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Applied Microbiology and Biotechnology (v.86, #2)

Peptide nucleic acids (PNAs) antisense effect to bacterial growth and their application potentiality in biotechnology by Masashi Hatamoto; Akiyoshi Ohashi; Hiroyuki Imachi (pp. 397-402).

Peptide nucleic acids (PNAs) are nucleic acid analogs having attractive properties such as quiet stability against nucleases and proteases, and they form strong complexes with complementary strands of DNA or RNA. Because of this attractive nature, PNA is often used in antisense technology to inhibit gene expression and microbial cell growth with high specificity. Many bacterial antisense or antiribosomal studies using PNA oligomers have been reported so far, and parameters to design effective antisense PNAs and to improve PNA cell entry for efficient inhibition of bacterial growth have been presented. However, there are still several obstacles such as low cellular uptake of PNA while applying antisense PNAs to a complex microbial community. On overcoming these problems, the PNA antisense technique might become a very attractive tool not only for controlling the microbial growth but also for further elucidating microbial ecology in complex microbial consortia. Here, we summarize and present recent studies on the development of antimicrobial PNAs targeting mRNAs and rRNAs. In addition, the application potentiality of antisense techniques in nonclinical biotechnology fields is discussed.

Keywords: Bacterial growth; Environmental microbiology; Antisense; rRNA

Engineering of protein secretion in yeast: strategies and impact on protein production by Alimjan Idiris; Hideki Tohda; Hiromichi Kumagai; Kaoru Takegawa (pp. 403-417).

Yeasts combine the ease of genetic manipulation and fermentation of a microorganism with the capability to secrete and modify foreign proteins according to a general eukaryotic scheme. Their rapid growth, microbiological safety, and high-density fermentation in simplified medium have a high impact particularly in the large-scale industrial production of foreign proteins, where secretory expression is important for simplifying the downstream protein purification process. However, secretory expression of heterologous proteins in yeast is often subject to several bottlenecks that limit yield. Thus, many studies on yeast secretion systems have focused on the engineering of the fermentation process, vector systems, and host strains. Recently, strain engineering by genetic modification has been the most useful and effective method for overcoming the drawbacks in yeast secretion pathways. Such an approach is now being promoted strongly by current post-genomic technology and system biology tools. However, engineering of the yeast secretion system is complicated by the involvement of many cross-reacting factors. Tight interdependence of each of these factors makes genetic modification difficult. This indicates the necessity of developing a novel systematic modification strategy for genetic engineering of the yeast secretion system. This mini-review focuses on recent strategies and their advantages for systematic engineering of yeast strains for effective protein secretion.

Keywords: Yeast secretion system; Secretion pathway; Protein folding; Membrane trafficking; Protease; Glycosylation

Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology by James M. Clomburg; Ramon Gonzalez (pp. 419-434).

The microbial production of biofuels is a promising avenue for the development of viable processes for the generation of fuels from sustainable resources. In order to become cost and energy effective, these processes must utilize organisms that can be optimized to efficiently produce candidate fuels from a variety of feedstocks. Escherichia coli has become a promising host organism for the microbial production of biofuels in part due to the ease at which this organism can be manipulated. Advancements in metabolic engineering and synthetic biology have led to the ability to efficiently engineer E. coli as a biocatalyst for the production of a wide variety of potential biofuels from several biomass constituents. This review focuses on recent efforts devoted to engineering E. coli for the production of biofuels, with emphasis on the key aspects of both the utilization of a variety of substrates as well as the synthesis of several promising biofuels. Strategies for the efficient utilization of carbohydrates, carbohydrate mixtures, and noncarbohydrate carbon sources will be discussed along with engineering efforts for the exploitation of both fermentative and nonfermentative pathways for the production of candidate biofuels such as alcohols and higher carbon biofuels derived from fatty acid and isoprenoid pathways. Continued advancements in metabolic engineering and synthetic biology will help improve not only the titers, yields, and productivities of biofuels discussed herein, but also increase the potential range of compounds that can be produced.

Keywords: Synthetic biology; Metabolic engineering; Biofuels production; Escherichia coli ; Biofuels

Nitrification and degradation of halogenated hydrocarbons—a tenuous balance for ammonia-oxidizing bacteria by Luis A. Sayavedra-Soto; Barbara Gvakharia; Peter J. Bottomley; Daniel J. Arp; Mark E. Dolan (pp. 435-444).

The process of nitrification has the potential for the in situ bioremediation of halogenated compounds provided a number of challenges can be overcome. In nitrification, the microbial process where ammonia is oxidized to nitrate, ammonia-oxidizing bacteria (AOB) are key players and are capable of carrying out the biodegradation of recalcitrant halogenated compounds. Through industrial uses, halogenated compounds often find their way into wastewater, contaminating the environment and bodies of water that supply drinking water. In the reclamation of wastewater, halogenated compounds can be degraded by AOB but can also be detrimental to the process of nitrification. This minireview considers the ability of AOB to carry out cometabolism of halogenated compounds and the consequent inhibition of nitrification. Possible cometabolism monitoring methods that were derived from current information about AOB genomes are also discussed. AOB expression microarrays have detected mRNA of genes that are expressed at higher levels during stress and are deemed “sentinel” genes. Promoters of selected “sentinel” genes have been cloned and used to drive the expression of gene-reporter constructs. The latter are being tested as early warning biosensors of cometabolism-induced damage in Nitrosomonas europaea with promising results. These and other biosensors may help to preserve the tenuous balance that exists when nitrification occurs in waste streams containing alternative AOB substrates such as halogenated hydrocarbons.

Keywords: Nitrification; Chlorinated aliphatic hydrocarbons; N. europaea ; Degradation; Cometabolism

Microbial l-methioninase: production, molecular characterization, and therapeutic applications by Ashraf S. El-Sayed (pp. 445-467).

l-Methioninase is ubiquitous in all organisms except in mammals. It mainly catalyzes the, α, γ-elimination of l-methionine to α-ketobutyrate, methanethiol, and ammonia. Unlike normal cells, methionine dependency was reported as a biochemical phenomenon among various types of cancer cells. Thus, l-methioninase is the universal protocol for triggering the majority of tumor cells. This review is an attempt to briefly describe the occurrence of the biochemical and molecular properties of l-methioninase by a comparative manner to the eukaryotic and prokaryotic source for the maximum exploitation in the therapeutic field. The combination of l-methioninase treatment, gene therapy, and chemotherapeutic drugs clearly explores the various therapeutic aspects of this enzyme. Finally, the perspectives for increasing the therapeutic efficacy of this enzyme were described.

