A novel phage genome integrated into a plasmid in Bacillus thuringiensis strain AF101

Bacillus thuringiensis strain AF101 possesses a single plasmid (pAF101) with a molecular size of 42 MDa (69 kb). During plasmid curing experiments in strain AF101, we found that a phage (J7W-1) was induced by ethidium bromide treatment. Moreover, the phage genome (48 kb) hybridized only with pAF101 on a Southern blot of the DNA of a cleared lysate prepared from strain AF101. Comparison of the restriction patterns of pAF101 and J7W-1 phage DNA revealed that pAF101 contains not only the entire phage DNA but also a plasmid-specific DNA region. These results indicate that the J7W-1 genome has been stably integrated into pAF101 in strain AF101. Integration of the J7W-1 genome into a plasmid was also observed after phage infection of the type strain of B. thuringiensis subsp. israelensis.     

Genomic Analysis of Mycobacterium massiliense Strain M115, an Isolate from Human Sputum

We report the draft genome sequence of a clinical isolate, strain M115, identified as Mycobacterium massiliense, a member of the newly created taxon of Mycobacterium abscessus subspecies bolletii comb. nov.     

Thioclava atlantica sp. nov., isolated from deep sea sediment of the Atlantic Ocean

A taxonomic study was carried out on strain 13D2W-2^T, which was isolated from a sulphur-oxidizing bacterial consortium, enriched by the deep-sea sediment of the Atlantic Ocean. The isolate was observed to be Gram-negative, oxidase- and catalase-positive, short rod-shaped and motile by means of a flagellum. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 4 to 41 °C, and the strain found to be able to reduce nitrate but not degrade gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 13D2W-2^T belongs to the genus Thioclava, with highest sequence similarity of 97.8 % to Thioclava dalianensis DLFJ1-1^T, followed by Thioclava pacifica TL 2^T (97.7 %), while the sequence similarities to other members of the genus were all below 97.0 %. The digital DNA:DNA hybridization estimated values between strain 13D2W-2^T and, respectively, T. dalianensis DLFJ1-1^T and T. pacifica TL 2^T were 22.6 ± 2.4 and 25.6 ± 2.4 %. The ANI values between strain 13D2W-2^T and T. dalianensis DLFJ1-1^T and T. pacifica TL 2^T were 78.49 and 81.91 % respectively. The principal fatty acid identified was Summed Feature 8 (C_18:1 ω7c/ω6c) (74.38 %). The isoprenoid quinone of strain 13D2W-2^T was identified as Q10 (100 %). The major polar lipids of strain 13D2W-2^T were found to be comprised of phosphatidylethanolamine, phosphatidylglycerol, an aminophospholipid, a glycolipid and three unknown phospholipids. The G+C content of the chromosomal DNA was determined to be 65.3 mol%. The combined genotypic and phenotypic data show that strain 13D2W-2^T represents a novel species of the genus Thioclava, for which the name Thioclava atlantica sp. nov. is proposed, with the type strain 13D2W-2^T ( = MCCC 1A02612^T = LMG 27145^T).     

Reidentification of cellulolytic enzyme-producing Trichoderma strains W-10 and G-39

Strain W-10, originally identified as Trichoderma koningii, and its supposed mutant G-39, published for production and gene expression of cellulase and xylanase, demonstrated morphological characteristics distinct from those of T. koningii, respectively. To clarify the identification derived from morphological characteristics, several methods were used, including electrophoretic karyotyping, internal transcribed spacer (ITS) analysis of rDNA, and polymerase chain reaction (PCR) fingerprinting using the universal primer L45. All the molecular characteristics showed that strains G-39 and W-10 were identical to T. reesei and T. longibrachiatum, respectively. The results strongly supported that T. koningii G-39 and W-10 should be reassigned as T. reesei and T. longibrachiatum, respectively. Strain G-39 should be considered a mutant from T. reesei QM9414 whose spores were contaminated with those of strain W-10 during a laboratory operation. According to this, we declare that T. koningii G-39 and W-10 must be renamed as T. reesei and T. longibrachiatum, respectively.     

