Characterization of 13 newly isolated strains of anaerobic, cellulolytic, thermophilic bacteria

Characteristics of 13 newly isolated thermophilic, anaerobic, and cellulolytic strains were compared with previously described strains of Clostridium thermocellum: ATCC 27405 and JW20 (ATCC 31549). Colony morphology, antibiotic sensitivity, fermentation end-products, and cellulose degradation were documented. All 13 strains were sensitive to erythromycin (5 μg/ml) and chloramphenicol (25 μg/ml), and all strains but one were sensitive to kanamycin (20 μg/ml). Polymerase chain reaction (PCR) amplification using primers based on gene sequences from C. thermocellum ATCC 27405 was successful for all 13 strains in the case of the hydrogenase gene and 11 strains in the case of phosphotransacetylase/acetate kinase genes. Ten strains amplified a product of the expected size with primers developed to be specific for C. thermocellum 16SrRNA primers. Two of the 13 strains did not amplify any product with the PCR primers designed for the phosphotransacetylase/acetate kinase and 16SrRNA primers. A MboI-like GATC- recognizing restriction activity was present in all of the five strains examined. The results of this study have several positive implications with respect to future development of a transformation system for cellulolytic thermophiles. Journal of Industrial Microbiology & Biotechnology (2001) 27, 275–280. Received 12 September 2000/ Accepted in revised form 20 November 2000     

Overexpression of Arylsulfate Sulfotransferase as Fusion Protein with GlutathioneS-Transferase

A procedure has been developed for the overexpression and purification of milligram quantities of theKlebsiellaK-36 arylsulfate sulfotransferase (ASST). The structural gene was amplified by means of a polymerase chain reaction (PCR) technique and inserted into the plasmid vector pGEX-3X. The plasmid pGEX-100, carrying theKlebsiellaK-36astAstructural gene under the control of theEscherichia coli tacpromoter, was transformed into theE. colistrain BL21 (DE3). The ASST was produced inE. colias a fusion with glutathioneS-transferase. Conditions for protein production, isolation on glutathione Sepharose 4B, and Xa cleavage to generate active ASST were developed. The purification yielded approximately 0.7 mg of pure enzyme per liter of bacterial culture. Kinetic analysis of the overexpressed enzyme indicated that it had kinetic properties almost the same as those of the enzyme purified fromKlebsiellaK-36 cells. The purification procedure was very rapid and is suitable for obtaining considerable amounts of enzyme at a relatively high yield compared with its purifying method from the culture of theKlebsiellaK-36 strain.     

New solvent-producing Clostridium sp. strains, hydrolyzing a wide range of polysaccharides, are closely related to Clostridium butyricum

Thirteen new Clostridium strains, previously isolated from soil and found to produce high amounts of solvents from glucose, hydrolyzed a great variety of α- and β-glycans, including raw starch, xylan, pectin, inulin and cellulose. The sequences of the PCR-amplified DNA fragments containing the variable 3′ part of one of the 16S rRNA genes were 99.5% identical. The macrorestriction pattern of two endonucleolytic digests of chromosomal DNA in the pulsed-field gel electrophoresis (PFGE) confirmed their high homogeneity on the DNA level. The complete 16S rRNA gene sequence of three selected strains was 99.8% identical to the 16S rRNA gene sequence from Clostridium butyricum and separates them from C. acetobutylicum. To the closely related four species of solventogenic clostridia a new group of strains has to be added, which has a great potential for the direct fermentation of biomass. Journal of Industrial Microbiology & Biotechnology (2001) 27, 329–335. Received 12 September 2000/ Accepted in revised form 25 July 2001     

Cloning, expression and characterization of l-aspartate β-decarboxylase gene from Alcaligenes faecalis CCRC 11585

