JournalTOCs API - Microbiology (20 articles)

Structure of the archaeal community in the Black Sea photic zone

2015-07-01

Structure of the archaeal community in the Black Sea photic zone

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Qualitative and quantitative analysis of the structure of the archaeal community of the photic zone of the Black Sea water column was carried out. Real-time PCR revealed 2 × 10⁴ archaeal cells/mL (4.2% of the total cell number) at a 15-m depth. The structure of archaeal communities in the subsurface water column was investigated using the sequencing by synthesis technology (Illumina/Solexa) of the 16S rRNA genes. The Marine Group II phylogenetic cluster belonging to the phylum Euryarchaeota was the most numerous archaeal group (1.2–1.7 × 10⁴ cells/mL). The Marine Group I phylogenetic cluster (phylum Thaumarchaeota) was the second most numerous group (40% of the free-living archaea or 7.7 × 10³ cells/mL). Sequences of the ‘Nitrosopumilus’ cluster were revealed among Marine Group I sequences due to high homology (over 90%). A group of archaea belonging to the Deep-sea Hydrothermal Vent Euryarchaeotic Group 6 (DHVEG-6) (phylum Euryarchaeota) was also detected. The 16S rRNA gene sequences belonging to this cluster were revealed only in the suspension fraction. High homology level (over 90%) suggested classification of most DHVEG-6 sequences within the ‘Parvarchaeum’ cluster. In spite of a noticeable methane peak detected at 15-m depth, no sequences of methanogens were found.

Molecular identification and resistance investigation of atrazine degrading bacteria in the sediments of Karun River, Ahvaz, Iran

2015-07-01

Molecular identification and resistance investigation of atrazine degrading bacteria in the sediments of Karun River, Ahvaz, Iran

Microbiology, Vol. , No. \ (2015) pp. -

Abstract

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Nowadays, the use of pesticides as plant protection products has become widely prevalent, leading to the entry of large amounts of pesticides into soil and water resources, and subsequently, a threat to the environment. The objective of this study was molecular identification and resistance investigation of atrazine degrading bacteria in the sediments of Karun River, Ahvaz, Iran. Nine samples were collected in both summer (Jul) and autumn (Nov) year 2012 from a depth of 3 to 5 cm of the sediments. Atrazine degrading bacteria were enriched in a culture containing atrazine with initial concentration of 30 mg/L. Identification of isolated bacteria was performed by morphological and biochemical test and molecular analysis based on 16S rDNA sequencing. The atrazine biodegradation rate was obtained by high-performance liquid chromatography (HPLC). Six strains was identified including Achromobacter insolitus strain F-N3, Delftia tsuruhatensis strain F-N4, Klebsiella pneumonia F-N1, Enterobacter ludwigii strain F-N5, Serratia marcescens strain F-N6 in both summer and autumn, and Exiguobacterium profundum strain F-N2 only in the summer. The minimum inhibitory concentration (MIC) of atrazine showed that the most resistant species belonged to E. ludwigii F-N5 and D. tsuruhatensis F-N4 in the both seasons. The atrazine degradation rates of the two strains reached 90 and 85%, respectively after 7 days culture. Result showed that indigenous bacteria in the Karun River can degrade the atrazine effectively.

Sulfate-reducing bacteria of the genus Desulfovibrio from south vietnam seacoast

2015-07-01

Sulfate-reducing bacteria of the genus Desulfovibrio from south vietnam seacoast

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Nine strains of sulfate-reducing bacteria were isolated from a biofouling of corroded steel samples incubated in a marine environment near Nha Trang, South Vietnam. Sulfate-reducing bacteria were obtained from all samples with black corrosion products (in rust-filled metal cavities, beneath the Balanus and oyster booths, and beneath Bryozoa or algal colonies). Analysis of the 16S rRNA gene sequences of these strains showed that they belonged to the genus Desulfovibrio, with D. salexigens, D. marinisediminis, D. alaskensis, D. bizertensis D. indonesiensis, and D. dechloracetivorans as the closest phylogenetic relatives (98–99% similarity). According to the 16S rRNA gene sequencing, one Desulfovibrio isolate was related to “D. caledoniensis”, although the similarity did not exceed 97.0%. All strains utilized hydrogen (in the presence of acetate and CO₂), lactate, pyruvate, formate, and fumarate, but not acetate. Utilization of other substrates varied from strain to strain. Some isolates were capable of slow autotrophic growth with H₂ as the sole electron donor. D. indonesiensis and D. alaskensis strains were tolerant to long-term exposure to atmospheric oxygen exposure and could grow in the presence of 0.1% O₂ in the gas phase.