Proposal of Mycobacterium peregrinum sp. nov., nom. rev., and elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to species status: Mycobacterium abscessus comb. nov.

We studied the taxonomic positions of the rapidly growing organism Mycobacterium fortuitum and phenotypically related organisms. We confirmed that "Mycobacterium peregrinum" ATCC 14467T (T = type strain) is genetically independent of M. fortuitum ATCC 6841T by using various DNA hybridization conditions. Strains that were genetically identified as "M. peregrinum" were phenotypically differentiated from M. fortuitum ATCC 6841T. Thus, we propose that "M. peregrinum" should be revived as an independent species, Mycobacterium peregrinum sp. nov., nom. rev. The type strain is strain ATCC 14467. M. fortuitum subsp. acetamidolyticum ATCC 35931T exhibited a high level of DNA relatedness to M. fortuitum ATCC 6841T. The hybridized DNAs maintained stable heteroduplexity at high stringency; thus, we confirmed that M. fortuitum subsp. acetamidolyticum is identical to M. fortuitum ATCC 6841T. We found that M. chelonae subsp. abscessus ATCC 19977T is genetically different from M. chelonae subsp. chelonae NCTC 946T on the basis of the results of quantitative hybridization even under optimal conditions. There was no reason to maintain this organism as a subspecies of M. chelonae. Thus, we propose that M. chelonae subsp. abscessus should be elevated to species status as Mycobacterium abscessus (Kubica et al.) comb. nov. The type strain is strain ATCC 19977.     

Induction of the acrosome reaction in guinea pig spermatozoa by calmodulin antagonist W-7

The effect of the calmodulin antagonist W-7 on the capacitation and the acrosome reaction of guinea pig spermatozoa was examined. The characteristic features of the acrosome reaction induced by W-7 were the dependence on the composition and pH of the medium and on the presence of sodium bicarbonate. The most effective concentration of W-7 for inducing the acrosome reaction was approximately 5 μM, which is far less than the Kd for calmodulin. Moreover, W-7 enhanced the ability of spermatozoa to acquire capacitation in a Ca²⁺-free medium. The spermatozoa induced to undergo the acrosome reaction by W-7 were capable of penetrating the zona-free hamster eggs. W-5, which has a lower affinity for calmodulin than W-7, also induced the acrosome reaction in the same manner as W-7. These results suggest that the naphthalenesulfonamide derivatives W-7 and W-5 can induce the acrosome reaction in guinea pig spermatozoa via capacitation in a pH-dependent, Ca²⁺-calmodulin-independent manner.     

Ethanol fermentation of beet molasses by a yeast resistant to distillery waste water and 2-deoxyglucose

A flocculent killer yeast, Saccharomyces cerevisiae strain H-1, which was selected for ethanol fermentation of beet molasses, has a tendency to lose its viability in distillery waste water (DWW) of beet molasses mash after ethanol fermentation. Through acclimations of strain H-1 in DWW, strain W-9, resistant to DWW, was isolated. Strain M-9, resistant to 2-deoxyglucose was further isolated through acclimations of strain W-9 in medium containing 150 ppm 2-deoxyglucose. A fermentation test of beet molasses indicated that the ethanol productivity and sugar consumption were improved by strain M-9 compared to the parental strain H-1 and strain W-9. The concentration of ethanol produced by strain M-9 was 107.2 g/l, and the concentration of residual sugars, which were mainly composed of sucrose and fructose, were lower than those produced by the parental strain H-1 and strain W-9 at the end of fermentation of beet molasses.     

Cross-resistance to insecticides in a malathion-resistant strain of Ceratitis capitata (Diptera: Tephritidae)

