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Applied Microbiology and Biotechnology (v.65, #2)
Small, basic antifungal proteins secreted from filamentous ascomycetes: a comparative study regarding expression, structure, function and potential application by F. Marx (pp. 133-142).
Peptides and proteins with antimicrobial activity are produced throughout all kingdoms in nature, from prokaryotes to lower and higher eukaryotes, including fungi, plants, invertebrates and vertebrates. These proteins contribute to an important constitutive or induced defense mechanism of the producer against microorganisms. According to their variety in structure and function, these proteins are classified arbitrarily into groups that are based on their mechanism of action, their structure and their similarity to other known proteins. The present review focuses on a new group of antimicrobial proteins, namely small, basic and cysteine-rich antifungal proteins, which are secreted from filamentous fungi of the group Ascomycetes. These proteins are encoded by orthologous genes and exhibit both similarities and differences concerning their species-specificity, primary structure, protein activity and target sites. The properties of these proteins, their possible mode of action and their potential application for human benefits are discussed in comparison with other already well known antimicrobial proteins.
The effects of extracellular polymeric substances on the formation and stability of biogranules by Yong-Qiang Liu; Yu Liu; Joo-Hwa Tay (pp. 143-148).
Biogranulation is a promising biotechnology developed for wastewater treatment. Biogranules exhibit a matrix microbial structure, and intensive research has shown that extracellular polymeric substances (EPS) are a major component of the biogranule matrix material in both anaerobic and aerobic granules. This paper aims to review the role of EPS in biogranulation, factors influencing EPS production, the effect of EPS on cell surface properties of biogranules, and the relationship of EPS to the structural stability of biogranules. EPS production is substantially enhanced when the microbial community is subject to stressful culture conditions, and the stimulated EPS production in the microbial matrix in turn favours the formation of anaerobic and aerobic granules. EPS can also play an essential role in maintaining the integrity and stability of spatial structure in mature biogranules. It is expected that this paper can provide deep insights into the functions of EPS in the biogranulation process.
Metabolic selectivity and growth of Clostridium thermocellum in continuous culture under elevated hydrostatic pressure by G. D. Bothun; B. L. Knutson; J. A. Berberich; H. J. Strobel; S. E. Nokes (pp. 149-157).
The continuous culture of Clostridium thermocellum, a thermophilic bacterium capable of producing ethanol from cellulosic material, is demonstrated at elevated hydrostatic pressure (7.0 MPa, 17.3 MPa) and compared with cultures at atmospheric pressure. A commercial limitation of ethanol production by C. thermocellum is low ethanol yield due to the formation of organic acids (acetate, lactate). At elevated hydrostatic pressure, ethanol:acetate (E/A) ratios increased >102 relative to atmospheric pressure. Cell growth was inhibited by approximately 40% and 60% for incubations at 7.0 MPa and 17.3 MPa, respectively, relative to continuous culture at atmospheric pressure. A decrease in the theoretical maximum growth yield and an increase in the maintenance coefficient indicated that more cellobiose and ATP are channeled towards maintaining cellular function in pressurized cultures. Shifts in product selectivity toward ethanol are consistent with previous observations of hydrostatic pressure effects in batch cultures. The results are partially attributed to the increasing concentration of dissolved product gases (H2, CO2) with increasing pressure; and they highlight the utility of continuous culture experiments for the quantification of the complex role of dissolved gas and pressure effects on metabolic activity.
Influence of media and temperature on bacteriocin production by Bacillus cereus 8A during batch cultivation by D. Bizani; A. Brandelli (pp. 158-162).
Cerein 8A is a bacteriocin produced by the soil bacterium Bacillus cereus 8A, isolated from native woodlands of Brazil. The influence of temperature and media on the growth of B. cereus 8A and the production of this bacteriocin was studied during batch cultivation. Maximum activity was detected by cultivation in brain/heart infusion broth, reaching 3200 activity units ml−1. Bacteriocin was also produced in peptone, MRS, Mueller–Hinton and nutrient broth, while no activity was observed during cultivation in thioglycollate or tryptic soy broth. Temperature had a strong influence on bacteriocin production, which was higher at 30 °C than at 25 °C. An important decrease in bacteriocin activity was observed at 37 °C. The relationship between growth and specific production rates, as a function of the temperature, showed different kinetics of production and there were several peaks in the specific production rates during growth. Bacteriocin was produced at the stationary phase, indicating it is synthesized as a secondary metabolite.