Keywords: Antitumor enzymes; l-Methioninase; Properties; Therapeutic application

Continuous 2-Keto-l-gulonic acid fermentation by mixed culture of Ketogulonicigenium vulgare DSM 4025 and Bacillus megaterium or Xanthomonas maltophilia by Yoshinori Takagi; Teruhide Sugisawa; Tatsuo Hoshino (pp. 469-480).

The fermentation process of 2-keto-L-gulonic acid (2KGA) from L-sorbose was developed using a two-stage continuous fermentation system. The mixed culture of Ketogulonicigenium vulgare DSM 4025 and Bacillus megaterium DSM 4026 produced 90 g/L of 2KGA from 120 g/L of L-sorbose at the dilution rate of 0.01 h⁻¹ in a single-stage continuous fermentation process. But after the production period was beyond 150 h, the significant decrease of 2KGA productivity was observed. When the non-spore forming bacteria Xanthomonas maltophilia IFO 12692 was used instead of B. megaterium DSM 4026 as a partner strain for K. vulgare DSM 4025, the 2KGA productivity was significantly improved in a two-stage continuous culture mode, in which two fermentors of the same size and volume were connected in series. In this mode, with two sets of 3-L jar fermentors, the steady state could be continued to over 1,331.5 h at least, when the dilution rates were 0.0382 h⁻¹ and 0.0380 hour⁻¹, respectively, for the first and second fermentors. The overall productivity was calculated to be 2.15 g/L/h at 113.1 g/L and a molar conversion yield of 90.1%. In the up-scaling fermentation to 30-L jar fermentors, 118.5 g/L of 2KGA was produced when dilution rates in both stages were 0.0430 hour⁻¹, and the overall productivity was calculated to be 2.55 g/L/h.

Keywords: 2-Keto-L-gulonic acid; L-Sorbose; Two-stage continuous mode; Mixed culture; Ketogulonicigenium vulgare ; Xanthomonas maltophilia

An efficient method for N-acetyl-d-neuraminic acid production using coupled bacterial cells with a safe temperature-induced system by Yinan Zhang; Fei Tao; Miaofen Du; Cuiqing Ma; Jianhua Qiu; Lichuan Gu; Xiaofei He; Ping Xu (pp. 481-489).

N-Acetyl-d-neuraminic acid (Neu5Ac) is a precursor for producing many pharmaceutical drugs such as zanamivir which have been used in clinical trials to treat and prevent the infection with influenza virus, such as the avian influenza virus H5N1 and the current 2009 H1N1. Two recombinant Escherichia coli strains capable of expressing N-acetyl-d-glucosamine 2-epimerase and N-acetyl-d-neuraminic acid aldolase were constructed based on a highly efficient temperature-responsive expression system which is safe compared to chemical-induced systems and coupled in Neu5Ac production. Carbon sources were optimized for Neu5Ac production, and the concentration effects of carbon sources on the production were investigated. With 2,200 mM pyruvate as carbon source and substrate, 61.9 mM (19.1 g l⁻¹) Neu5Ac was produced from 200 mM N-acetyl-d-glucosamine (GlcNAc) in 36 h by the coupled cells. Our Neu5Ac biosynthetic process is favorable compared with natural product extraction, chemical synthesis, or even many other biocatalysis processes.

Keywords: N-Acetyl-d-glucosamine 2-epimerase; N-Acetyl-d-neuraminic acid aldolase; N-Acetyl-d-neuraminic acid production; Epimerization; Temperature-induced expression system

Microbial conversion of ruscogenin by Gliocladium deliquescens NRRL1086: glycosylation at C-1 by Nai-Dong Chen; Jian Zhang; Ji-Hua Liu; Bo-Yang Yu (pp. 491-497).

The glycosylation of ruscogenin (1) by Gliocladium deliquescens NRRL 1086 was observed and gave a regioselectively glycosylated product identified as ruscogenin 1-O-β-D-glucopyranoside (2) by infrared, mass spectrometry, and nuclear magnetic resonance spectra. Time-course studies indicated that it appeared to be favorable to accumulate 2 when ruscogenin was added to the 24-h-old stage II culture, and the yield of 2 was about 20.1% during 120∼168 h. It was noted that additional carbohydrates could significantly increase glycoside formation and the yield of 2 even reached as high as 68% compared with the control 20.1%. The primary investigation about the characteristics of the enzyme resulted that the reaction was blocked by β-glycosidase inhibitor imidazole, however, was enhanced remarkably by glycosyltransferase inhibitor sodium dodecyl sulfate. To our knowledge, this is the first reported case of producing steroidal saponin by microbial transformation, and G. deliquescens NRRL1086 would be a practical and highly efficient tool in producing natural ruscogenin monoside.

Keywords: Gliocladium deliquescens NRRL1086; Biotransformation; Ruscogenin; Microbial glycosylation

A downstream process for production of a viable and stable Bacillus cereus aquaculture biological agent by Rajesh Lalloo; Dheepak Maharajh; Johann Görgens; Neil Gardiner (pp. 499-508).

Biological products offer advantages over chemotherapeutics in aquaculture. Adoption in commercial application is lacking due to limitations in process and product development that address key end user product requirements such as cost, efficacy, shelf life and convenience. In previous studies, we have reported on the efficacy, physiological robustness and low-cost spore production of a Bacillus cereus isolate (NRRL 100132). This study examines the development of suitable spore recovery, drying, formulation and tablet production from the fermentation product. Key criteria used for such downstream process unit evaluation included spore viability, recovery, spore balance, spore re-germination, product intermediate stability, end product stability and efficacy. A process flow sheet comprising vertical tube centrifugation, fluidised bed agglomeration and tablet pressing yielded a suitable product. The formulation included corn steep liquor and glucose to enhance subsequent spore re-germination. Viable spore recovery and spore balance closure across each of the process units was high (>70% and >99% respectively), with improvement in recovery possible by adoption of continuous processing at large scale. Spore re-germination was 97%, whilst a product half-life in excess of 5 years was estimated based on thermal resistance curves. The process resulted in a commercially attractive product and suitable variable cost of production.

Keywords: Bacillus cereus ; Downstream processing; Biological agent; Aquaculture

Investigation of acetic acid-catalyzed hydrothermal pretreatment on corn stover by Jian Xu; Mette Hedegaard Thomsen; Anne Belinda Thomsen (pp. 509-516).