l -Aspartate β-decarboxylase (Asd) is an important enzyme to produce l-alanine and d-aspartate. The genomic library of Alcaligenes faecalis CCRC 11585 was cloned into pBK-CMV and transformed into Escherichia coli. One clone, which carried the asd gene and expressed Asd activity, was isolated and chosen for further study. PBK-asdAE1 was subcloned and its sequence analysis revealed an open reading frame, consisting of 1599 bp, that encodes a 533-amino-acid polypeptide. The nucleotide sequence of the asd gene from A. faecalis CCRC 11585 (asdA) showed 84% identity with that from Pseudomonas dacunhae CCRC 12623, and the amino acid sequence showed 93% identity. The amino acid sequence of the AsdA showed 51–58% homology with various aminotransferases. Alignment of the AsdA with several aspartate or tyrosine aminotransferases revealed 17 conserved amino acids that appeared in most of the conserved amino acid residues within the pyridoxal-5′-phosphate (PLP) binding domains of aminotransferases. Furthermore, the asdA gene was cloned into expression vector pET-21a and transformed into E. coli BL21(DE3). A protein band sized at 61 kDa is present on the SDS-PAGE gel from the intracellular soluble form of E. coli BL21(DE3)/pET-asdA. The specific activities of the pET-AsdA purified by using His-Bind chromatography is 215 U/mg at 45°C and pH 5.0, which is 1000-fold higher than that of the A. faecalis crude extract. This is the first report of an asdA gene sequence from A. faecalis and represents the potential application of a recombinant AsdA for production of l-alanine or d-aspartic acid. Journal of Industrial Microbiology & Biotechnology (2000) 25, 132–140. Received 02 November 1999/ Accepted in revised form 23 June 2000     

Development of marker-free strains of Bacillus subtilis capable of secreting high levels of industrial enzymes

Different strategies have been employed to achieve high-level expression of single-copy genes encoding secreted enzymes in Bacillus subtilis. A model system was developed which utilizes the aprL gene from Bacillus clausii as a reporter gene for monitoring expression levels during stationary phase. An exceptionally strong promoter was constructed by altering the nuceotide sequence in the −10 and −35 regions of the promoter for the amyQ gene of Bacillus amyloliquefaciens. In addition, two or three tandem copies of this promoter were shown to increase expression levels substantially in comparison to the monomer promoter alone. Finally, the promoter and mRNA stabilization sequences derived from the cry3A gene of Bacillus thuringiensis were used in combination with the mutant amyQ promoter to achieve the highest levels of aprL expression. These promoters were shown to be fully functional in a high-expressing Bacillus strain grown under industrial fermentation conditions. The ability to obtain maximum expression levels from a single copy gene now makes it feasible to construct environmentally friendly, marker-free industrial strains of B. subtilis. Journal of Industrial Microbiology & Biotechnology (2000) 25, 204–212. Received 05 January 2000/ Accepted in revised form 26 June 2000     

Regulation of Arksulfate Sulfotransferase from a Human Intestinal Bacterium by Nucleotides and Magnesium Ion

Abstract

Arylsulfate sulfotransferase (ASST) from a human intestinal bacterium stoichiometrically catalyzed the transfer of a sulfate group from phenylsulfate esters to phenolic compounds. Pentachlorophenol, one of the selective inhibitors of phenol sulfoconjugation in mammalian tissues, inhibited both phenol and tyramine sulfation by ASST Nucleotide triphosphaies such as ATP, GTP, UTP and CTP, and pyrophosphate inhibited the ASST activity, whereas Mg²⁺ and Mn²⁺ activated the enzyme and prevented its inhibition by ATP and pyrophosphate. Equimolar binding of [α-] and [γ-³²P]ATP to the enzyme showed that the enzyme protein was not phospholylated, but bound ATP. These results suggest that nucleotide triphosphates and divalent cations are important modulators in the control of ASST activity.     

Characterization of an echinocandin B-producing strain blocked for sterigmatocystin biosynthesis reveals a translocation in the stcW gene of the aflatoxin biosynthetic pathway

Echinocandin B (ECB), a lipopolypeptide used as a starting material for chemical manufacture of the anti-Candida agent LY303366, is produced by fermentation using a strain of Aspergillus nidulans. In addition to ECB, the wild-type strain also produces a significant level of sterigmatocystin (ST), a potent carcinogen structurally related to the aflatoxins. Characterization of a mutant designated A42355-OC-1 (OC-1), which is blocked in ST biosynthesis, was the result of a chromosomal translocation. The chromosomal regions containing the breakpoints of the translocation were isolated and DNA sequencing and PCR analysis of the chromosomal breakpoints demonstrated the translocation occurred within the stcW gene of the ST biosynthetic pathway, resulting in disruption of the open reading frame for this gene. Biochemical feeding studies indicate the involvement of this gene product in the conversion of averufin to 1-hydroxy versicolorone. This work demonstrates an effective synergy between classical strain improvement methods and molecular genetics. Journal of Industrial Microbiology & Biotechnology (2000) 25, 333–341. Received 27 April 2000/ Accepted in revised form 25 November 2000     