Resistance to malathion has been reported in field populations of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), in areas of Spain where an intensive use of this insecticide was maintained for several years. The main goal of this study was to determine whether resistance to malathion confers cross-resistance to different types of insecticides. Susceptibility bioassays showed that the malathion-resistant W-4Km strain (176-fold more resistant to malathion than the susceptible C strain) has moderate levels of cross-resistance (three- to 16-fold) to other organophosphates (trichlorphon, diazinon, phosmet and methyl-chlorpyrifos), the carbamate carbaryl, the pyrethroid lambda-cyhalothrin, and the benzoylphenylurea derivative lufenuron, whereas cross-resistance to spinosad was below two-fold. The W-4Km strain was selected with lambda-cyhalothrin to establish the lambda-cyhalothrin-resistant W-1Klamda strain (35-fold resistant to lambda-cyhalothrin). The synergistic activity of the esterase inhibitor DEF with lambda-cyhalothrin and the increase in esterase activity in the W-1Klamda strain suggests that esterases may be involved in the development of resistance to this insecticide. Our results showed that resistance to malathion may confer some degree of cross-resistance to insecticides currently approved for the control of Mediterranean fruit fly in citrus crops (lambda-cyhalothrin, lufenuron, and methyl-chlorpyrifos). Especially relevant is the case of lambda-cyhalothrin, because we have shown that resistance to this insecticide can rapidly evolve to levels that may compromise its effectiveness in the field.     

Combined use of <Emphasis Type="Italic">GAP</Emphasis> and <Emphasis Type="Italic">AOX1</Emphasis> promoters and optimization of culture conditions to enhance expression of <Emphasis Type="Italic">Rhizomucor miehei</Emphasis> lipase

Rhizo mucor miehei lipase (RML) is an industrially important enzyme, but its application is limited due to its high cost. In this study, a series of measures such as codon optimization, propeptide addition, combined use of GAP and AOX1 promoters, and optimization of culture conditions were employed to increase the expression of RML. Three transformants of the constitutive-inducible combined Pichia pastoris strains were generated by transforming the pGAPZαA-rml vector into the pPIC9K-rml/GS115 strain, which resulted in high-expression yields of RML. Using the shake flask method, highest enzyme activity corresponding to 140 U/mL was observed in the strain 3-17, which was about sixfold higher than that of pPIC9K-rml/GS115 or pGAPZαA-rml/GS115. After optimization of culture conditions by response surface methodology, the lipolytic activity of strain 3-17 reached 175 U/mL in shake flasks. An increase in the copy number simultaneously with the synergistic effect provided by two promoters led to enhanced degree of protein expression.     

Comparison of NaOH-N-acetyl cysteine and sulfuric acid decontamination methods for recovery of mycobacteria from clinical specimens

We compared the NaOH-N-acetyl cysteine (NaOH-NALC) and the sulfuric acid decontamination procedure in the detection of mycobacteria using the Mycobacteria Growth Indicator Tube (MGIT). In total 219 sputum specimens were collected from 142 Zambian patients and subjected to mycobacterial culture. One half of the specimen was decontaminated with NaOH-NALC and the other half was decontaminated with sulfuric acid. From the 438 samples a total of 261 (60%) cultures yielded growth of mycobacteria, consisting of 22 different species. The sulfuric acid method was more successful than the NaOH-NALC method in recovering mycobacteria in MGITs (146 versus 115 respectively, p = 0.001). Of the 146 positive mycobacterial cultures recovered after sulfuric acid decontamination 28 were Mycobacterium tuberculosis, 84 nontuberculous mycobacteria (NTM) and 34 acid fast bacterial isolates which could not be identified to the species level. The 115 mycobacteria recovered by the NaOH-NALC method consisted of 34 M. tuberculosis strains, 55 NTM and 26 acid fast bacteria that could not be identified. The most frequently isolated NTM were Mycobacterium lentiflavum and Mycobacterium intracellulare. Comparing the two decontamination methods the recovery of NTM in the sulfuric acid group was significant higher than in the NaOH-NALC group (p = 0.001). In contrast, no significant difference was found for the recovery of M. tuberculosis. These results show that the decontamination method used affects the recovery of nontuberculous mycobacteria in particular.     

O-chain expression in the rough Brucella melitensis strain B115: induction of O-polysaccharide-specific monoclonal antibodies and intracellular localization demonstrated by immunoelectron microscopy.