Acetic acid (AA)-catalyzed liquid hot water (LHW) pretreatments on raw corn stover (RCS) were carried out at 195 °C at 15 min with the acetic acid concentrations between 0 and 400 g/kg RCS. After pretreatment, the liquor fractions and water-insoluble solids (WIS) were collected separately and tested in terms of the recoveries of glucan and xylan from both the liquor fractions and the WIS, toxicity level of the liquors, and the convertibility of WIS to ethanol. The highest glucan recoveries was found to be 97.42% and 97.94% when 15 and 30 g AA/kg RCS were employed, respectively. The highest xylan recovery of 81.82% was observed by the pretreatment with 10 g AA/kg RCS. The toxic test on liquors showed that the inhibition effect happened to Baker's yeast when the acetic acid used in the pretreatment was higher than 100 g/kg RCS. The WIS obtained from the pretreatment with 15 g and 30 g/kg RCS were subjected to enzymatic hydrolysis and more easily converted to ethanol by Baker's yeast, which gave the ethanol concentration of 33.72 g/L and 32.06 g/L, respectively, higher than 22.04 g/L which was from the non-catalyzed LHW pretreatment (195 °C, 15 min). The ethanol concentration from the RCS was only 8.02 g/L.

Keywords: Pretreatment; Baker's yeast; Glucan/xylan recovery; Convertibility; Fermentability

A novel acid-stable, acid-active β-galactosidase potentially suited to the alleviation of lactose intolerance by Shane O’Connell; Gary Walsh (pp. 517-524).

Extracellular β-galactosidase produced by a strain of Aspergillus niger van Tiegh was purified to homogeneity using a combination of gel filtration, ion-exchange, chromatofocusing, and hydrophobic interaction chromatographies. The enzyme displayed a temperature optimum of 65 °C and a low pH optimum of between 2.0 and 4.0. The monomeric glycosylated enzyme displayed a molecular mass of 129 kDa and an isoelectric point of 4.7. Protein database similarity searching using mass spectrometry-derived sequence data indicate that the enzyme shares homology with a previously sequenced A. niger β-galactosidase. Unlike currently commercialised products, the enzyme displayed a high level of stability when exposed to simulated gastric conditions in vitro, retaining 68 ± 2% of original activity levels. This acid-stable, acid-active β-galactosidase was formulated, along with a neutral β-galactosidase from Kluyveromyces marxianus DSM5418, in a novel two-segment capsule system designed to ensure delivery of enzymes of appropriate physicochemical properties to both stomach and small intestine. When subjected to simulated full digestive tract conditions, the twin lactase-containing capsule hydrolyzed, per unit activity, some 3.5-fold more lactose than did the commercial supplemental enzyme. The acid-stable, acid-active enzyme, along with the novel two-segment delivery system, may prove beneficial in the more effective treatment of lactose intolerance.

Keywords: Lactase; β-galactosidase; Aspergillus niger van Tiegh; Lactose intolerance; Two-segment capsule

The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity by Xiao-Zhou Zhang; Zuoming Zhang; Zhiguang Zhu; Noppadon Sathitsuksanoh; Yunfeng Yang; Y.-H. Percival Zhang (pp. 525-533).

Family 48 glycoside hydrolases (cellobiohydrolases) are among the most important cellulase components for crystalline cellulose hydrolysis mediated by cellulolytic bacteria. Open reading frame (Cphy_3368) of Clostridium phytofermentans ISDg encodes a putative family 48 glycoside hydrolase (CpCel48) with a family 3 cellulose-binding module. CpCel48 was successfully expressed as two soluble intracellular forms with or without a C-terminal His-tag in Escherichia coli and as a secretory active form in Bacillus subtilis. It was found that calcium ion enhanced activity and thermostability of the enzyme. CpCel48 had high activities of 15.1 U μmol⁻¹ on Avicel and 35.9 U μmol⁻¹ on regenerated amorphous cellulose (RAC) with cellobiose as a main product and cellotriose and cellotetraose as by-products. By contrast, it had very weak activities on soluble cellulose derivatives (e.g., carboxymethyl cellulose (CMC)) and did not significantly decrease the viscosity of the CMC solution. Cellotetraose was the smallest oligosaccharide substrate for CpCel48. Since processivity is a key characteristic for cellobiohydrolases, the new initial false/right attack model was developed for estimation of processivity by considering the enzyme's substrate specificity, the crystalline structure of homologous Cel48 enzymes, and the configuration of cellulose chains. The processivities of CpCel48 on Avicel and RAC were estimated to be ∼3.5 and 6.0, respectively. Heterologous expression of secretory active cellobiohydrolase in B. subtilis is an important step for developing recombinant cellulolytic B. subtilis strains for low-cost production of advanced biofuels from cellulosic materials in a single step.

Keywords: Clostridium phytofermentans ; Cellobiohydrolase; Family 48 exoglucanase; Bacillus subtilis ; Characterization; Processivity

Factors affecting production and stability of the AcAFP antifungal peptide secreted by Aspergillus clavatus by Houda Skouri-Gargouri; Neila Jellouli-Chaker; Ali Gargouri (pp. 535-543).

We have previously reported the identification of a small, basic and cysteine-rich antifungal peptide (AcAFP) secreted by Aspergillus clavatus and shown its ability to prevent growth of various human- and plant-pathogenic filamentous fungi. In this study, we sought to determine the physiological/microbiological requirements to enhance the AcAFP production and the conditions influencing its stability. The maximum of AcAFP production was obtained when A. clavatus was grown on 2% glycerol as sole carbon source and 100 mM NaCl. The AcAFP expression was shown to be influenced by pH, being suppressed under acidic (pH 5) and strongly induced under alkaline conditions. The activity of the purified AcAFP was not affected by temperature; it loosed approximately 20% of its activity after 3 h at 100°C and was efficient through a large pH range (pH 5-12) with an optimum at pH 8. AcAFP activity decreased at high ionic strength and in the presence of 10 mM of divalent cations (Mn²⁺, Fe²⁺ and Ca²⁺).

Keywords: Aspergillus clavatus ; Antifungal activity; Salt effect; Thermostability; Carbon sources

Synthesis of dextrans with controlled amounts of α-1,2 linkages using the transglucosidase GBD–CD2 by Yoann Brison; Emeline Fabre; Claire Moulis; Jean-Charles Portais; Pierre Monsan; Magali Remaud-Siméon (pp. 545-554).

GBD–CD2 is an α-1,2 transglucosidase engineered from DSR-E, a glucansucrase naturally produced by Leuconostoc mesenteroides NRRL B-1299. This enzyme catalyses from sucrose, the α-1,2 transglucosylation of glucosyl moieties onto α-1,6 dextran chains. Steady-state kinetic studies showed that hydrolysis and transglucosylation reactions occurred at the early stage of the reaction in the presence of 70 kDa dextran as acceptor and sucrose. The transglucosylation reaction catalysed by GBD–CD2 follows a Ping Pong Bi Bi mechanism with a high k _cat value of 970 s⁻¹. The amount of the synthesised α-1,2 side chains was found to be directly dependent on the initial molar ratio [Sucrose]/[Dextran]. Dextrans with controlled α-1,2 linkage contents ranging from 13% to 40% were synthesised. The procedure resulted in the production of dextrans with the highest content of α-1,2 linkages ever reported.

