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Applied Microbiology and Biotechnology (v.58, #1)
Biotechnologically relevant enzymes from Thermus thermophilus by A. Pantazaki; A. Pritsa; D. Kyriakidis (pp. 1-12).
Enzymes produced by Thermus thermophilus are of considerable biotechnological interest. This review covers industrial applications of several protein products of this thermophilic bacterium that are functional under extreme conditions. The purification of proteins from T. thermophilus using either conventional methods or in the light of the cloning of their genes and expression in mesophilic microorganisms is discussed. Enzymes that biodegrade proteins, polysaccharides or key enzymes that are involved in amino acid metabolism, protein folding or in other fundamental biological processes such as DNA replication, DNA repair, and RNA maturation, with potential use in different biotechnological processes are reviewed as well.
Quinoproteins: structure, function, and biotechnological applications by K. Matsushita; H. Toyama; M. Yamada; O. Adachi (pp. 13-22).
A new class of oxidoreductase containing an amino acid-derived o-quinone cofactor, of which the most typical is pyrroloquinoline quinone (PQQ), is called quinoproteins, and has been recognized as the third redox enzyme following pyridine nucleotide- and flavin-dependent dehydrogenases. Some quinoproteins include a heme c moiety in addition to the quinone cofactor in the molecule and are called quinohemoproteins. PQQ-containing quinoproteins and quinohemoproteins have a common structural basis, in which PQQ is deeply embedded in the center of the unique superbarrel structure. Increased evidence for the structure and function of quinoproteins has revealed their unique position within the redox enzymes with respect to catalytic and electron transfer properties, and also to physiological and energetic function. The peculiarities of the quinoproteins, together with their unique substrate specificity, have encouraged their biotechnological application in the fields of biosensing and bioconversion of useful compounds, and also to environmental treatment.
Biosynthesis, biotechnological production and applications of 5-aminolevulinic acid by K. Sasaki; M. Watanabe; T. Tanaka; T. Tanaka (pp. 23-29).
Microbial production of 5-aminolevulinic acid (ALA) by photosynthetic bacteria compared to other bacteria and algae is reviewed. During aerobic-microaerobic cultivation of Rhodobacter sphaeroides mutant strain CR520, control of the redox potential was effective for producing large amounts of extracellular ALA. ALA has been practically applied in agriculture as an herbicide, an insecticide and a growth-promoting factor for plants. New agricultural applications including salt tolerance and cold temperature tolerance of plants are also described. Finally, recent medical applications for cancer treatment, tumor diagnosis and other clinical uses are discussed.
Microbial degradation of polyethers by F. Kawai (pp. 30-38).
This paper summarizes studies on microbial degradation of polyethers. Polyethers are aerobically metabolized through common mechanisms (oxidation of terminal alcohol groups followed by terminal ether cleavage), well-characterized examples being found with polyethylene glycol (PEG). First the polymer is oxidized to carboxylated PEG by alcohol and aldehyde dehydrogenases and then the terminal ether bond is cleaved to yield the depolymerized PEG by one glycol unit. Most probably PEG is anaerobically metabolized through one step which is catalyzed by PEG acetaldehyde lyase, analogous to diol dehydratase. Whether aerobically or anaerobically, the free OH group is necessary for metabolization of PEG. PEG with a molecular weight of up to 20,000 was metabolized either in the periplasmic space (Pseudomonas stutzeri and sphingomonads) or in the cytoplasm (anaerobic bacteria), which suggests the transport of large PEG through the outer and inner membranes of Gram-negative bacterial cells. Membrane-bound PEG dehydrogenase (PEG-DH) with high activity towards PEG 6,000 and 