Spleen cells from mice infected with the rough Brucella melitensis strain B115 were fused with NSO myeloma cells. Hybridoma supernatants were screened in ELISA with cell walls (CW), sonicated cell extracts (CE) and rough lipopolysaccharide (R-LPS) of B. melitensis strain B115 and whole B. melitensis B115 cells. Surprisingly, 22 monoclonal antibodies (mAbs) reacting in ELISA with both CW and CE but not with R-LPS and bacterial cells were shown by immunoblot analysis and ELISA to react with smooth lipopolysaccharide (S-LPS). These mAbs also reacted in ELISA with O polysaccharides (OPS) from the smooth Brucella abortus strain 99 and the smooth B. melitensis strain 16M and thus recognize epitopes present on the O-chain. Proteinase K LPS preparations from B. melitensis B115 analysed by immunoblotting with one mAb (12G12) recognizing S-LPS of both A and M specificity displayed the typical S-LPS high-molecular-mass ladder pattern but no S-LPS was detected in the phenol/water/chloroform/light petroleum LPS preparation of the same strain. mAb 12G12, specific for S-LPS, and a mAb (A68/03F03/D05) specific for R-LPS were used to localize the O-chain and R-LPS expressed in B. melitensis strain B115 by immunoelectron microscopy. Immunogold labelling was observed at the surface of B. melitensis B115 cells with the anti-R-LPS mAb but not with the anti-S-LPS mAb. In ultrathin sections, immunogold labelling with the S-LPS specific mAb was observed in the cytoplasm and in the periphery of the cytoplasm, probably at the cytoplasmic membrane.(ABSTRACT TRUNCATED AT 250 WORDS)     

Influence of Bacteriophage PBS1 and φW-14 Deoxyribonucleic Acids on Homologous Deoxyribonucleic Acid Uptake and Transformation in Competent Bacillus subtilis

Both bacteriophage PBS1 deoxyribonucleic acid (DNA) (in which all the thymine residues are replaced by uracil) and phage W-14 DNA [in which half the thymine residues are replaced by 5-(aminobutylaminomethyl)uracil or 5-putrescinylthymine] exhibit comparable competing abilities for uptake of homologous DNA in a Bacillus subtilis competent system. But, whereas PBS1 DNA leads to a decrease in transformation frequencies compatible with its competing ability for DNA uptake, W-14 DNA decreases transformation frequencies by a factor up to eightfold higher. The effect of W-14 DNA on transformation frequencies is visible even at a concentration level that does not decrease transforming DNA uptake. No such effect was observed with heterologous DNA containing presumably ionically bound putrescine. Low concentrations of W-14 DNA decreased the number of double (nonlinked) transformants more than single transformants. The influence on transformation was abolished when W-14 DNA was added 20 min after addition of transforming DNA, i.e., when the recombination process was terminated. The putrescine-containing DNA also decreased retention of trichloroacetic acid-precipitable radioactivity of homologous DNA taken up. We conclude that W-14 DNA inhibits some intracellular process(es) at the level of recombination. In addition, there is evidence that W-14 DNA, but not heterologous DNA with ionically bound putrescine, binds also to site(s) on the cell surface other than receptors for homologous DNA.     

Comparison of the Pathogenicity for Mice of Mycobacterium fortuitum and Mycobacterium abscessus

The pathogenicity for mice of 12 strains of Mycobacterium abscessus was compared with that for 8 strains of M. fortuitum. Both species caused lesions in kidneys and produced "spinning disease" resulting from inner ear infections. No major differences in pathogenicity of these two species were demonstrated. Strain to strain variation was marked, especially with M. abscessus. For example, 1.6 x 10(6) organisms of strain 11188 of M. abscessus produced death in four of five animals within 42 days, whereas strain 380 of M. abscessus failed to produce any deaths within 42 days. In the case of M. fortuitum, the greatest mortality observed was one of five animals, yet the incidence of spinning disease and kidney disease occurred earlier postinfection than in mice infected with M. abscessus. Histologically, abscess formation by a strain of M. abscessus was greater than by a strain of M. fortuitum, but this difference cannot be interpreted as a species difference.     