Keywords: Kinetic mechanism; Alpha-1,2 transglucosylation; Ping Pong Bi Bi; Engineered glucansucrase; Dextran

Characterization of an exo-acting intracellular α-amylase from the hyperthermophilic bacterium Thermotoga neapolitana by Kyung-Min Park; So-Young Jun; Kyoung-Hwa Choi; Kwan-Hwa Park; Cheon-Seok Park; Jaeho Cha (pp. 555-566).

We cloned and expressed the gene for an intracellular α-amylase, designated AmyB, from the hyperthermophilic bacterium Thermotoga neapolitana in Escherichia coli. The putative intracellular amylolytic enzyme contained four regions that are highly conserved among glycoside hydrolase family (GH) 13 α-amylases. AmyB exhibited maximum activity at pH 6.5 and 75°C, and its thermostability was slightly enhanced by Ca²⁺. However, Ca²⁺ was not required for the activity of AmyB as EDTA had no effect on enzyme activity. AmyB hydrolyzed the typical substrates for α-amylase, including soluble starch, amylose, amylopectin, and glycogen, to liberate maltose and minor amount of glucose. The hydrolytic pattern of AmyB is most similar to those of maltogenic amylases (EC 3.2.1.133) among GH 13 α-amylases; however, it can be distinguished by its inability to hydrolyze pullulan and β-cyclodextrin. AmyB enzymatic activity was negligible when acarbose, a maltotetraose analog in which a maltose residue at the nonreducing end was replaced by acarviosine, was present, indicating that AmyB cleaves maltose units from the nonreducing end of maltooligosaccharides. These results indicate that AmyB is a new type exo-acting intracellular α-amylase possessing distinct characteristics that distinguish it from typical α-amylase and cyclodextrin-/pullulan-hydrolyzing enzymes.

Keywords: GH 13 α-amylases; Hyperthermophiles; Intracellular α-amylase; Thermostability; Thermotoga neapolitana

Analysis of extracellular alginate lyase and its gene from a marine bacterial strain, Pseudoalteromonas atlantica AR06 by Ryoji Matsushima; Hiroko Danno; Motoharu Uchida; Kenji Ishihara; Toshiyuki Suzuki; Masaki Kaneniwa; Yoshiyuki Ohtsubo; Yuji Nagata; Masataka Tsuda (pp. 567-576).

Pseudoalteromonas atlantica AR06 is a marine bacterial strain that can utilize alginate as a sole source of carbon and energy. The extracellular protein fraction prepared from the AR06 cultivation media exhibited alginate lyase activity to depolymerize the alginate molecules having homopolymeric and heteropolymeric forms of mannuronate and guluronate so as to mainly convert into the dimer to tetramer. A DNA fragment encoding a portion of alginate lyase was amplified from AR06 genomic DNA by PCR using a set of degenerated primers, and then the whole alginate lyase gene, named alyA, and its flanking regions were obtained from a cosmid library of AR06 genomic DNA. The alyA mutant of AR06 showed (1) the loss of alginate depolymerization activity on alginate agar plate and (2) significant growth defects in alginate minimal medium; these defects were complemented by the introduction of the alyA gene. Furthermore, zymography and biochemical analyses revealed that three extracellular protein bands of AR06 had alginate lyase activities and that all three protein bands were derived from the nascent alyA gene product. These results clearly indicated that the alyA gene greatly contributes to the assimilation of alginate in AR06. The transcription of the alyA gene was induced by the presence of alginate in minimal medium, but its obvious induction was not observed in rich medium even in the presence of alginate.

Keywords: Pseudoalteromonas atlantica ; Bifunctional alginate lyase; Extracellular enzyme; Expression of alyA gene

Purification, characterization, and mode of action of a rhamnogalacturonan hydrolase from Irpex lacteus, tolerant to an acetylated substrate by Jessica Normand; Marie-Christine Ralet; Jean-François Thibault; Hélène Rogniaux; Philippe Delavault; Estelle Bonnin (pp. 577-588).

A novel rhamnogalacturonase (RGase) acting on an acetylated substrate was detected in the commercial preparation Driselase, an enzymatic mixture derived from the basidiomycete Irpex lacteus. The activity was isolated by hydrophobic interaction chromatography, gel filtration, and preparative isoelectric focusing, resulting in the isolation of five different rhamnogalacturonan hydrolases exhibiting various isoelectric points from 6.2 to 7.7. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and mass spectrometry analyses after trypsin cleavage of the five fractions revealed that the five rhamnogalacturonases have a molar mass of 55 kDa without any divergences in the identified peptides. The RGase with a pI of 7.2 exhibited a pH optimum between 4.5 and 5 and a temperature optimum between 40°C and 50°C. Its mode of action was analyzed by mass spectrometry of the oligosaccharides produced after hydrolysis of acetylated and nonacetylated rhamnogalacturonan. Oligomers esterified by an acetyl group on the reducing galacturonic acid residue or fully acetylated were detected in the hydrolysate showing that the novel enzyme is able to bind acetylated galacturonic acid in its active site.

Keywords: Rhamnogalacturonase; Acetylated rhamnogalacturonan; Irpex lacteus ; Rhamnogalacturonan oligomer mass spectroscopy

Collagenolytic subtilisin-like protease from the deep-sea bacterium Alkalimonas collagenimarina AC40^T by Atsushi Kurata; Kohsuke Uchimura; Tohru Kobayashi; Koki Horikoshi (pp. 589-598).

A new alkaline protease (AcpII) was purified from a culture of the deep-sea bacterium Alkalimonas collagenimarina AC40^T. AcpII degraded collagen three times faster than it degraded casein. The optimal pH was 8.5–9, and the optimal temperature was 45°C for the degradation of collagen. AcpII was completely inhibited by phenylmethylsulfonyl fluoride and partially by EDTA. Cloning and sequencing the gene for AcpII revealed a 2,283-bp open reading frame encoding a protein of 760 amino acids. AcpII comprises a prepropeptide, a catalytic domain that includes a protease-associated domain (PA domain), and tandem repeat prepeptidase C-terminal domains. To elucidate the role of the PA domain of AcpII, we constructed genes for two enzyme derivatives that possessed the catalytic domains with or without the PA domain and expressed them in Escherichia coli. The derivative without the PA domain showed increased specific activities toward all proteinaceous substrates tested, including gelatin, casein, and collagen, compared with those of the derivative with the PA domain.

Keywords: Collagenolytic protease; Subtilisin; Subtilase family A; PA domain; Deep-sea; Alkalimonas collagenimarina

Heterologous expression of an Agaricus meleagris pyranose dehydrogenase-encoding gene in Aspergillus spp. and characterization of the recombinant enzyme by Ines Pisanelli; Magdalena Kujawa; Doris Gschnitzer; Oliver Spadiut; Bernhard Seiboth; Clemens Peterbauer (pp. 599-606).

