such irregularities. The next most common were aortic arch anomalies and tetralogy of Fallot. (3) Cardiac anomalies derived from infundibular maldevelopment such as tetralogy of Fallot and pulmonary atresia with ventricular septal defect were observed only in the group treated with nitrofen on the 11th gestational day. (4) Aortic arch anomalies were very frequent; the great majority were anomalous right subclavian artery with left aortic arch.

CONCLUSION

This animal model is suitable for further embryological investigation of the development of congenital cardiovascular anomalies.

Diagnostic pitfalls of Merkel cell carcinoma and dramatic response to chemotherapy

Merkel cell carcinoma (MCC) is an unusual malignant tumor that arises from neuroendocrine cells with features of epithelial differentiation. We describe a MCC patient with unusual clinical, histopathological, and immunohistochemical features. Although the microscopic, immunohistochemical, and ultrastructural characteristics of MCC have been well defined, diagnostic difficulties remain, particularly in distinguishing it from lymphoma involving the skin, as suggested by our case. This is an unusual case in which dense lymphoid infiltration masked the true tumor. All the immunohistochemical markers of MCC except neuron-specific enolase (NSE) were negative. The dramatic response to primary chemotherapy was also very noteworthy.

Polyamine profiles in the urine of patients with leukemia

Eleven urinary polyamine levels were determined in controls (32 cases) and 43 patients with varying stages of leukemia including initial, relapse and complete remission, using gas chromatography nitrogen-phosphorus detection. Also, to indirectly evaluate the possible involvement of enzymes, precursor to product concentration ratios were compared between controls and patients with each stage of leukemia. As a result, it is confirmed that the ratio of N1-acSpd/N8-acSpd could be used as a diagnostic marker and the level of N1,N12-diacetylspermine could be used for determining disease stage and as a malignancy marker for leukemia. An altered metabolic pathway related to leukemia is also proposed in which N1,N12-diacetylspermine can be produced directly from spermine and N1,N12-diacetylspermine is a major source of N1-acetylspermidine.

GC-MS determination of organic acids with solvent extraction after cation-exchange chromatography

We combined column and partition chromatography to isolate, purify, and quantify biological organic acids in urine and cerebrospinal fluid (CSF). Urine and CSF samples were introduced onto a preconditioned cation-exchange column (Dowex 50 W x 8 resin) to remove the biological interferences. The effluent with water was extracted with ethyl acetate two times (pH 1 and 3) and the organic acids were quantitatively converted into their trimethylsilyl derivatives for detection by gas chromatography-mass spectrometry. The good quality-control data were obtained through precision and accuracy tests. Inter- and intraassay CVs were 0.01-10.2% and 0.02-12.2%, respectively. Analytical recoveries compared favorably with results from the commonly used solvent extraction method. This method was used for the measurement of the 14 organic acids in the urine and CSF of healthy volunteers. The values obtained were in the range of the published data.

Do sheep really have problems with cardiopulmonary bypass for total artificial heart implantation?

Although the use of sheep in total artificial heart (TAH) implantation has many advantages, they are known to show a significant morbidity rate on cardiopulmonary bypass (CPB); this has been considered to be a major limiting factor in using them for TAH experiments. We conducted a series of ovine CPB experiments to evaluate the sheep's pathophysiological response to CPB. CPB-related hemolysis, bleeding, and lung dysfunction were analyzed in 5 sheep, which had undergone CPB, used at our hospital for TAH implantation. Four of the 5 sheep survived the experimental procedures, and 3 of them survived on a long-term basis. Unacceptable degrees of hemolysis related to CPB were not observed. Postoperative bleeding was not remarkable, and coagulation test results did not show significant abnormal findings. Acute lung injuries of a mild to moderate degree were found mainly at the microscopic level, but rarely had clinical significance. In conclusion, this experiment suggests that sheep can be used for the animal model for TAH implantation with acceptable risk on CPB circuits and techniques are used.

Urinary polyamine evaluation for effective diagnosis of various cancers

With a newly modified analytical method, the concentrations of free and acetylated urinary polyamines were simultaneously determined in a control group (32 cases) and patients with various types of cancers (104 cases, 20 males and 84 females) by gas chromatography-nitrogen-phosphorus detection. Significant concentration differences between normal subjects and various cancer patients were found. The various types of cancers (advanced gastric carcinoma, ovarian cancer, acute myelocyte leukemia, non-Hodgkin's lymphoma) gave unique patterns of urinary polyamine profile as well as significant differences of concentration. To indirectly evaluate the possible involvement of enzymes, precursor-to-product concentration ratios were compared between controls and patients with various types of cancers.