Occurrence, diversity, and abundance of methanogenic archaea in terrestrial hot springs of Kamchatka and Saõ Miguel Island

2015-07-01

Occurrence, diversity, and abundance of methanogenic archaea in terrestrial hot springs of Kamchatka and Saõ Miguel Island

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Detection and analysis of the mcrA gene encoding methyl-coenzyme M reductase, the key enzyme of methanogenesis, was used to assess occurrence and diversity of methanogenic archaea in terrestrial hot springs of Kamchatka and Sa~o Miguel Island (the Azores). For this analysis, phylogeny of methanogens was initially reconstructed based on available sequences of the mcrA gene, which is a common functional and phylogenetic marker for this physiological group of prokaryotes. Methanogens were revealed in most of the studied terrestrial hot springs with temperatures from 51 to 89°C, although they constituted an insignificant portion of the microbial population. The mcrA gene sequences revealed in the samples belonged to members of the genera Methanothermobacter, Methanothermus, and Methanothrix, previously detected in hot springs, as well as to methanogens not found earlier in these environments. The latter belonged to Methanomassiliicoccales, Methanocellales, and Methanomethylovorans, as well as to MCR-2a, the new deep phylogenetic cluster of uncultured methanogenic archaea; its phylotypes were present in all springs where the mcrA gene was detected. Our results indicate high diversity of the thermophilic methanogens inhabiting terrestrial hot springs and the presence among them of new groups with yet unknown substrate specificity.

Bacterial photosensory proteins: Regulatory functions and optogenetic applications

2015-07-01

Bacterial photosensory proteins: Regulatory functions and optogenetic applications

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Three classes of light-sensory regulatory proteins, which have been identified in genomes of numerous phototrophic and nonphotosynthetic bacteria, are discussed: the UVA/blue light sensitive BLUF and LOV domain-containing proteins and red/far-red light-sensitive phytochromes. Light perception by these chromoproteins is provided by the flavin or bilin (in phytochromes) chromophores binding to their photosensory domains. Bacterial photoreceptors also contain a variety of effector domains with enzymatic DNA-binding and other functions, which compose modular light-switchable systems. In recent years, progress was achieved in uncovering the photoactivation mechanisms of such systems. Based on the chromophore phototransformation-induced changes in the domain structures, these mechanisms cause the biochemical signal cascades which can control the light-dependent physiological responses of the cells. The new information obtained is important not only for understanding the fundamental mechanisms of light perception and signal transduction by bacterial photosensory proteins but also as a basis for designing photo-switchable enzymes and light-inducible gene expression systems, which may be used in optogenetics, a new field in cell biology and biotechnology. The presents review is focused on the structural aspects of signal transduction in light-activated bacterial photoreceptors, on their regulatory functions, and on some recent advances in using LOV and BLUF photosensors in optogenetics for the regulation of biological processes.

The production of exopolysaccharide by Pseudomonas putida GAP-P45 under various abiotic stress conditions and its role in soil aggregation

2015-07-01

The production of exopolysaccharide by Pseudomonas putida GAP-P45 under various abiotic stress conditions and its role in soil aggregation

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Exopolysaccharides (EPS) production is modified in response to environmental changes and is believed to protect bacteria. In the present study Pseudomonas putida strain GAP-P45 identified by 16S rDNA sequence analysis was exposed to stresses such as drought, temperature and salt to test the ability to tolerate and produce EPS. Strain GAP-P45 could tolerate matric stress up to −0.73 MPa, Temperature of 50°C and 1.4 M salt and produced EPS, which increased with increase in stress levels. Among all stress conditions, the production was high under drought stress. HPLC analysis revealed that monosaccharide composition and ratio of sugars in EPS increased under stress that might induce osmotic and thermal tolerance in GAP-P45. Rhamnose was reported as major sugar under all stress conditions. Among the different carbon sources tested, glycerol was found to be best for EPS production under stressed as well as non-stressed conditions. Inoculation with GAP-P45 resulted in better soil aggregation and aggregate stability under different stress conditions. However inoculation effect was more under drought-stress. The significance of these findings shows that abiotic stresses influence the EPS composition and ratios of sugars, which influence the tolerance of the microorganisms which can be employed for improvement in water holding capacity under unfavorable environmental conditions.