Pyranose dehydrogenase (PDH) is a flavin-dependant sugar oxidoreductase found in the family Agaricaceae, basidiomycetes that degrade lignocellulose-rich forest litter, and is catalytically related to the fungal enzymes pyranose 2-oxidase and cellobiose dehydrogenase. It has broad substrate specificity and displays similar activities with most sugar constituents of lignocellulose including disaccharides and oligosaccharides, a number of (substituted) quinones, and metal ions are suitable electron acceptors rather than molecular oxygen. In contrast to pyranose 2-oxidase and cellobiose dehydrogenase, which oxidize regioselectively at C-2 and C-1, respectively, PDH is capable of oxidation on C-1 to C-4 as well as double oxidations, depending on the nature of the substrate. This makes it a very interesting enzyme for biocatalytic applications, as many of the reaction products are otherwise unaccessible by chemical or enzymatic means. PDH was characterized in detail in a limited number of fungi, and the first encoding genes were isolated only recently. We report here, for the first time, the heterologous expression of one of these genes, encoding the major PDH protein in Agaricus meleagris, in the filamentous fungi Aspergillus nidulans, and Aspergillus niger.

Engineered amadoriase II exhibiting expanded substrate range by Jing Zheng; Hong Guan; Lihua Xu; Rong Yang; Zhanglin Lin (pp. 607-613).

Amadori compounds are ubiquitous in vivo as well as in food and have been implicated in diabetic complications and aging. In recent years, fructosyl amine oxidases (FAOXs) which cleave Amadori products are gaining increasing attention. Until now, however, all FAOXs can only react with small glycated substrates (such as fructosyl amino acids or dipeptides), which has hindered the applications of this new class of enzymes in diagnosis, therapeutics, and detergents. In this study, Aspergillus fumigatus amadoriase II was engineered with the aim to expand its substrate range, using a heat-inducible autolytic vector and fructosyl–polylysine (3–13 lysines) as an intermediate-sized model substrate. After two rounds of directed evolution, a mutant (SII-82) was obtained that showed an 8.78-fold increase in the activity toward fructosyl–polylysine and which also performed several fold better than the wild-type on real gravy stains at concentrations of 10–100 µg/ml (parts per million). Mutational analyses revealed useful clues for altering the substrate-binding pocket. This study suggests that it is possible to manipulate fructosyl amine oxidases to accommodate larger substrates, and that mutant SII-82 might serve as a template for further engineering.

Keywords: Fructosyl amine oxidase; FAOX; Amadoriase II; Directed evolution; Heat inducible autolysis; High-throughput screening

The inhibitory effects of mushroom extracts on sucrose-dependent oral biofilm formation by Akira Yano; Sayaka Kikuchi; Yoshihisa Yamashita; Yuichi Sakamoto; Yuko Nakagawa; Yasuo Yoshida (pp. 615-623).

Mushrooms contain large quantities of α-glucans. Shiitake (Lentinula edodes), Japan’s most popular edible mushroom, has been reported to contain about 6% (weight/dried weight) of α-(1,3)-glucan. This glucan is one of the major components of oral biofilm formed by the cariogenic bacteria Streptococcus mutans and Streptococcus sobrinus. We found that extracts from shiitake and other edible mushrooms could reduce preformed biofilms of S. mutans and S. sobrinus in the presence of dextranase. We also investigated the α-glucanase activities of shiitake mushroom extracts and their effects on biofilm formation. The extracts possessed α-glucanase activity and degraded water-insoluble glucans from mutans streptococci. The extracts strongly inhibited the sucrose-dependent formation of biofilms by S. mutans and S. sobrinus in the presence of dextranase. Our results suggest that some components of mushrooms, including α-glucanases, might inhibit the sucrose-induced formation of oral biofilms.

Keywords: Lentinula edodes ; Shiitake mushroom; Streptococcus mutans ; Streptococcus sobrinus ; Oral biofilm; Mutanase

Purification and characterization of acetophenone reductase with excellent enantioselectivity from Geotrichum candidum NBRC 4597 by Yasuo Nakata; Takuro Fukae; Ryoji Kanamori; Shuji Kanamaru; Tomoko Matsuda (pp. 625-631).

NADH-dependent enzyme reducing acetophenone derivatives with high stereoselectivities and wide substrate specificities from Geotrichum candidum NBRC 4597 was isolated, purified, characterized, and used for asymmetric synthesis. Through five-step purification including ammonium sulfate fractionation and a series of chromatographies, the enzyme was purified about 150-fold with a yield of 5.6%. The active enzyme has a molecular mass of 73 kDa determined by gel filtration chromatography, and the SDS-PAGE result reveals that the molecular size of the subunit is 36 kDa. These results indicate that the enzyme consists of a homodimer of a 36 kDa subunit. The acetophenone reductase exhibited the highest activity at 50°C and optimal pH at 5.5. The enzyme was the most stable at 40°C. No metal ions considerably activated the enzyme, and such metal ions as Cu²⁺, Cd²⁺, and Zn²⁺ strongly inhibited the activity of the enzyme. The V _max and the apparent K _m value of the reductase were 77.0 µmol/min per milligram of protein and 0.296 mM for acetophenone, respectively. The N-terminal and internal amino acid sequences were determined by peptide sequencer. Furthermore, the purified enzyme was used for asymmetric reduction of acetophenone, resulting in the formation of corresponding (S)-alcohol with 99% ee.

Keywords: Reductase; Asymmetric reduction; Enantioselective; Acetophenone; (S)-1-Phenylethanol

DnaK/DnaJ-assisted recombinant protein production in Trichoplusia ni larvae by Mónica Martínez-Alonso; Silvia Gómez-Sebastián; José M. Escribano; Juan-Carlos Saiz; Neus Ferrer-Miralles; Antonio Villaverde (pp. 633-639).

The DnaK/DnaJ Escherichia coli chaperone pair, co-produced along with recombinant proteins, has been widely used to assist protein folding in bacterial cells, although with poor consensus about the ultimate effect on protein quality and its general applicability. Here, we have evaluated for the first time these bacterial proteins as folding modulators in a highly promising recombinant protein platform based on insect larvae. Intriguingly, the bacterial chaperones enhanced the solubility of a reporter, misfolding-prone GFP, doubling the yield of recombinant protein that can be recovered from the larvae extracts in a production process. This occurs without negative effects on the yield of total protein (extractable plus insoluble), indicative of a proteolytic stability of the chaperone substrate. It is in contrast with what has been observed in bacteria for the same reporter protein, which is dramatically degraded in a DnaK-dependent manner. The reported data are discussed in the context of the biotechnological potential and applicability of prokaryotic chaperones in complex, eukaryotic factories for recombinant protein production.