Excretion study of furazabol, an anabolic steroid, in human urine

Furazabol and 16-hydroxyfurazabol represented the most abundant peaks in urinary metabolic profiles for two men obtained by gas chromatography-mass spectrometry (GC-MS) after oral administration of 5 mg furazabol. The excreted amounts of unchanged furazabol were determined and its response in GC-MS was compared with that of the 16-hydroxy metabolite. The maximum excretion rates of these compounds were reached 2-3 h after oral administration. The half-lives of unchanged furazabol for two human subjects, were 1.87 and 1.29 h respectively and the recovered amount in 48 h was 24% (33% for one, 15% for the other). Also the spectrum of an unidentified metabolite is reported.

Genetic and transcriptional organization of the Bacillus subtilis spc-alpha region

We used chromosomal walking methods to isolate a 10.8-kb region from the major ribosomal protein (r-protein) gene cluster of Bacillus subtilis (Bs). The gene order in this region, given by gene product, was r-proteins L16-L29-S17-L14-L24-L5-S14-S8-L6-L18-S5-L30-L15-SecY-adenylate kinase (Adk)-methionine aminopeptidase (Map)-initiation factor 1 (IF1)-L36-S13-S11-alpha subunit of RNA polymerase-L17. The region cloned, therefore, contains the homologues for the last three genes of the Escherichia coli (Ec) S10 operon, together with entire spc and alpha operons. This Bs organization differs from the corresponding region in Ec by the inclusion of the genes encoding Adk, Map and IF1 between the genes encoding SecY and L36. Plasmid integration experiments indicated that all 22 genes comprise a single large transcriptional unit controlled from a major promoter which lies upstream from the gene encoding r-protein L16. Promoter probe experiments located lesser activities internal to this large transcriptional unit, the secY and map promoters. The secY promoter region (psecY) contained two activities, each principally functioning in the stationary growth phase when high protein export is required. Thus, the Bs S10-spc-alpha region differs from its Ec counterpart in both genetic and transcriptional organization. Given this difference in transcriptional organization, the mechanisms coordinating expression of the translational apparatus are also likely to differ between Ec and Bs.

AL072, a novel anti-Legionella antibiotic produced by Streptomyces sp

AL072 is a potent anti-Legionella antibiotic produced by Streptomyces strain AL91. The compound was isolated from the fermentation broth with 1 volume of isopropyl alcohol, followed by an ethyl acetate extraction and subsequent concentration under reduced pressure. Purification was performed on an octadecyl silica gel column followed by preparative HPLC. AL072 purified as mentioned above showed extremely specific activity only towards Legionella pneumophila. No antibacterial activity against any other bacteria tested was demonstrable. Its molecular weight was determined by FAB-MS (m/z 648) and the compound was identified as a novel 1,3-diacyl glycerol with the molecular formula C41H76O5. One of the two acyl groups is linoleyl and the other is 3,5-dimethyl octadecanoyl.

Cepacidine A, a novel antifungal antibiotic produced by Pseudomonas cepacia. I. Taxonomy, production, isolation and biological activity

Cepacidine A is a potent antifungal antibiotic produced by Pseudomonas cepacia AF 2001. The compound was isolated from the fermentation broth with 1 vol isopropyl alcohol, followed by the collection of the precipitation formed upon concentration of the extract. Purification was effected by chromatography on Diaion HP-20, alumina and reversed phase C18 followed by TLC on silica gel. These techniques afforded the two closely related compounds, cepacidine A1 and cepacidine A2. A mixture of these two compounds called capacidine A, showed high in vitro antifungal activity against the various animal and plant pathogenic fungi. The activity was diminished by the presence of serum. No antibacterial activity was demonstrable.