Active sulfate reduction in acidic sediments of gold mine tailings

2015-05-01

Active sulfate reduction in acidic sediments of gold mine tailings

Microbiology, Vol. , No. (2015) pp. -
\nArticle URL: http://link.springer.com/10.1134/S0026261715030157\nCitation: \ (2015) \nPublication Date: 2015-05-01\nJournal: Microbiology

Activated sludge bacteria transforming cyanopyridines and amides of pyridinecarboxylic acids

2015-05-01

Activated sludge bacteria transforming cyanopyridines and amides of pyridinecarboxylic acids

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Species diversity of bacteria from the activated sludge of Perm biological waste treatment facilities capable of transformation of cyanopyridines and amides of pyridinecarboxylic acids was investigated. Enrichment cultures in mineral media with 3-cyanopyridine as the sole carbon and nitrogen source were used to obtain 32 clones of gram-negative heterotrophic bacteria exhibiting moderate growth on solid and liquid media with 3- and 4-cyanopyridine. Sequencing of the 16S rRNA gene fragments revealed that the clones with homology of at least 99% belonged to the genera Acinetobacter, Alcaligenes, Delftia, Ochrobactrum, Pseudomonas, Stenotrophomonas, and Xanthobacter. PCR analysis showed that 13 out of 32 isolates contained the sequences (~1070 bp) homologous to the nitrilase genes reported previously in Alcaligenes faecalis JM3 (GenBank, D13419.1). Nine clones were capable of nitrile and amide transformation when grown on minimal salt medium. Acinetobacter sp. 11h and Alcaligenes sp. osv transformed 3-cyanopyridine to nicotinamide, while most of the clones possessed amidase activity (0.5 to 46.3 mmol/(g h) for acetamide and 0.1 to 5.6 mmol/(g h) for nicotinamide). Nicotinamide utilization by strain A. faecalis 2 was shown to result in excretion of a secondary metabolite, which was identified as dodecyl acrylate at 91% probability.

1-aminocyclopropane-1-carboxylate deaminase of the aerobic facultative methylotrophic actinomycete Amycolatopsis methanolica 239

2015-07-01

1-aminocyclopropane-1-carboxylate deaminase of the aerobic facultative methylotrophic actinomycete Amycolatopsis methanolica 239

Microbiology, Vol. , No. (2015) pp. \ -
\nArticle URL: http://link.springer.com/10.1134/S0026261715040074\nCitation: \ (2015) \nPublication Date: 2015-07-01\nJournal: Microbiology

The yeast Komagataella : A genetic genus in accordance with interspecies hybridization

2015-07-01

The yeast Komagataella : A genetic genus in accordance with interspecies hybridization

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Using induced complementary auxotrophic mutants and selective growth of prototrophic hybrids on minimal medium, hybridization of the type strain of Komagataella kurtzmanii VKPM Y-727 with the type strains of K. pastoris VKPM Y-3262, K. phaffii NRRL Y-7556, K. populi NRRL YB-455, K. pseudopastoris NRRL Y-27603, and K. ulmi NRRL YB-407 was demonstrated. The data obtained suggest that the genus Komagataella, established previously by phylogenetic analysis, corresponds well to the concept of genetic genus in ascomycetous fungi. According to this concept, a genetic genus is a group of hybridized species having a common mating type system. Application of the concept of genetic genus for different yeast genera is discussed.