Keywords: Protein folding; Chaperones; Insect larvae; Protein quality; DnaK; Protein factories

Molecular design of yeast cell surface for adsorption and recovery of molybdenum, one of rare metals by Takashi Nishitani; Mariko Shimada; Kouichi Kuroda; Mitsuyoshi Ueda (pp. 641-648).

In modern industrial society, molybdenum is one of the important metals for development of the industry of rare metals. It is important to recycle the rare metals from wastes because they are technically and economically difficult to be dug and be purified, and they exist in only a few regions in the world. In this study, ModE protein derived from Escherichia coli, which is a molybdate-dependent transcriptional regulator with the ability to bind molybdate as a form of soluble molybdenum, was displayed on the yeast cell surface by α-agglutinin-based cell surface display system for the adsorption and recovery of molybdate. Displayed ModE, confirmed by immunofluorescence labeling, caught molybdate more preferably at pH 3.0 than at basic pH. Yeast cells displaying C-terminal domain of ModE, which lacks N-terminal DNA binding domain, more effectively adsorbed molybdate than those displaying full-length ModE, suggesting that the deletion of the domain unrelated to metal binding enhanced the binding ability. Our results indicated that the adsorption system on cell surface of yeast cells displaying ModE is effective not only for adsorption of molybdate as a rare metal bioadsorbent but also for the easy recovery of molybdate located on the cell surface.

Keywords: Cell surface engineering; Rare metal; Molybdenum; ModE; Bioadsorption

Halophilic β-lactamase as a new solubility- and folding-enhancing tag protein: production of native human interleukin 1α and human neutrophil α-defensin by Hiroko Tokunaga; Shoko Saito; Kazuki Sakai; Rui Yamaguchi; Iwao Katsuyama; Tomohiro Arakawa; Kikuo Onozaki; Tsutomu Arakawa; Masao Tokunaga (pp. 649-658).

The amino acid composition of halophilic enzymes is characterized by an abundant content of acidic amino acid, which confers to the halophilic enzymes extensive negative charges at neutral pH and high aqueous solubility. This negative charge prevents protein aggregation when denatured and thereby leads to highly efficient protein refolding. β-Lactamase from periplasmic space of moderate halophile (BLA), a typical halophilic enzyme, can be readily expressed as a native, active form in Escherichia coli cytoplasm. Similar to other halophilic enzymes, BLA is soluble upon denaturation by heat or urea treatments and, hence, can be efficiently refolded. Such high solubility and refolding efficiency make BLA a potential fusion partner for expression of aggregation-prone heterologous proteins to be expressed in E. coli. Here, we succeeded in the soluble expression of several “difficult-to-express” proteins as a BLA fusion protein and verified biological activities of human interleukin 1α and human neutrophil α-defensin, HNP-1.

Keywords: Halophilic; β-Lactamase; Interleukin 1α; α-Defensin; Solubility-enhancing tag; Folding-enhancing tag

A novel expression system for intracellular production and purification of recombinant affinity-tagged proteins in Aspergillus niger by Andreas H. F. J. Roth; Petra Dersch (pp. 659-670).

A set of different integrative expression vectors for the intracellular production of recombinant proteins with or without affinity tag in Aspergillus niger was developed. Target genes can be expressed under the control of the highly efficient, constitutive pkiA promoter or the novel sucrose-inducible promoter of the β-fructofuranosidase (sucA) gene of A. niger in the presence or absence of alternative carbon sources. All expression plasmids contain an identical multiple cloning sequence that allows parallel construction of N- or C-terminally His₆- and StrepII-tagged versions of the target proteins. Production of two heterologous model proteins, the green fluorescence protein and the Thermobifida fusca hydrolase, proved the functionality of the vector system. Efficient production and easy detection of the target proteins as well as their fast purification by a one-step affinity chromatography, using the His₆- or StrepII-tag sequence, was demonstrated.

Keywords: Aspergillus niger ; Affinity-tagged proteins; Protein production; Inducible promoter; Expression vectors; sucA promoter

Evidence for the in vivo expression of a distant downstream gene under the control of ColE1 replication origin by Sofia C. Ribeiro; Duarte M. F. Prazeres; Gabriel A. Monteiro (pp. 671-679).

ColE1-like plasmids are widely used as expression vectors and as gene delivery vehicles. We have recently described a naturally occurring plasmid deletion phenomenon in the ColE1-type plasmid, pCI-neo, which leads to the detectable expression of an apparently promotorless kanamycin resistance gene. In the current work, we found that the expression of that aminoglycoside phosphotransferase (aph) gene is regulated by an RNAII preprimer promoter located within the plasmid ColE1 replication origin, as a consequence of the extension of the RNA II species for at least 1.5 kb, up to the aph gene. This mechanism is dependent on the nonformation and/or dissociation of the hybrid between plasmid DNA and RNA II preprimer transcript. This is the first in vivo description of RNA II transcription beyond ori in wild-type Escherichia coli strains and nonmutated RNAII plasmid sequences resulting in productive transcription of distant downstream genes. Our results raise questions about unwanted expression of genes from expression or cloning vectors of ColE1 type and highlight the importance of a more careful design of ColE1-derived plasmid vectors.

Keywords: Plasmid; ColE1-type replication; RNA II transcription read through

Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing by Anthony R. Borneman; Eveline J. Bartowsky; Jane McCarthy; Paul J. Chambers (pp. 681-691).

Many bacteria display substantial intra-specific genomic diversity that produces significant phenotypic variation between strains of the same species. Understanding the genetic basis of these strain-specific phenotypes is especially important for industrial microorganisms where these characters match individual strains to specific industrial processes. Oenococcus oeni, a bacterium used during winemaking, is one such industrial species where large numbers of strains show significant differences in commercially important industrial phenotypes. To ascertain the basis of these phenotypic differences, the genomic content of ten wine strains of O. oeni were mapped by array-based comparative genome hybridization (aCGH). These strains comprised a genomically diverse group in which large sections of the reference genome were often absent from individual strains. To place the aCGH results in context, whole genome sequence was obtained for one of these strains and compared with two previously sequenced, unrelated strains. While the three strains shared a core group of conserved ORFs, up to 10% of the coding potential of any one strain was specific to that isolate. The genome of O. oeni is therefore likely to be much larger than that present in any single strain and it is these strain-specific regions that are likely to be responsible for differences in industrial phenotypes.

Keywords: Comparative genomics; Whole genome sequencing; Lactic acid bacteria; Oenococcus

Very early acetaldehyde production by industrial Saccharomyces cerevisiae strains: a new intrinsic character by Naoufel Cheraiti; Stéphane Guezenec; Jean-Michel Salmon (pp. 693-700).