Stably Sustained Hydrogen Production with High Molar Yield through a Combination of a Marine Green Alga and a Photosynthetic Bacterium

Stably sustained continuous production of hydrogen with high molar yield was achieved through a combination of dark fermentative hydrogen evolution by Chlamydomonas sp. strain MGA161 and hydrogen photoevolution by a marine photosynthetic bacterium W-1S in an alternating light-dark cycle as a model of the day-night cycle. The newly isolated strain W-1S could use acetic acid and ethanol excreted by strain MGA161 as electron donors for hydrogen photoevolution. The fermentation broth of strain MGA161 stimulated the hydrogen photoproduction of strain W-1S. This alga-bacterial combination had a high conversion yield of 8 mol H₂/mol of glucose of starch, with the possibility of improvement up to 10.5.     

Detection of genes encoding cholera toxin (CT), zonula occludens toxin (ZOT), accessory cholera enterotoxin (ACE) and heat-stable enterotoxin (ST) in Vibrio mimicus clinical strains

A total of 51 clinical strains of Vibrio mimicus were searched for the presence of virulence-associated genes, like ctx, zot or ace genes which locate in "cholera virulence cassette," and the st gene by polymerase chain reaction. Moreover, the pathological potential of each clinical strain was also examined by rabbit ileal loop (RIL). Three strains showed to have the ctx gene, of which only one strain was zot gene-positive. Meanwhile, one other strain was zot+ but ctx-. All of these four strains were found to have the ace gene and to belong to serogroup O115. Nine strains showed to carry the st gene. However, none of these ST-gene-positive strains was indicated to contain the genes located in the "cholera virulence cassette." It is of interest to note that all of the RIL-positive and/or virulence gene-positive strains were restricted to three serogroups, O20, O41 and O115. These results suggest a significant association between O antigens and enterotoxic activities in V. mimicus clinical strains, and clearly demonstrate multifactorial virulence potentials of this human pathogen.     

金针菇漆酶基因的克隆及其在毕赤酵母中的表达研究

综合运用cDNA末端快速扩增 (RapidAmplificationofcDNAEnds ,RACE )和基因组步行等技术克隆到一个金针菇 (Flammulinavelutipes)的漆酶结构基因和其对应的全长cDNA ,经测序和BLAST比对分析表明该基因属于多铜氧化酶基因家族 ,与已发表的漆酶基因 (AF176 2 30 )的同源性最高 ,在氨基酸水平为 72 %。该结构基因命名为gl ccFv,cDNA命名为lccFv ,其序列提交GenBank ,登录号分别为AY4 85 82 6和AY4 5 0 4 0 6。将lccFv的开放阅读框克隆到毕赤酵母表达载体pHBM90 6 ,转化毕赤酵母GS115且实现了分泌表达。将重组毕赤酵母GS115 (pHBM5 6 5 )诱导产酶 ,在培养温度 2 0℃、甲醇流加量为 1 0 % (V V)的情况下 ,其分泌表达的LCCFv的最高酶活为 0 10 70U mL ,最适反应温度为 4 5℃ ,最适反应pH值为 3 9,在最适反应条件下其热稳定性和pH值稳定性均较好     

Quantitative radioautographic study of intracellular localization of calmodulin antagonist,W-7, in Chinese-hamster ovary cells

Summary The purpose of the present study was to analyse quantitatively the localization of calmodulin antagonist, n-(6-aminohexyl)-5-chloro-1-naphthalene-sulfonamide (W-7) in CHO-Kl cells. The cultured CHO-Kl cells were labelled with 1 (16.7 M), 2 (33.4 M), 5 (83.5 M) and 10 Ci/ml (167 M) tritiated W-7. Some cells were preincubated in 10, 50 and 100 M unlabelled W-7 for 30 min and then labelled with 2 or 5 Ci/ml tritiated W-7 for 1 h. The cells were doubly fixed in glutaraldehyde and osmium-tetroxide solution, and embedded in Epon. For light-microscopic radioautography, 2 m-thick sections were wet mounted with radioautographic emulsion and exposed for 1 month. The radioautograms showed that large numbers of silver grains were mainly localized in the cytoplasm as well as in the nucleus. Quantitative analysis demonstrated that, in both the cytoplasm and nucleus, the number of silver grains was dependent on the concentration of the administered tritiated W-7 and the number was dramatically decreased by the pretreatment of unlabelled W-7. These results show that, in CHO-Kl cells, the W-7 binding sites are saturable. It is concluded that W-7 may get into CHO-Kl cells and be bound to a specific protein that may be calmodulin protein.     