Trophic patterns of functioning and microbial profile of the evolutionally established associated kefir grains culture

2015-07-01

Trophic patterns of functioning and microbial profile of the evolutionally established associated kefir grains culture

Microbiology, Vol. , No. (2015) pp. -

Abstract

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The associated culture of kefir grains was analyzed by molecular methods for determination of the functional activity of microbial isolates and molecular genetic techniques for their identification. A combination of 16S rRNA analysis and denaturing gradient gel electrophoresis was used to determine the microbial profile of kefir grains and to reveal lactic acid bacteria of two physiological groups, differing in their ability to use lactose for lactic acid fermentation. The role of inducible β-galactosidase of lactic acid bacteria for the functional stability of the microbial community was shown in the study of the functional activity and microbial profile of the kefir grains after long-time cultivation (over 4 years) on lactose-free milk. The results obtained improve our understanding of the possible trophic interactions in such microbial communities and may be used to develop the algorithm for experimental production of a stably associated culture of kefir grains.

Disruption of bacterial biofilms using recombinant dispersin B

2015-07-01

Disruption of bacterial biofilms using recombinant dispersin B

Microbiology, Vol. , No. (2015) pp. -

Abstract

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A synthetic gene encoding dispersin B of Aggregatibacter actinomycetemcomitans was cloned and expressed in Escherichia coli cells. Procedure for purification of recombinant dispersin B was developed, and its in vitro activity was determined. The enzyme was used in experiments on disruption of the biofilms formed by various microorganisms. It exhibited high activity against Staphylococcus epidermidis biofilms. The biofilms formed by Burkholderia cenocepacia and Achromobacter xylosoxidans were more resistant to the recombinant enzyme.

Methylopila turkiensis sp. nov., a new aerobic facultatively methylotrophic phytosymbiont

2015-07-01

Methylopila turkiensis sp. nov., a new aerobic facultatively methylotrophic phytosymbiont

Microbiology, Vol. , No. (2015) pp. -

Abstract

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A new facultative methylotroph, strain Side1^T, was isolated from the phyllosphere of Bougainvillea sp. L. The isolate is represented by rod-shaped, aerobic gram-negative asporogenous bacteria which divide by binary fission. Methanol and mono- and trimethylamine were utilized, as well as a limited spectrum of polycarbon substrates, while methane and dichloromethane were not used. Growth occurred at pH 6.0–9.0 with the optimum at pH 7.0 within the temperature range from 20 to 40°C (optimum at 28–30°C) and 0–2.5% NaCl in the medium. The predominant fatty acids were cis-11-octadecenoic (C18:1ω7c), 11-methyl-octadecenoic (C18:ω7c11Me), and stearic (C18:0) acids. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, and diphosphatidylglycerol were the dominant phospholipids. Q₁₀ was the dominant ubiquinone. The isolate oxidized methanol and methylamine by the appropriate dehydrogenases. The isocitrate lyase-negative variant of the serine pathway was used. Ammonium assimilation involved glutamate dehydrogenase and the glutamate cycle (glutamate synthase and glutamine synthetase). The strain synthesized indole and siderophores; it solubilized insoluble phosphates. The DNA G+C content (T\n \ _m) was 65.4 mol %. While the nucleotide sequence of the 16S rRNA gene of strain Side1 exhibited high similarity to those of Methylopila species (M. musalis MUSA^T and M. capsulata IM1^T), DNA-DNA homology with these cultures was 32–37%. The results obtained supported classification of strain Side1^T as a new species Methylopila turkiensis sp. nov. (VKM B-2748^T= DSM 27566^T).

Statistical medium optimization for the production of collagenolytic protease by Pseudomonas sp. SUK using response surface methodology

2015-07-01

Statistical medium optimization for the production of collagenolytic protease by Pseudomonas sp. SUK using response surface methodology