Expression of the creatininase gene from Pseudomonas putidaRS65 in Escherichia coli

The gene encoding creatininase from Pseudomonas putida RS65 was cloned, sequenced and expressed in Escherichia coli. One plasmid containing a 7.0-kb HindIII insert was selected by its ability to express creatininase activity. After deletion of the adjacent restriction fragments, a 1.1-kb SphI fragment, which contained the full length of the creatininase gene, was subcloned into a pUC18 vector and the nucleotide sequence of the creatininase gene was determined. The gene consists of 771 base pairs and encodes a protein of 257 amino acids. The constitutive creatininase productivity of E. coli DH5α (pCRN741) cultured in broth was about 8.5-fold higher than that of P. putida RS65 cultured in a creatinine-containing medium. The creatininase gene was expressed efficiently in E. coli from its own promoter. Journal of Industrial Microbiology & Biotechnology (2000) 24, 2–6. Received 02 April 1999/ Accepted in revised form 31 July 1999     

Cultural and biochemical diversity of pink-pigmented bacteria isolated from paper mill slimes

A study of 25 paper mill slime deposits and one additive revealed nine pink-pigmented bacterial isolates, eight of which were different from pink-pigmented bacteria identified in the paper industry in the middle 1900s. The pink-pigmented bacteria described previously in pulp and paper included Micrococcus agilis, Bacillus subtilis, Serratia sp. and Alcaligenes viscosus. With the exception of one isolate, Micrococcus sp., these isolates possessed many cultural, biochemical and chemical properties which were different from the ones previously reported for paper mills. Eight of these bacteria were Gram-negative rods or filamentous, aerobic and positive for catalase production. Two isolates were methylotrophic, oxidizing methanol and identified as Methylobacterium zatmanii. Cellular fatty acid analysis and other characteristics showed one isolate to be Roseomonas sp. Using 16S rRNA gene sequencing, one isolate which was a Gram-negative rod was identified as Deionococcus grandis. Four bacteria had cells that were long or filamentous and these were isolated from mills with pink slime problems. The identity of one of the filamentous bacteria was determined by 16S rRNA gene sequencing to be close to Flectobacillus sp. strain MWH38. Most of the isolates were susceptible to 11 industrial biocides. Journal of Industrial Microbiology & Biotechnology (2000) 25, 74–80. Received 28 January 2000/ Accepted in revised form 09 June 2000     

The catechol 2,3-dioxygenase gene and toluene monooxygenase genes from Burkholderia sp. AA1, an isolate capable of degrading aliphatic hydrocarbons and toluene

Burkholderia sp. AA1 isolated from a diesel fuel-contaminated site degraded toluene, as well as a wide range of alkanes from decane (C₈) to pentacosane (C₂₅) as sole carbon and energy sources. This strain also utilized m-toluate, p-toluate, o-toluate, and m-cresol as sole carbon and energy sources. Toluene- and toluate-grown cells showed catechol 2,3-dioxygenase activity and indole oxidation activity that is exhibited by some toluene oxygenation enzymes. The catechol 2,3-dioxygenase gene (catB) was cloned and sequenced. Its deduced amino acid sequence is analogous to the extradiol dioxygenases cloned from a variety of microorganisms. A DNA fragment containing the genes for the indole oxidation activity was cloned and sequenced. A seven-gene cluster designated as tbhABCDEFG was identified. Significant similarities were found with multicomponent monooxygenase systems for toluene, benzene and phenol from different bacterial strains. Journal of Industrial Microbiology & Biotechnology (2000) 25, 127–131. Received 28 July 1999/ Accepted in revised form 28 June 2000     

Characterization of a maltose transport system in Clostridium acetobutylicum ATCC 824

The utilization of maltose by Clostridium acetobutylicum ATCC 824 was investigated. Glucose was used preferentially to maltose, when both substrates were present in the medium. Maltose phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) activity was detected in extracts prepared from cultures grown on maltose, but not glucose or sucrose, as the sole carbon source. Extract fractionation and PTS reconstitution experiments revealed that the specificity for maltose is contained entirely within the membrane in this organism. A putative gene system for the maltose PTS was identified (from the C. acetobutylicum ATCC 824 genome sequence), encoding an enzyme II^Mal and a maltose 6-phosphate hydrolase. Journal of Industrial Microbiology & Biotechnology (2001) 27, 298–306. Received 12 September 2000/ Accepted in revised form 30 November 2000     