Folate requirements of the 2-keto-l-gulonic acid-producing strain Ketogulonigenium vulgare LMP P-20356 in l-sorbose/CSL medium by S. Leduc; J.-C. de Troostembergh; J.-M. Lebeault (pp. 163-167).
In this study, the requirements for growth factors of Ketogulonigenium vulgare LMP P-20356, a 2-keto-l-gulonic acid-producing strain of particular interest for the manufacture of vitamin C, were assessed. Various growth factors were studied in order to obtain improved growth of the strain when cultured in an l-sorbose/corn steep liquor medium. Cultures grown in the presence of reduced mono- and polyglutamated folate derivatives showed a 15- to 20-fold higher biomass content than control cultures lacking these supplements, indicating that the strain has a requirement for folate. Although most folate derivatives used in this study promoted growth, the amplitude of the response varied depending on the compound used. Dihydrofolic acid was found to be the most active form, followed by 5-formyltetrahydrofolic acid, 5-methyltetrahydrofolic acid and tetrahydrofolic acid. Folic acid had no effect. The effectiveness of polyglutamated derivatives was inversely proportional to the polyglutamated chain-length of the derivative used. Our results suggest that the rate-limiting step in the utilisation of monoglutamated folates is most probably related to their transport and/or their intracellular interconversion rather than their polymerisation into polyglutamated forms (physiological forms). The industrial production of 2-keto-l-gulonic acid by K. vulgare LMP P-20356 could be improved by using media in which low-molecular-weight reduced folates are present.
Indene bioconversion by a toluene inducible dioxygenase of Rhodococcus sp. I24 by Horst Priefert; Xian M. O’Brien; Philip A. Lessard; Annette F. Dexter; Ellen E. Choi; Sladjana Tomic; Geeta Nagpal; Jennie J. Cho; Melina Agosto; Lucy Yang; Sheri L. Treadway; Lance Tamashiro; Matthew Wallace; Anthony J. Sinskey (pp. 168-176).
Rhodococcus sp. I24 can oxygenate indene via at least three independent enzyme activities: (i) a naphthalene inducible monooxygenase (ii) a naphthalene inducible dioxygenase, and (iii) a toluene inducible dioxygenase (TID). Pulsed field gel analysis revealed that the I24 strain harbors two megaplasmids of ∼340 and ∼50 kb. Rhodococcus sp. KY1, a derivative of the I24 strain, lacks the ∼340 kb element as well as the TID activity. Southern blotting and sequence analysis of an indigogenic, I24-derived cosmid suggested that an operon encoding a TID resides on the ∼340 kb element. Expression of the tid operon was induced by toluene but not by naphthalene. In contrast, naphthalene did induce expression of the nid operon, encoding the naphthalene dioxygenase in I24. Cell free protein extracts of Escherichia coli cells expressing tidABCD were used in HPLC-based enzyme assays to characterize the indene bioconversion of TID in vitro. In addition to 1-indenol, indene was transformed to cis-indandiol with an enantiomeric excess of 45.2% of cis-(1S,2R)-indandiol over cis-(1R,2S)-indandiol, as revealed by chiral HPLC analysis. The K m of TID for indene was 380 μM. The enzyme also dioxygenated naphthalene to cis-dihydronaphthalenediol with an activity of 78% compared to the formation of cis-indandiol from indene. The K m of TID for naphthalene was 28 μM. TID converted only trace amounts of toluene to 1,2-dihydro-3-methylcatechol after prolonged incubation time. The results indicate the role of the tid operon in the bioconversion of indene to 1-indenol and cis-(1S,2R)-indandiol by Rhodococcus sp. I24.
A cloned Bacillus halodurans multicopper oxidase exhibiting alkaline laccase activity by H. J. Ruijssenaars; S. Hartmans (pp. 177-182).
The gene product of open reading frame bh2082 from Bacillus halodurans C-125 was identified as a multicopper oxidase with potential laccase activity. A homologue of this gene, lbh1, was obtained from a B. halodurans isolate from our culture collection. The encoded gene product was expressed in Escherichia coli and showed laccase-like activity, oxidising 2,2′-azino-bis(3-ethylbenz-thiazoline-6-sulfonic acid), 2,6-dimethoxyphenol and syringaldazine (SGZ). The pH optimum of Lbh1 with SGZ is 7.5–8 (at 45°C) and the laccase activity is stimulated rather than inhibited by chloride. These unusual properties make Lbh1 an interesting biocatalyst in applications for which classical laccases are unsuited, such as biobleaching of kraft pulp for paper production.