Microbiology, Vol. , No. (2015) pp. -

Abstract

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\n Pseudomonas sp. SUK producing an extracellular collagenolytic protease was isolated from soil samples from meat and poultry industrial area based in Kolhapur, India. Response surface methodology was employed for the optimization of different nutritional parameters influencing production of collagenolytic protease by newly isolated Pseudomonas sp. SUK in submerged fermentation. Initial screening of production parameters was performed using Plackett-Burman design and the variables with statistically significant effects on collagenolytic protease production were identified as gelatin, peptone, and K₂HPO₄. Further, optimization by response surface methodology (RSM) using Central Composite Design showed optimum production of collagenolytic protease with 12.05 g L⁻¹ of gelatin, 12.26 g L⁻¹ of peptone and 1.29 g L⁻¹ of K₂HPO₄. Collagenolytic protease production obtained experimentally has very close agreement with the model prediction value and the model was proven to be adequate. The statistical optimization by response surface methodology upsurges collagenolytic protease yield by 2.9 fold, hence the experimental design is effective towards process optimization. Moreover, ammonium sulphate precipitated, partially purified enzyme has shown to cleave collagen from bovine achilles tendon, which was observed by phase contrast microscopy, and SDS-PAGE. Hence, extracellular collagenolytic protease of Pseudomonas sp. SUK could have considerable potential for industrial as well as medical applications.

Structural characterization of the extracellular peptide metabolites of Luteococcus japonicus subsp. casei and their protective effect on probiotic bacteria

2015-07-01

Structural characterization of the extracellular peptide metabolites of Luteococcus japonicus subsp. casei and their protective effect on probiotic bacteria

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Protective effect of Luteococcus japonicus subsp. casei exometabolites on the cells of transient probiotic Propionibacterium strains, Enterococcus faecium, and the yeasts Saccharomyces cerevisiae Boulardii under exposure to bile salts (BS) and acid stress was studied. The extracellular peptide reactivating factor (RF) and the peptide component of the culture liquid (CL) after RF removal possessed a protective effect. Protective (preventive) and reactivating (after stress impact) application of RF resulted in 1.5- to 2.0-fold increased survival of the human transient probiotics P. freudenreichii, P. acidipropionici and E. faecium subjected to BS treatment of acid stress. The CL peptide fraction had a stronger protective effect. Its application for preincubation of P. acidipropionici cells resulted in 14-fold (BS treatment) and 8-fold (acid stress) increased survival compared to the control. Yeasts exhibited very high resistance to the stress factors used. Two active glycopeptide fractions with molecular masses of 1.8 and 2.4 kDa were found in RF. Analysis of their amino acid composition revealed the residues of glycine, leucine, proline, arginine, and aspartate/asparagine, while no residues of aromatic and sulfur-containing amino acids, or the disulfide bridge-type posttranslational modifications, were found. The possible mechanisms of reactivating and the protective effect of RF are discussed.

Formation of 55-kDa fragments under impaired coordination bonds and hydrophobic interactions in peripheral light-harvesting complexes isolated from photosynthetic purple bacteria

2015-05-01

Formation of 55-kDa fragments under impaired coordination bonds and hydrophobic interactions in peripheral light-harvesting complexes isolated from photosynthetic purple bacteria

Microbiology, Vol. , No. (2015) pp. -

Abstract

Size exclusion chromatography was used to assess the relative size of intact and diphenylamine-treated (DPA, with suppressed carotenoid synthesis) peripheral light-harvesting complexes (LH2 complexes) of the sulfur bacterium Allochromatium minutissimum. Both LH2 complexes were nonamers and had the same elution volume V_e, coinciding with that for the LH2 complex of Rhodoblastus acidophilus (strain 10050). Their molecular weight was 150 kDa. Both pheophytinization of bacteriochlorophyll (BChl) at low pH and treatment with the detergent LDAO, which affects the hydrophobic interactions between the neighboring protomers, result in the fragmentation of the ring of the isolated LH2 complexes and formation of 55-kDa fragments with molecular weights corresponding to one-third of the initial value. Fragmentation caused by both pheophytinization and detergent treatment was much more rapid in DPA LH2 complexes than in the intact ones. The 55-kDa fragments formed at low pH values contained monomeric bacteriopheophytin, while the fragments of a similar molecular weight formed at pH 8.0 in the presence of the detergent contained monomeric BChl. The observed fragmentation was hypothesized to reflect the inherent C₃ symmetry of the LH2 complexes, with the preliminarily assembled trimers used as building blocks.