Large-scale production of GDP-fucose and Lewis X by bacterial coupling

A large-scale production system of GDP-fucose (GDP-Fuc) and fucosylated oligosaccharides was established by the combination of recombinant Escherichia coli cells overexpressing GDP-Fuc biosynthetic genes and Corynebacterium ammoniagenes cells. E. coli cells overexpressed the genes for glucokinase, phosphomannomutase, mannose-1-phosphate guanylyltransferase, GDP-mannose (GDP-Man) dehydratase, and GDP-4-keto-6-deoxy-mannose (GKDM) epimerase/reductase as well as phosphoglucomutase and phosphofructokinase. C. ammoniagenes contributed to the formation of GTP from GMP. GDP-Fuc accumulated to 29 mM (18.4 g l⁻¹) after a 22-h reaction starting with GMP and mannose through introducing the two-step reaction to overcome the inhibition of GDP-Fuc on GDP-Man dehydratase activity. When E. coli cells overexpressing the α1,3-fucosyltransferase gene of Helicobacter pylori were put into the GDP-Fuc production system, Lewis X [Galβ1–4(Fucα1–3)GlcNAc] was produced at an amount of 40 mM (21 g l⁻¹) for 30 h from GMP, mannose, and N-acetyl lactosamine. The production system through bacterial coupling can be applied to the industrial manufacture of fucosylated oligosaccharides. Journal of Industrial Microbiology & Biotechnology (2000) 25, 213–217. Received 01 May 2000/ Accepted in revised form 20 July 2000     

Oxidative-stress-induced production of pyocyanin by Xanthomonas campestris and its effect on the indicator target organism, Escherichia coli

Pyocyanin, a potential antimicrobial agent, was secreted by Xanthomonas campestris. Treatments with agents causing oxidative stress in the organism caused up to 4.4-fold increase in pyocyanin production. Pyocyanin added in the extracellular space did not affect growth rate of X. campestris, but decreased maximum cell concentration and specific product formation. However, the growth of Escherichia coli, the indicator target organism, was affected by pyocyanin. There was also a significant increase in the intracellular reactive oxygen species (ROS) concentration and antioxidant enzyme [catalase, superoxide dismutase (SOD)] concentrations, in the presence of pyocyanin. The intracellular ROS concentrations in E. coli formed upon exposure to pyocyanin, which is an indicator of the toxicity, was dependent on the growth phase of the organism. Studies with mutants of E. coli showed that intracellular ROS concentration was not significantly affected by the absence of the regulon OxyR, but, was significantly higher in cases when the regulon rpoS or the genes katG or katE were absent. Journal of Industrial Microbiology & Biotechnology (2000) 25, 266–272. Received 08 May 2000/ Accepted in revised form 04 August 2000     

A series of laboratory exercises utilizing luxR gene of Vibrio fischeri and gfp gene of Aequoria victoria to teach the broad applications of polymerase chain reaction

Three experiments are described; directional cloning of the luxR gene from the bioluminescent marine bacterium, Vibrio fischeri, directional cloning of the gfpgene from the marine jelly fish, Aequoria victoria, and the construction of a LuxR-GFP fusion protein. Experiments are presented using lux and gfp in an undergraduate biology curriculum. Journal of Industrial Microbiology & Biotechnology (2000) 24, 345–352. Received 02 April 1999/ Accepted in revised form 19 November 1999     

Development of an Escherichia coli expression system and thermostability screening assay for libraries of mutant xylanase

A thermostability screening assay was developed using an Escherichia coli expression system to express Streptomyces lividans xylanase A (XlnA). The screening system was tested using mutants randomized at position 49 of the S. lividans XlnA gene, a position previously shown to confer thermostability with a I49P point mutation. The library was cloned into an E. coli expression vector and transformed into XL1-blue bacteria. The resulting clones were screened for increased thermostability with respect to wild-type XlnA. Using this assay, we isolated the I49P mutant previously shown to be thermostable, as well as novel I49A and I49C mutants. The I49A and I49C mutants were shown to have 2.8- to 8-fold increase in thermostability over that of wild-type XlnA. The results show that the screening assay can selectively enrich for clones with increased thermostability and is suitable for screening small- to medium-sized libraries of 5000–20,000 clones. Journal of Industrial Microbiology & Biotechnology (2000) 25, 310–314. Received 18 May 2000/ Accepted in revised form 19 September 2000     