During a general survey of the acetaldehyde-producing properties of commercially available wine yeast strains, we discovered that, although final acetaldehyde production cannot be used as a discriminating factor between yeast strains, initial specific acetaldehyde production rates were of highly interest for classifying yeast strains. This parameter is very closely related to the growth- and fermentation-lag phase durations. We also found that this acetaldehyde early production occurs with very different extent between commercial active dry yeast strains during the rehydration phase and could partially explain the known variable resistance of yeast strains to sulfites. Acetaldehyde production appeared, therefore, as very precocious, strain-dependent, and biomass-independent character. These various findings suggest that this new intrinsic characteristic of industrial fermenting yeast may be likely considered as an early marker of the general fermenting activity of industrial fermenting yeasts. This phenomenon could be particularly important for understanding the ecology of colonization of complex fermentation media by Saccharomyces cerevisiae.

Keywords: Yeast; Acetaldehyde; Anaerobiosis; Alcoholic fermentation

Consequences of cps mutation of Klebsiella pneumoniae on 1,3-propanediol fermentation by Ni-Ni Guo; Zong-Ming Zheng; Yu-Lin Mai; Hong-Juan Liu; De-Hua Liu (pp. 701-707).

The filtration in 1,3-propanediol (1,3-PD) downstream process is influenced by the large amounts of capsular polysaccharides (CPS) produced by Klebsiella pneumoniae CGMCC 1.6366. The morphological and fermentation properties were investigated with the CPS-deficient mutant K. pneumoniae CGMCC 1.6366 CPS. Similar biomass was obtained with CGMCC 1.6366, and the mutant strain in batch cultures indicating the cell growth was slightly inhibited by CPS defection. The viscosity of fermentation broth by mutant strain decreased by 27.45%. The flux with ceramic membrane filter was enhanced from 168.12 to 303.6 l h⁻¹ m⁻², exhibiting the great importance for downstream processing of 1,3-PD fermentation. The products spectrum of mutant isolate changed remarkably regarding to the concentration of fermentation products. The synthesis of important 1,3-PD and 2,3-butanediol was enhanced from 9.73 and 4.06 g l⁻¹ to 10.37 and 4.77 g l⁻¹ in batch cultures. The noncapsuled K. pneumoniae provided higher 1,3-PD yield of 0.54 mol mol⁻¹ than that of encapsuled wild parent in batch cultures. The fed-batch fermentation of mutant strain resulted in 1,3-PD concentration, yield, and productivity of 78.13 g l⁻¹, 0.53 mol mol⁻¹, and 1.95 g l⁻¹ h⁻¹, respectively.

Keywords: Capsule; Downstream process; Glycerol; Klebsiella pneumoniae ; 1,3-Propanediol

Purple nonsulfur bacteria diversity in activated sludge and its potential phosphorus-accumulating ability under different cultivation conditions by Chih-Ming Liang; Chun-Hsiung Hung; Shu-Chuan Hsu; Ing-Chih Yeh (pp. 709-719).

This study investigates the diversity and the potential phosphorus-accumulating ability among the purple nonsulfur (PNS) bacteria. Traditional methods and molecular biotechniques were applied. Microscopic visualization using 4′,6-diamidino-2-phenylindole staining as well as chemical analysis demonstrated that most of the isolated PNS bacteria presented different levels of phosphorus accumulation. Four of the pure cultures, denoted as Rhodopseudomonas palustris CC1, CC7, G11, and GE1, based on their differences in the PNS’s pufM gene, exhibited higher internal phosphorus content compared to other isolated strains in this study. In addition, substantial polyphosphate accumulation was observed after the bacteria entered their stationary growth phase. Among them, the isolated R. palustris G11 could accumulate internal phosphorus up to 13%–15% of its cell dry weight under anaerobic illuminated incubation conditions. When the incubation status was switched from anaerobic to aerobic, the bacterial phosphorus content had a tendency to decrease slightly or remain about the same throughout the whole aerobic stage. The growth rate and biomass were higher when the PNS bacteria grew under photoheterotrophic conditions rather than the chemoheterotrophic ones. Furthermore, the environmental pH value could affect the contents of internal bacterial phosphate. Results of this study demonstrated that PNS bacteria are a group of the polyphosphate-accumulating organisms, of which this ability had never been properly studied. The conditions that PNS bacteria accumulating polyphosphate presented from this study were unique and showed characteristics that were different from the well-known enhanced biological phosphorus removal model.

Keywords: Chemoheterotrophic; Phosphorus removal; Photoheterotrophic; PNS; Polyphosphate; Wastewater treatment plants

Inhibitory effect of hydroxycinnamic acids on Dekkera spp. by Victoria Harris; Vladimir Jiranek; Christopher M. Ford; Paul R. Grbin (pp. 721-729).

Simple phenolic components of wine, hydroxycinnamic acids (HCAs) are known to have antimicrobial properties. This study sought to determine the potential of ferulic acid as an antifungal agent for the control of Dekkera. Growth was inhibited by all HCAs examined in this study, with ferulic acid being the most potent at all concentrations. In the presence of ethanol, the inhibitory effects of ferulic acid were amplified. Scanning electron microscopy images reveal cellular damage upon exposure to ferulic acid. Thus, manipulation of ferulic acid concentrations could be of industrial significance for control of Dekkera and may be the basis for differences in susceptibility of wines to Dekkera spoilage.

Keywords: Antimicrobial; Brettanomyces ; Spoilage; Scanning electron microscopy; Phenolic acids; Wine

Synthesis of γ-aminobutyric acid (GABA) by Lactobacillus plantarum DSM19463: functional grape must beverage and dermatological applications by Raffaella Di Cagno; Francesco Mazzacane; Carlo Giuseppe Rizzello; Maria De Angelis; Giammaria Giuliani; Marisa Meloni; Barbara De Servi; Marco Gobbetti (pp. 731-741).

Agriculture surplus were used as substrates to synthesize γ-aminobutyric acid (GABA) by Lactobacillus plantarum DSM19463 for the manufacture of a functional beverage or as a novel application for dermatological purposes. Dilution of the grape must to 1 or 4% (w/v) of total carbohydrates favored higher cell yield and synthesis of GABA with respect to whey milk. Optimal conditions for synthesizing GABA in grape must were: initial pH 6.0, initial cell density of Log 7.0 cfu/mL, and addition of 18.4 mM l-glutamate. L. plantarum DSM19463 synthesized 4.83 mM of GABA during fermentation at 30°C for 72 h. The fermented grape must also contain various levels of niacin, free minerals, and polyphenols, and Log 10.0 cfu/g of viable cells of L. plantarum DSM19463. Freeze dried preparation of grape must was applied to the SkinEthic® Reconstructed Human Epidermis or multi-layer human skin model (FT-skin tissue). The effect on transcriptional regulation of human beta-defensin-2 (HBD-2), hyaluronan synthase (HAS1), filaggrin (FGR), and involucrin genes was assayed through RT-PCR. Compared to GABA used as pure chemical compound, the up-regulation HBD-2 was similar while the effect on the expression of HAS1 and FGR genes was higher.