Preparations of Bacillus pumilus secreted RNase: One enzyme or two'

2015-07-01

Preparations of Bacillus pumilus secreted RNase: One enzyme or two'

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Immunochemical analysis of the following purified preparations of Bacillus pumilus RNase (binase) was carried out: industrially manufactured enzyme (Institute of Organic Synthesis, Riga, Latvia) and the enzymes isolated from the culture liquid of the native B. pumilus producer and from the Escherichia coli BL21 recombinant strain bearing the pGEMGX1/ent/Bi plasmid. Electrophoresis of all three samples of purified binase revealed two protein fractions with ribonuclease activity possessing molecular masses of ∼12 and 25 kDa. The possible presence of binase II, a second secreted RNase, was ruled out. Both high- and low-molecular mass proteins interacted with binase-specific antibodies in the immunoblotting reaction, which indicated their antigenic identity. The difference in molecular mass between these proteins indicated the possible presence of two forms of binase in solution, a monomer and a dimer.

Metabolic properties of Pachysolen tannophilus mutants producing xylitol and ethanol from D-xylose

2015-07-01

Metabolic properties of Pachysolen tannophilus mutants producing xylitol and ethanol from D-xylose

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Activity of the major enzymes of D-xylose metabolism in the mutants of xylose-utilizing yeasts Pachysolen tannophilus selectively producing xylitol or ethanol was studied. The xylitol-producing strain exhibited low activities of xylitol dehydrogenase, xylose reductase with preferential affinity to NADPH, NAD⁺-dependent malate dehydrogenase, and cytochrome c oxidase (4.40, 4.80, 1.87, and 0.28 μmol mg⁻¹ min⁻¹, respectively). The cells of the ethanol-producing mutants exhibited elevated activity of NADH/NADPH-xylose reductase, xylitol dehydrogenase, 1-glycerophosphate dehydrogenase, and lactate dehydrogenase to 6.80, 8.60, 4.68, and 16.48 μmol mg⁻¹ min⁻¹, respectively. Effect of the NADPH/NADH imbalance on ethanol production accumulation and xylitol accumulation is discussed.

Transmembrane adenylate cyclase controls the virulence factors of plant pathogenic Pseudomonas siringae and mutualistic Rhizobium leguminosarum

2015-07-01

Transmembrane adenylate cyclase controls the virulence factors of plant pathogenic Pseudomonas siringae and mutualistic Rhizobium leguminosarum

Microbiology, Vol. , No. (2015) pp. -

Abstract

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The possible role of transmembrane adenylate cyclase of a plant pathogen Pseudomonas siringae pv. pisi and of a symbiotroph Rhizobium leguminosarum bv. viceae in control of the activity of their virulence factors (cellulases and pectinases, the enzymes degrading plant cell walls) was investigated. While transmembrane adenylate cyclase was found to control the activity of virulence factors in both pathogens and symbionts, the strategies employed by these microorganisms in molecular dialogue with plants involving the adenylate cylcase signal system exhibited both similarities and cardinal differences.

Production of xylitol and ethanol and activity of the key enzymes of D-xylose consumption in Pachysolen tannophilus mutant strains

2015-07-01

Production of xylitol and ethanol and activity of the key enzymes of D-xylose consumption in Pachysolen tannophilus mutant strains

Microbiology, Vol. , No. (2015) pp. -

Abstract

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Production of xylitol and ethanol, as well as activities of the key enzymes of D-xylose consumption, were studied in Pachysolen tannophilus mutants with altered growth on D-xylose, xylitol, ethanol, or D-glucose as sole carbon sources. Suppressed activity of xylose reductase with preferential affinity for NADPH and of xylitol dehydrogenase to 4.40 and 4.80 μmol mg⁻¹ min⁻¹, respectively, resulted in accumulation of xylitol (0.25 g per 1 g D-xylose consumed). The highest levels of NADH/NADPH-xylose reductase and xylitol dehydrogenase (6.00–6.80 and 6.80–8.40 μmol mg⁻¹ min⁻¹, respectively) were found in the strains producing 0.24–0.26 g ethanol per 1 g D-xylose. Application of Pa. tannophilus mutants for analysis of the regulation of D-xylose catabolism in yeasts is discussed.