Size does matter: overcoming the adeno-associated virus packaging limit

Recombinant adeno-associated virus (rAAV) vectors mediate long-term gene transfer without any known toxicity. The primary limitation of rAAV has been the small size of the virion (20 nm), which only permits the packaging of 4.7 kilobases (kb) of exogenous DNA, including the promoter, the polyadenylation signal and any other enhancer elements that might be desired. Two recent reports (D Duan et al: Nat Med 2000, 6:595-598; Z Yan et al: Proc Natl Acad Sci USA 2000, 97:6716-6721) have exploited a unique feature of rAAV genomes, their ability to link together in doublets or strings, to bypass this size limitation. This technology could improve the chances for successful gene therapy of diseases like cystic fibrosis or Duchenne muscular dystrophy that lead to significant pulmonary morbidity.     

Increasing the yield and viscosity of exopolysaccharides secreted by Sphingomonas by augmentation of chromosomal genes with multiple copies of cloned biosynthetic genes

Certain bacteria of the Sphingomonas genus secrete structurally related capsular polysaccharides. Due to their unique properties, three (gellan, welan and rhamsan) are produced commercially by submerged fermentation and are used as modifiers of aqueous rheology and as gelling agents. However, conversion of glucose into these polysaccharides is relatively inefficient. To identify general methods for increasing the productivity of Sphingomonas, we augmented the normal chromosomal copy of the phosphoglucomutase gene (pgm) and the cluster of genes (sps) required for assembly of the carbohydrate repeat unit for strain S7 with multiple copies of plasmids carrying these genes. Although a sixfold increase in Pgm activity only lead to a small percentage increase in conversion of glucose to the S-7 polysaccharide, multiple sps genes caused a nearly 20% increase in the yield from glucose and an even larger increase in culture viscosity. The increased viscosity was accompanied by a change in the sugar composition of the secreted polymer. Journal of Industrial Microbiology & Biotechnology (2000) 25, 49–57. Received 18 February 2000/ Accepted in revised form 29 April 2000     

Molecular characterization of xynX, a gene encoding a multidomain xylanase with a thermostabilizing domain from Clostridium thermocellum

A Clostridium thermocellum gene, xynX, coding for a xylanase was cloned and the complete nucleotide sequence was determined. The xylanase gene of Clostridium thermocellum consists of an ORF of 3261 nucleotide encoding a xylanase (XynX) of 1087 amino acid residues (116 kDa). Sequence analysis of XynX showed a multidomain structure that consisted of four different domains: an N-terminal thermostabilizing domain homologous to sequences found in several thermophilic enzymes, a catalytic domain homologous to family 10 glycosyl hydrolases, a duplicated cellulose-binding domain (CBD) homologous to family IX CBDs, and a triplicated S-layer homologous domain. A deletion mutant of xynX having only the catalytic region produced a mutant enzyme XynX-C which retained catalytic activity but lost thermostability. In terms of half-life at 70 °C, the thermostability of XynX-C was about six times lower than that of the other mutant enzyme, XynX-TC, produced by a mutant containing both the thermostabilizing domain and the catalytic domain. The optimum temperature of XynX-C was about 5–10 °C lower than that of XynX-TC. Received: 12 January 2000 / Received revision: 24 April 2000 / Accepted: 1 May 2000     

Novel N-quinonyl amino acids and their transformation to 3-substituted p-isoxazinones

Summary. Quinonyl amino acids are building blocks in the preparation of peptides which target the quinonic drug to cancer damaged area. Novel N-(3-chloro-1,4-dihydro-1,4-dioxonaphthalen-2-yl)-α-amino acids 1a–f were prepared by direct substitution of 2,3-dichloro-1,4-naphthoquinone. The quinonic moiety was reduced by NaBH₄ to yield the corresponding hydroquinones 2a–f, which in acidic conditions underwent internal cyclization to yield the 3,4-dihydro-2H-naphth[1,2-b]-1,4-oxazine-2-ones (six-membered azlactones) 3a–f. Received February 2, 2000 Accepted March 29, 2000