20,000 was purified from PEG-utilizing sphingomonads. Sequencing of PEG-DH revealed that the enzyme belongs to the group of GMC flavoproteins, FAD being the cofactor for the enzyme. On the other hand, alcohol dehydrogenases purified from other bacteria that cannot grow on PEG oxidized PEG. Cytoplasmic NAD-dependent alcohol dehydrogenases with high specificity towards ether-alcohol compound, either crude or purified, showed appreciable activity towards PEG 400 or 600. Liver alcohol dehydrogenase (equine) also oxidized PEG homologs, which might cause fatal toxic syndrome in vivo by carboxylating PEG together with aldehyde dehydrogenase when PEG was absorbed. An ether bond-cleaving enzyme was detected in PEG-utilizing bacteria and purified as diglycolic acid (DGA) dehydrogenase from a PEG-utilizing consortium. The enzyme oxidized glycolic acid, glyoxylic acid, as well as PEG-carboxylic acid and DGA. Similarly, dehydrogenation on polypropylene glycol (PPG) and polytetramethylene glycol (PTMG) was suggested with cell-free extracts of PPG and PTMG-utilizing bacteria, respectively. PPG commercially available is atactic and includes many structural (primary and secondary alcohol groups) and optical (derived from pendant methyl groups on the carbon backbone) isomers. Whether PPG dehydrogenase (PPG-DH) has wide stereo- and enantioselective substrate specificity towards PPG isomers or not must await further purification. Preliminary research on PPG-DH revealed that the enzyme was inducibly formed by PPG in the periplasmic, membrane and cytoplasm fractions of a PPG-utilizing bacterium Stenotrophomonas maltophilia. This finding indicated the intracellular metabolism of PPG is the same as that of PEG. Besides metabolization of polyethers, a biological Fenton mechanism was proposed for degradation of PEG, which was caused by extracellular oxidants produced by a brown-rot fungus in the presence of a reductant and Fe3+, although the metabolism of fragmented PEG has not yet been well elucidated.
Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies by L. Wackett; M. Sadowsky; B. Martinez; N. Shapir (pp. 39-45).
s-Triazine ring compounds are common industrial chemicals: pesticides, resin intermediates, dyes, and explosives. The fate of these compounds in the environment is directly correlated with the ability of microbes to metabolize them. Microbes metabolize melamine and the triazine herbicides such as atrazine via enzyme-catalyzed hydrolysis reactions. Hydrolytic removal of substituents on the s-triazine ring is catalyzed by enzymes from the amidohydrolase superfamily and yields cyanuric acid as an intermediate. Cyanuric acid is hydrolytically processed to yield 3 mol each of ammonia and carbon dioxide. In those cases studied, the genes underlying the hydrolytic reactions are localized to large catabolic plasmids. One such plasmid, pADP-1 from Pseudomonas sp. ADP, has been completely sequenced and contains the genes for atrazine catabolism. Insertion sequence elements play a role in constructing different atrazine catabolic plasmids in different bacteria. Atrazine chlorohydrolase has been purified to homogeneity from two sources. Recombinant Escherichia coli strains expressing atrazine chlorohydrolase have been constructed and chemically cross-linked to generate catalytic particles used for atrazine remediation in soil. The method was used for cleaning up a spill of 1,000 pounds of atrazine to attain a level of herbicide acceptable to regulatory agencies.
Antifungal antibiotics by M. Gupte; P. Kulkarni; B. Ganguli (pp. 46-57).
The search for new drugs against fungal infections is a major challenge to current research in mycotic diseases. The present article reviews the current types of antifungal infections, the current scenario of antifungal antibiotics, and the need and approaches to search for newer antifungal antibiotics and antifungal drug targets.
Vacuum-soaking of wood chip shiitake (Lentinula edodes) logs to reduce soak time and log weight variability and to stimulate mushroom yield by D. Royse; T. Rhodes; J. Sanchez (pp. 58-62).