Isolation and characterization of a Mycobacterium strain that metabolizes the insecticide endosulfan

AIM: The aim of this study was to isolate and characterize a bacterium capable of metabolizing endosulfan. METHODS AND RESULTS: A endosulfan-degrading bacterium (strain ESD) was isolated from soil inoculum after repeated culture with the insecticide as the sole source of sulfur. Analysis of its 16S rRNA gene sequence, and morphological and physiological characteristics revealed it to be a new fast-growing Mycobacterium, closely related to other Mycobacterium species with xenobiotic-degrading capabilities. Degradation of endosulfan by strain ESD involved both oxidative and sulfur-separation reactions. Strain ESD did not degrade endosulfan when sulfite, sulphate or methionine were present in the medium along with the insecticide. Partial degradation occurred when the culture was grown, with endosulfan, in the presence of MOPS (3-(N-morpholino)propane sulphonic acid), DMSO (dimethyl sulfoxide), cysteine or sulphonane and complete degradation occurred in the presence of gutathione. When both beta-endosulfan and low levels of sulphate were provided as the only sources of sulfur, biphasic exponential growth was observed with endosulfan metabolism being restricted to the latter phase of exponential growth. CONCLUSIONS: This study isolated a Mycobacterium strain (strain ESD) capable of metabolizing endosulfan by both oxidative and sulfur-separation reactions. The endosulfan-degrading reactions are a result of the sulfur-starvation response of this bacterium. SIGNIFICANCE AND IMPACT OF THE STUDY: This describes the isolation of a Mycobacterium strain capable of degrading the insecticide endosulfan. This bacterium is a valuable source of enzymes for use in enzymatic bioremediation of endosulfan residues.     

新型抗结核分枝杆菌药物筛选模型的建立

为建立基于酶水平和细胞水平的新型抗结核分枝杆菌（Mycobacterium tuberculosis）药物的筛选模型,以M.tuberculosis H37Rv基因组DNA为模板,PCR特异性扩增异柠檬酸裂解酶（ICL）基因,构建表达载体,在E.coli BL21（DE3）中高效表达,使用N i2＋亲和层析柱纯化重组ICL,检测其活性。优化ICL酶反应条件,考察待筛选样品溶剂对酶活性的影响,建立ICL抑制剂酶水平筛选模型;考察与优化耻垢分枝杆菌（Mycobacterium smegma）在以乙酸盐为唯一碳源的培养基中的生长状况,建立基于M.sm egma的乙醛酸代谢途径抑制剂的细胞水平筛选模型;利用上述2种筛选模型对1 060种可能具有拮抗活性的微生物代谢样品进行初筛和复筛,两者筛选结果正相关性较好。     

Genomic stability over 9 years of an isoniazid resistant Mycobacterium tuberculosis outbreak strain in Sweden

In molecular epidemiological studies of drug resistant Mycobacterium tuberculosis (TB) in Sweden a large outbreak of an isoniazid resistant strain was identified, involving 115 patients, mainly from the Horn of Africa. During the outbreak period, the genomic pattern of the outbreak strain has stayed virtually unchanged with regard to drug resistance, IS6110 restriction fragment length polymorphism and spoligotyping patterns. Here we present the complete genome sequence analyses of the index isolate and two isolates sampled nine years after the index case as well as experimental data on the virulence of this outbreak strain. Even though the strain has been present in the community for nine years and passaged between patients at least five times in-between the isolates, we only found four single nucleotide polymorphisms in one of the later isolates and a small (4 amino acids) deletion in the other compared to the index isolate. In contrast to many other evolutionarily successful outbreak lineages (e.g. the Beijing lineage) this outbreak strain appears to be genetically very stable yet evolutionarily successful in a low endemic country such as Sweden. These findings further illustrate that the rate of genomic variation in TB can be highly strain dependent, something that can have important implications for epidemiological studies as well as development of resistance.