Keywords: γ-Aminobutyric acid; Functional grape must; Human skin protection; Lactobacillus plantarum

Two different electron transfer pathways may involve in azoreduction in Shewanella decolorationis S12 by Xingjuan Chen; Meiying Xu; Jinbo Wei; Guoping Sun (pp. 743-751).

Electron transfer pathways for azoreduction by S. decolorationis S12 were studied using a mutant S12-22 which had a transposon insertion in ccmA. The results imply that there are two different pathways for electron transport to azo bonds. The colony of S12-22 was whitish and incapable of producing mature c-type cytochromes whose α-peak was at 553 nm in the wild type S12. The mutant S12-22 could not use formate as the sole electron donor for azoreduction either in vivo or in vitro, but intact cells of S12-22 were able to reduce azo dyes of low polarity, such as methyl red, when NADH was served as the sole electron donor. Although the highly polar-sulfonated amaranth could not be reduced by intact cells of S12-22, it could be efficiently reduced by cell extracts of the mutant when NADH was provided as the sole electron donor. These results suggest that the mature c-type cytochromes are essential electron mediators for the extracellular azoreduction of intact cells, while the other pathway without the involvement of mature c-type cytochromes, NADH-dependent oxidoreductase-mediated electron transfer pathway can reduce lowly polar sulfonated azo dyes inside the whole cells or highly polar sulfonated azo dyes in the cell extracts without bacterial membrane barriers.

Keywords: Electron transfer pathways; Azoreduction; ccmA ; Azo dyes; Shewanella decolorationis S12

Engineering expression of the heavy metal transporter MerC in Saccharomyces cerevisiae for increased cadmium accumulation by Masako Kiyono; Kiyomi Miyahara; Yuka Sone; Hidemitsu Pan-Hou; Shimpei Uraguchi; Ryosuke Nakamura; Kou Sakabe (pp. 753-759).

The merC gene from the Tn21-encoded mer operon has potential uses as a molecular tool for bioremediation. It was overexpressed as the fusion proteins MerC-Sso1p or MerC-Vam3p in Saccharomyces cerevisiae. Green fluorescent protein (GFP)-MerC-Sso1p fusion proteins located primarily in the plasma membrane, although some protein was detected in the endoplasmic reticulum. In contrast, GFP-MerC-Vam3p was expressed in the vacuolar membranes. These results suggest that yeast Sso1p and Vam3p are essential for targeting molecules to the plasma and vacuolar membranes, respectively. Significantly more cadmium ions were accumulated by yeast cells expressing MerC-Sso1p than with MerC-Vam3p or control cells. These results suggest that expression of MerC in the plasma membrane may be a particularly promising strategy for improving accumulation of cadmium in yeast.

Keywords: Bioremediation; Bacterial heavy metal transport; MerC; SNARE; Cadmium

Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments by Jasperien De Weert; Marc Viñas; Tim Grotenhuis; Huub Rijnaarts; Alette Langenhoff (pp. 761-771).

Nonylphenol (NP) is an estrogenic pollutant which is widely present in the aquatic environment. Biodegradation of NP can reduce the toxicological risk. In this study, aerobic biodegradation of NP in river sediment was investigated. The sediment used for the microcosm experiments was aged polluted with NP. The biodegradation of NP in the sediment occurred within 8 days with a lag phase of 2 days at 30°C. During the biodegradation, nitro-nonylphenol metabolites were formed, which were further degraded to unknown compounds. The attached nitro-group originated from the ammonium in the medium. Five subsequent transfers were performed from original sediment and yielded a final stable population. In this NP-degrading culture, the microorganisms possibly involved in the biotransformation of NP to nitro-nonylphenol were related to ammonium-oxidizing bacteria. Besides the degradation of NP via nitro-nonylphenol, bacteria related to phenol-degrading species, which degrade phenol via ring cleavage, are abundantly present.

Keywords: Nonylphenol; Nitro-nonylphenol; Aerobic degradation; Nitrosomonas

Metabolism of mono- and dichloro-dibenzo-p-dioxins by Phanerochaete chrysosporium cytochromes P450 by Noriyuki Kasai; Shin-ichi Ikushiro; Raku Shinkyo; Kaori Yasuda; Shinji Hirosue; Akira Arisawa; Hirofumi Ichinose; Hiroyuki Wariishi; Toshiyuki Sakaki (pp. 773-780).

The white-rot fungus Phanerochaete chrysosporium possesses biodegradative capabilities of polychlorinated dibenzo-p-dioxins (PCDDs). One hundred twenty yeast clones expressing individual P450s of P. chrysosporum (PcCYPs), generated in our previous efforts, were screened for transformation of dioxin, and 40 positive clones were obtained. Of these clones, six clones showed metabolism of 2-chloro-dibenzo-p-dioxin, and a microsomal PcCYP designated as PcCYP11a3 showed much higher activity than any other PcCYPs. The turnover numbers of hydroxylation activities of PcCYP11a3 toward 1-MCDD (58 min⁻¹) and 2-MCDD (13 min⁻¹) are more than 200 times higher than those of previously reported PcCYP65a2. In addition, PcCYP11a3 catalyzes hydroxylation of 2,3-dichloro-dibenzo-p-dioxin. To our best knowledge, PcCYP11a3 has the highest activity toward PCDDs among the known CYPs derived from microorganisms. Although PcCYP11a3 showed no detectable activity toward 2,7-dichloro-dibenzo-p-dioxin and 2,3,7-trichloro-dibenzo-p-dioxin, PcCYP11a3 is promising as a template whose activity would be enhanced by site-directed mutagenesis.

Keywords: Cytochrome P450; Dioxin; PCDD; Metabolism; P. chrysosporium

A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments by Meng Li; Yiguo Hong; Martin Gunter Klotz; Ji-Dong Gu (pp. 781-790).

Published polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in the Candidatus “Scalindua” group. Furthermore, four primer sets used in detecting the hzo gene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longer hzo gene segments suitable for phylogenetic analysis. The optimized primer set for the 16S rRNA gene and the newly designed primer set for the hzo gene were successfully applied to identify anammox bacteria from marine sediments of aquaculture zone, coastal wetland, and deep ocean where the three ecosystems form a gradient of anthropogenic impact. Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem.

Keywords: Anammox bacteria; Primer sets; 16S RNA gene; hzo gene; Marine sediments

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Applied Microbiology and Biotechnology (v.86, #2)

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Applied Microbiology and Biotechnology (v.86, #2)