Synthetic logs were vacuum-soaked or regular-soaked to determine the effects of soaking on yield and mushroom size, log weight variability and water distribution within the log. Yields (g/log) from substrates vacuum-soaked were higher by 26.7%, 18.6% and 35.8% (mean = 27.2%) for crops I, II and III, respectively, when compared with regular-soaked. However, mushroom size averaged only 11.2 g for vacuum-soaked logs vs 17 g for regular-soaked logs (51.8% larger for regular-soaked). The time required for vacuum-soaking logs was generally less than 3 min, compared with regular-soaking times ranging over 3–15 h. Water tended to accumulate more in the outside zone in the vacuum-soaked logs, compared with regular-soaked logs. Mean moisture contents for crops I and II for outside, middle and interior zones of vacuum-soaked logs were 66%, 47.5% and 42.2%, respectively, while regular-soaked logs for the same zones were 62.4%, 52.1% and 50.9%, respectively. Vacuum-soaked log weights had lower standard deviations than weights for regular-soaked logs in four out of six soaks, indicating a more uniform soaking process.
Production of teicoplanin by valine analogue-resistant mutant strains of Actinoplanes teichomyceticus by Z. Jin; M. Wang; P. Cen (pp. 63-66).
Teicoplanin is a glycopeptide antibiotic produced by Actinoplanes teichomyceticus. A strain improvement to increase the productivity of the major component, teicoplanin A2-2, was carried out. As the fatty moiety of teicoplanin A2-2 is derived from L-valine, L-valine analogue (valine hydroxamate)-resistant mutants were derived. One of the mutants, 98-1-227, overproduced valine and produced a higher titer of total teicoplanin with higher A2-2 content. In a pilot fermentor (7 m3), the total productivity of teicoplanin was 1,800 units/ml and the A2-2 content was 58%.
Evaluation of an endo-β-mannanase produced by Streptomyces ipomoea CECT 3341 for the biobleaching of pine kraft pulps by M. Montiel; M. Hernández; J. Rodríguez; M. Arias (pp. 67-72).
An endo-β-mannanase (EC 3.2.1.78) from Streptomyces ipomoea CECT 3341 was purified and applied to the biobleaching of pine kraft pulps. The maximum level of endo-β-mannanase activity (0.6 units ml–1) was achieved after 4 days of growth in a medium containing locust bean gum and yeast extract. Zymograms revealed mannanase bands (Man) with high and low electrophoretic mobility on the second and seventh days of incubation (Man1, Man3) and three bands of high, medium and low mobility from the third to sixth days of growth (Man1, Man2, Man3). Although these exhibited different molecular masses, their amino-terminal sequences were identical. The action of proteases detected in the culture supernatant could be responsible for such events, suggesting that only one endo-β-mannanase is produced by S. ipomoea. The purified Man3 exhibited a molecular mass of 40 kDa, an isoelectric point of 4.0 and an optimal temperature and pH reaction of 55 °C and 7.5, respectively. It was strongly inhibited by Ag+, Hg2+, Al3+ and Fe3+, and was strongly activated by Mn2+. The ability of the purified endo-β-mannanase to improve the bleachability of pine kraft pulp, when applied with alkaline extraction, was demonstrated by an increase in the pulp brightness (1.7%, using the International Standards Organisation's test) and an absence of variations in the viscosity values. A relationship between the increase in pulp brightness and the presence of manganese in the pulps could be established.
Microencapsulation of Aerococcus viridans with catalase and its application for the synthesis of dihydroxyacetone phosphate by S. A. Streitenberger; M. J. Villaverde; Á. Sánchez-Ferrer; F. García-Carmona (pp. 73-76).
Dihydroxyacetone phosphate is essential for the synthesis of polyhydroxylated compounds used as components or precursors of active pharmaceutical substances, such as antibiotics or glycosidase inhibitors. Dihydroxyacetone phosphate was produced by enzymatic oxidation of L-α-glycerophosphate in the presence of glycerophosphate oxidase or Aerococcus viridans coimmobilized with a hydrogen peroxide-decomposing enzyme. The microencapsulation of A. viridans with catalase in sodium alginate showed a conversion of 98.5%; the conversion percentage remained constant in all five runs. Liquid chromatography of the product revealed that the product peak corresponded to that of the dihydroxyacetone phosphate internal standard. This indicated a high degree of product purity.
Dereplication for biotechnology screening: PyMS analysis and PCR–RFLP–SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes by Pedro F. Brandão; Masaki Torimura; Ryuichiro Kurane; Alan T. Bull (pp. 77-83).