Improving the insecticidal activity of Bacillus thuringiensis subsp. aizawai against Spodoptera exigua by chromosomal expression of a chitinase gene by S. Thamthiankul; W. J. Moar; M. E. Miller; W. Panbangred (pp. 183-192).
A transcriptionally fused gene comprising the P19 gene from Bacillus thuringiensis subsp. israelensis fused with a chitinase gene (chiBlA) from B. licheniformis was integrated into the B. thuringiensis subsp. aizawai BTA1 genome by homologous recombination. The resulting B. thuringiensis subsp. aizawai strain (INT1) showed growth and sporulation comparable with that of the wild-type strain. INT1 produced four chitinases of different molecular masses (i.e., 66, 55, 39, 36 kDa). Three of these (66, 55, 36 kDa) were derived from the cloned chiBlA gene, whereas the 39-kDa chitinase originated from BTA1. Using surface contamination bioassays, the 50% lethal concentration of lyophilized whole culture broth of INT1 against Spodoptera exigua neonate larvae was 12.2 μg/cm2, compared with 30.8 μg/cm2 for BTA1. Bioassays using filtered culture supernatant of INT1 (110 μg/cm2) together with trypsin-activated purified Cry1C protein of B. thuringiensis (1,280 ng/cm2) showed 75.0% mortality, compared with 56.7% mortality for Cry1C combined with BTA1 at the same concentration. Using scanning electron microscopy, clear perforations were observed in S. exigua fifth instar peritrophic membranes incubated with either crude or purified chitinase, or isolated from fifth instar S. exigua fed purified chitinase since the first instar. These results show that chitinase can increase the activity of B. thuringiensis subsp. aizawai against S. exigua. This is the first documentation of expressing a chimeric chitinase gene on the chromosome of B. thuringiensis; and chromosomal integration might be used as a potential technique for strain improvement.
Structural and functional characterization of the Bacillus megaterium uvrBA locus and generation of UV-sensitive mutants by H. Nahrstedt; F. Meinhardt (pp. 193-199).
The Bacillus megaterium genes uvrB and uvrA, encoding two subunits of the (A)BC excinuclease, which is responsible for nucleotide excision repair, were isolated and functionally characterized. RNA analyses revealed co-transcription of both genes probably forming a bicistronic operon. Expression of uvrB and uvrA was inducible by the DNA-damaging agent mitomycin C. This finding agrees with the presence of a potential DinR box within the uvrBA promoter. Single inactivation of uvrB or uvrA as well as the parallel knockout of both genes resulted in mutants highly sensitive to UV irradiation. Thus, this locus represents an attractive target for generating biologically safe containment strains of B. megaterium.
An equation for calculating the volumetric ratios required in a ligation reaction by R. M. Cranenburgh (pp. 200-202).
The ligation of two DNA fragments to create a new plasmid DNA molecule is a key reaction in molecular biology. Where the fragment lengths and concentrations are known, existing equations allow the desired relative molar ratio to be calculated, but this must then be related to the required volumes. Further calculations are then necessary if the maximum available volume is to consist of DNA solutions. The equation presented here allows the simple calculation of volumes of DNA solutions required to obtain a desired molar insert-to-vector ratio, and these can comprise all of the available volume in a ligation if required, thus maximising the yield of the recombinant plasmid.
Phylogenetic analysis based on genome-scale metabolic pathway reaction content by S. H. Hong; T. Y. Kim; S. Y. Lee (pp. 203-210).
Phylogenetic classifications based on single genes such as rRNA genes do not provide a complete and accurate picture of evolution because they do not account for evolutionary leaps caused by gene transfer, duplication, deletion and functional replacement. Here, we present a whole-genome-scale phylogeny based on metabolic pathway reaction content. From the genome sequences of 42 microorganisms, we deduced the metabolic pathway reactions and used the relatedness of these contents to construct a phylogenetic tree that represents the similarity of metabolic profiles (relatedness) as well as the extent of metabolic pathway similarity (evolutionary distance). This method accounts for horizontal gene transfer and specific gene loss by comparison of whole metabolic subpathways, and allows evaluation of evolutionary relatedness and changes in metabolic pathways. Thus, a tree based on metabolic pathway content represents both the evolutionary time scale (changes in genetic content) and the evolutionary process (changes in metabolism).
Degradation of polycyclic aromatic hydrocarbons by a newly isolated dibenzofuran-utilizing Janibacter sp. strain YY-1 by A. Yamazoe; O. Yagi; H. Oyaizu (pp. 211-218).