Cepacidine A, a novel antifungal antibiotic produced by Pseudomonas cepacia. II. Physico-chemical properties and structure elucidation

Cepacidine A is a novel glycopeptide with a potent antifungal activity, which is produced by Pseudomonas cepacia AF 2001. Its molecular weight was determined by FAB-MS (m/z 1215). The compound is comprised of glycine (1), serine (2), 2,4-diaminobutyric acid (1), aspartic acid (1), beta-hydroxy tyrosine (1), beta-hydroxy asparagine (1), xylose (1) and 5,7-dihydroxy-3,9-diamino-octadecanoic acid (1). Unfortunately, cepacidine A is a mixture of A1 and A2, either of which is barely distinguishable. Cepacidine A2 includes asparagine (1) instead of beta-hydroxy asparagine (1) of cepacidine A1. The MS data and the NOESY, TOCSY and HMBC spectra show that cepacidine A is a cyclic peptide and xylose is connected to 5,7-dihydroxy-3,9-diaminooctadecanoic acid.

Isolation of a secY homologue from Bacillus subtilis: evidence for a common protein export pathway in eubacteria

Genetic and biochemical studies have shown that the product of the Escherichia coli secY gene is an integral membrane protein with a central role in protein secretion. We found the Bacillus subtilis secY homologue within the spc-alpha ribosomal protein operon at the same position occupied by E. coli secY. B. subtilis secY coded for a hypothetical product 41% identical to E. coli SecY, a protein thought to contain 10 membrane-spanning segments and 11 hydrophilic regions, six of which are exposed to the cytoplasm and five to the periplasm. We predicted similar segments in B. subtilis SecY, and the primary sequences of the second and third cytoplasmic regions and the first, second, fourth, fifth, seventh, and tenth membrane segments were particularly conserved, sharing greater than 50% identity with E. coli SecY. We propose that the conserved cytoplasmic regions interact with similar cytoplasmic secretion factors in both organisms and that the conserved membrane-spanning segments actively participate in protein export. Our results suggest that despite the evolutionary differences reflected in cell wall architecture, Gram-negative and Gram-positive bacteria possess a similar protein export apparatus.

Gene encoding the alpha core subunit of Bacillus subtilis RNA polymerase is cotranscribed with the genes for initiation factor 1 and ribosomal proteins B, S13, S11, and L17

We describe the genetic and transcriptional organization of the promoter-distal portion of the Bacillus subtilis alpha operon. By DNA sequence analysis of the region surrounding rpoA, the gene for the alpha core subunit of RNA polymerase, we identified six open reading frames by the similarity of their products to their counterparts in the Escherichia coli transcriptional and translational apparatus. Gene order in this region, given by gene product, was IF1-B-S13-S11-alpha-L17. Gene order in E. coli is similar but not identical: SecY-B-S13-S11-S4-alpha-L17. The B. subtilis alpha region differed most strikingly from E. coli in the presence of IF1 and the absence of ribosomal protein S4, which is the translational regulator of the E. coli alpha operon. In place of the gene for S4, B. subtilis had a 177-base-pair intercistronic region containing two possible promoter sequences. However, experiments with S1 mapping of in vivo transcripts, gene disruptions in the alpha region, and a single-copy transcriptional fusion vector all suggested that these possible promoters were largely inactive during logarithmic growth, that the major promoter for the alpha operon lay upstream from the region cloned, and that the genes in the IF1 to L17 interval were cotranscribed. Thus, the transcriptional organization of the region resembles that of E. coli, wherein the alpha operon is transcribed primarily from the upstream spc promoter, but the absence of the S4 gene suggests that the translational regulation of the region may differ more fundamentally.

Gene for the alpha subunit of Bacillus subtilis RNA polymerase maps in the ribosomal protein gene cluster

We isolated the gene encoding the alpha subunit of Bacillus subtilis RNA polymerase from a lambda gt11 expression vector library by using anti-alpha antibody as a probe. Four unique clones were isolated, one carrying a lacZ-alpha gene fusion and three carrying the entire alpha coding region together with additional sequences upstream. The identity of the cloned alpha gene was confirmed by the size and immunological reactivity of its product expressed in Escherichia coli. Further, a partial DNA sequence found the predicted NH2 terminus of alpha homologous with E. coli alpha. By plasmid integration and PBS1 transduction, we mapped alpha near rpsE and within the major ribosomal protein gene cluster on the B. subtilis chromosome. Additional DNA sequencing identified rpsM (encoding S13) and rpsK (encoding S11) upstream of alpha, followed by a 180-base-pair intercistronic region that may contain two alpha promoters. Although the organization of the alpha region resembles that of the alpha operon of E. coli, the putative promoters and absence of rpsD (encoding S4) immediately preceding the B. subtilis alpha gene suggest a different regulation.