The search for exploitable biology is a major task for biotechnology-based industries. In this context, discrimination between previously tested or recovered micro-organisms (dereplication) is imperative, in order to reduce screening costs by sorting large collections of isolates, which are then subjected to further detailed evaluation. Pyrolysis mass spectrometry (PyMS) is a whole-cell fingerprinting technique that enables the rapid and reproducible sorting of micro-organisms, uses small samples and has the advantage of being fully automated. In this study, we compare chemometric fingerprinting with a ribotyping fingerprinting method, in order to investigate the extent to which pyrogroups formed by PyMS analysis relate to genetic diversity, using polymerase chain reaction–restriction fragment length polymorphism–single-strand conformational polymorphism (PRS). A mixture of environmental strains of mycolic acid containing actinomycetes was used to mimic the selection of colonies from primary isolation plates. The congruence found between the clusters defined by the chemometric and molecular fingerprinting techniques was very high and demonstrated the effectiveness of PyMS as a rapid sorting and dereplicating procedure for putatively novel strains, criteria that are critical for biotechnological screens. Moreover, PyMS analysis revealed significant variation within pyrogroups that contained strains with the same genotypic (PRS) characteristics, thus emphasising its discriminatory capacity at the infraspecies level.
A spontaneous runaway vector for production-scale expression of bovine somatotropin from Escherichia coli by C. Trepod; J. Mott (pp. 84-88).
An Escherichia coli expression vector was constructed for the production-scale fermentation of recombinant bovine somatotropin (rBST). Gene expression is regulated by a spontaneous increase in copy number at a constant low temperature without the need for an external inducer. This vector, designated pURA-4, contains the ampicillin resistance gene, the replication origin from pBR322, the R1 temperature-inducible runaway replicon, and a gene encoding rBST. Optimized rBST expression levels of >35% total cell protein were achieved at a constant 28°C. Shake-flask analysis of pURA-4 shows that the copy number spontaneously increases approximately 6-fold during rBST production. Investigation into the mechanism of pURA-4 spontaneous runaway shows that the increase in copy number is directed by the pBR322 ori and not by the R1 replicon. Although the R1 temperature-inducible replicon does not mediate spontaneous runaway, it does have a positive effect on rBST expression. Copy number analysis also confirmed the stability of pURA-4 spontaneous runaway from the shake-flask scale through the production scale.
Expression of genes of lipid synthesis and altered lipid composition modulates L-glutamate efflux of Corynebacterium glutamicum by K. Nampoothiri; C. Hoischen; B. Bathe; B. Möckel; W. Pfefferle; K. Krumbach; H. Sahm; L. Eggeling (pp. 89-96).
L-Glutamate is made with Corynebacterium glutamicum on a scale of more than 106 tons/year. Nevertheless, formation of this amino acid is enigmatic and there is very limited molecular information available to unravel the apparently complex conditions leading to L-glutamate efflux. Here, we report the isolation and overexpression of the genes involved in lipid synthesis: acp, fadD15, cma, cls, pgsA2, cdsA, gpsA, and plsC, and the inactivation of cma and cls. In addition, the consequences for phospholipid content, temperature sensitivity, as well as detergent-independent and detergent-dependent L-glutamate efflux were quantified. An in part strong alteration of the phospholipid composition was achieved; for instance, overexpression of fadD15 encoding an acyl-CoA ligase resulted in an increase of phosphatidyl inositol from 12.6 to 30.2%. All strains, except that overexpressing acp (acyl carrier protein), exhibited increased temperature sensitivity, with the strongest sensitivity present upon cls (cardiolipin synthetase) inactivation. As a consequence of the genetically modified lipid synthesis, L-glutamate efflux changed quite dramatically; for instance, overexpression of plsC (acylglycerolacyl transferase) resulted in a detergent-triggered increase of L-glutamate accumulation from 92 mM to 108 mM, whereas acp overexpression reduced the accumulation to 24 mM. With some of the overexpressed genes, substantial L-glutamate excretion even without detergent addition was obtained when the fermentation temperature was elevated. These data show that the chemical and physical properties of the cytoplasmic membrane are altered and suggest that this is a necessary precondition to achieve L-glutamate efflux.