The dibenzofuran (DF)-utilizing bacterium strain YY-1 was newly isolated from soil. The isolate was identified as Janibacter sp. with respect to its 16S rDNA sequence and fatty acid profiles, as well as various physiological characteristics. In addition to DF, strain YY-1 could grow on fluorene and dibenzothiophene as sole sources of carbon and energy. It was also able to cometabolize a variety of polycyclic aromatic hydrocarbons including dibenzo-p-dioxin, phenanthrene, and anthracene. The major metabolites formed from DF, biphenyl, dibenzothiophene, and naphthalene were identified by using gas chromatography-mass spectrometry as 2,3,2′-trihydroxybiphenyl, biphenyl-dihydrodiol, dibenzothiophene 5-oxide, and coumarin, respectively. These results indicate that strain YY-1 can catalyze angular dioxygenation, lateral dioxygenation, and sulfoxidation.
Physico-chemical and transglucosylation properties of recombinant sucrose phosphorylase from Bifidobacterium adolescentis DSM20083 by L. A. M. van den Broek; E. L. van Boxtel; R. P. Kievit; R. Verhoef; G. Beldman; A. G. J. Voragen (pp. 219-227).
Clones of a genomic library of Bifidobacterium adolescentis were grown in minimal medium with sucrose as sole carbon source. An enzymatic fructose dehydrogenase assay was used to identify sucrose-degrading enzymes. Plasmids were isolated from the positive colonies and sequence analysis revealed that two types of insert were present, which only differed with respect to their orientation in the plasmid. An open reading frame of 1,515 nucleotides with high homology for sucrose phosphorylases was detected on these inserts. The gene was designated SucP and encoded a protein of 56,189 Da. SucP was heterologously expressed in Escherichia coli, purified, and characterized. The molecular mass of SucP was 58 kDa, as estimated by SDS-PAGE, while 129 kDa was found with gel permeation, suggesting that the native enzyme was a dimer. The enzyme showed high activity towards sucrose and a lower extent towards α-glucose-1-phosphate. The transglucosylation properties were investigated using a broad range of monomeric sugars as acceptor substrate for the recombinant enzyme, while α-glucose-1-phosphate served as donor. d- and l-arabinose, d- and l-arabitol, and xylitol showed the highest production of transglucosylation products. The investigated disaccharides and trisaccharides were not suitable as acceptors. The structure of the transglucosylation product obtained with d-arabinose as acceptor was elucidated by NMR. The structure of the synthesized non-reducing dimer was α-Glcp(1→1)β-Araf.
Stoichiometry of microbial continuous-flow purification of toluene-contaminated air by S. Mutafov; B. Angelova; H.-P. Schmauder; T. Avramova; L. Boyadjieva (pp. 228-234).
The applicability of a recently published modification of the chemostat, named “titrostat”, for microbial continuous-flow purification of toluene-contaminated air is discussed. This article describes the operative range and the toluene elimination efficiency of a 2-l titrostat running with a mixed bacterial culture dominated by two Acinetobacter species: A. calcoaceticus and A. radioresistens. The study focuses on the kinetics and stoichiometry of the process. Special attention is paid to the peculiarities of toluene as an unconventional growth substrate having high carbon and energy content. Removal productivity as high as 2.24 g l−1 h−1 with 99.9% elimination efficiency was observed at air flow rate 60 l h−1, temperature 32°C, pH 6.2, toluene concentration in the inlet air 37.4 mg l−1 and titrant solution containing NH3 at 1.87 g l−1. The maximum biomass yield from assimilated toluene, Y s m=0.880±0.011, and a rate of substrate expenditures for cell maintenance, m s=0.022±0.002 h−1, were estimated.
Biofiltration of waste gases containing a mixture of formaldehyde and methanol by Óscar J. Prado; María C. Veiga; Christian Kennes (pp. 235-242).
Several biofilters and biotrickling filters were used for the treatment of a mixture of formaldehyde and methanol; and their efficiencies were compared. Results obtained with three different inert filter bed materials (lava rock, perlite, activated carbon) suggested that the packing material had only little influence on the performance. The best results were obtained in a biotrickling filter packed with lava rock and fed a nutrient solution that was renewed weekly. A maximum formaldehyde elimination capacity of 180 g m−3 h−1 was reached, while the methanol elimination capacity rose occasionally to more than 600 g m−3 h−1. Formaldehyde degradation was affected by the inlet methanol concentration. Several combinations of load vs empty bed residence time (EBRTs of 71.9, 46.5, 30.0, 20.7 s) were studied, reaching a formaldehyde elimination capacity of 112 g m−3 h−1 with about 80% removal efficiency at the lowest EBRT (20.7 s).