Identification and characterization of novel cytochrome P450 genes from the white-rot basidiomycete, Coriolus versicolor by H. Ichinose; H. Wariishi; H. Tanaka (pp. 97-105).
Using a reverse-transcription polymerase chain reaction (RT-PCR) technique, cytochrome P450 genes were cloned from the lignin-degrading basidiomycete, Coriolus versicolor. One possible P450 gene was identified, which consisted of 1,672 nucleotides and a poly(A) tail and encoded a deduced protein containing 449 amino acids. The deduced amino acid sequence revealed the presence of the P450 heme-binding motif, strongly suggesting that this protein belongs to the P450 superfamily, then designated CYP512A1. The deduced protein showed sequential similarity to other known P450s from several micro-organisms, such as Aspergillus terreus, Gibberella fujikuroi, and Neurospora crassa, with 30–35% identity. Since the identity of the amino acid sequence was less than 40% with any other P450s, this protein was suggested to be the first member of a new family of cytochrome P450. In addition, a differential display RT-PCR analysis showed the expression of the other P450 genes, which were up-regulated by the addition of dibenzothiophene and 4-methyldibenzothiophene-5-oxide. Using the 5′ rapid amplification of cDNA ends method, a 520-nucleotide sequence, including the P450 motif-coding region, was determined for one clone. The deduced protein showed high similarity to CYP512A1 but less than 40% identity with P450s from other organisms. A chemical stress-responsive expression of P450 is suggested for the first time in basidiomycetes.
Selective enrichment and characterization of a phosphorus-removing bacterial consortium from activated sludge by J. Hollender; U. Dreyer; L. Kornberger; P. Kämpfer; W. Dott (pp. 106-111).
Under alternating aerobic/anaerobic conditions and without additional carbon sources, a bacterial consortium consisting initially of 18 bacterial strains was obtained in a sequence batch reactor. The phosphorus removal capability could only be maintained using sterile filtrate of activated sludge as medium. The addition of calcium and magnesium salts, as well as vitamins and trace elements, to autoclaved sterile filtrate of activated sludge was not sufficient to achieve stable phosphorus removal. A further enrichment by subcultivation on solid agar, freezing, and shortening of the aerobic and anaerobic phases led to a defined bacterial consortium consisting of four strains. On the basis of physiological and chemotaxonomic characterization, and partial 16-S rRNA sequencing, one of the organisms was identified as Delftia acidovorans. A further isolate belonged to the Bacillus cereus group, and the third isolate was identified as Microbacterium sp.. The remaining strain seems to represent a new genus within the Flavobacteriaceae. Under continuous chemostat conditions, this consortium was able to remove up to 9.6 mg P/l phosphate in the aerobic phase and released up to 8.5 mg/l in the anaerobic phase. Up to 25 mg P-polyphosphate/g dry mass was stored under aerobic conditions.
Microbial diversity of a mesophilic hydrogen-producing sludge by H. Fang; T. Zhang; H. Liu (pp. 112-118).
A hydrogen-producing sludge degraded 99% of glucose at 36 °C and pH 5.5, producing a methane-free biogas (comprising 64% hydrogen) and an effluent comprising mostly butyrate, acetate, and ethanol. The yield was 0.26 l H2 g–1 glucose and the production rate per gram of volatile suspended solids was 4.6 l H2 day–1. A 16S rDNA library was constructed from the sludge for microbial species determination. A total of 96 clones were selected for plasmids recovery, screened by denaturing gradient gel electrophoresis, and sequenced for rDNA. Based on the phylogenetic analysis of the rDNA sequences, 64.6% of all the clones were affiliated with three Clostridium species (Clostridiaceae), 18.8% with Enterobacteriaceae, and 3.1% with Streptococcus bovis (Streptococcaceae). The remaining 13.5% belonged to eight operational taxonomic units, the affiliations of which were not identified.