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Applied Microbiology and Biotechnology (v.86, #5)

Genetic improvement of brewer’s yeast: current state, perspectives and limits by Sofie M. G. Saerens; C. Thuy Duong; Elke Nevoigt (pp. 1195-1212).

Brewer’s yeast strain optimisation may lead to a more efficient beer production process, better final quality or healthier beer. However, brewer’s yeast genetic improvement is very challenging, especially true when it comes to lager brewer’s yeast (Saccharomyces pastorianus) which contributes to 90% of the total beer market. This yeast is a genetic hybrid and allopolyploid. While early studies applying traditional genetic approaches encountered many problems, the development of rational metabolic engineering strategies successfully introduced many desired properties into brewer’s yeast. Recently, the first genome sequence of a lager brewer’s strain became available. This has opened the door for applying advanced omics technologies and facilitating inverse metabolic engineering strategies. The latter approach takes advantage of natural diversity and aims at identifying and transferring the crucial genetic information for an interesting phenotype. In this way, strains can be optimised by introducing “natural” mutations. However, even when it comes to self-cloned strains, severe concerns about genetically modified organisms used in the food and beverage industry are still a major hurdle for any commercialisation. Therefore, research efforts will aim at developing new sophisticated screening methods for the isolation of natural mutants with the desired properties which are based on the knowledge of genotype–phenotype linkage.

Keywords: Beer; Brewer’s yeast; S. pastorianus ; Metabolic engineering; Strain improvement; S. cerevisiae

Cyanobactins—ribosomal cyclic peptides produced by cyanobacteria by Kaarina Sivonen; Niina Leikoski; David P. Fewer; Jouni Jokela (pp. 1213-1225).

Cyanobactins are small cyclic peptides that are produced by a diverse selection of cyanobacteria living in symbioses as well as terrestrial, marine, or freshwater environments. They include compounds with antimalarial, antitumor, and multidrug reversing activities and potential as pharmaceutical leads. Cyanobactins are produced through the proteolytic cleavage and cyclization of precursor peptides coupled with further posttranslational modifications such as heterocyclization, oxidation, or prenylation of amino acids. Cyanobactin gene clusters encode two proteases which cleave and cyclisize the precursor peptide as well as proteins participating in posttranslational modifications. The bioinformatic mining of cyanobacterial genomes has led to the discovery of novel cyanobactins. Heterologous expression of these gene clusters provided insights into the role of the genes participating in the biosynthesis of cyanobactins and facilitated the rational design of novel peptides. Enzymes participating in the biosynthesis of cyanobactins may prove useful as catalysts for producing novel cyclic peptides in the future. The recent discovery of the cyanobactin biosynthetic pathway in cyanobacteria extends our knowledge of their potential as producers of interesting metabolites.

Keywords: Cyanobacteria; Cyanobactins; Peptides; Bioactive compounds

Marine yeasts as biocontrol agents and producers of bio-products by Zhen-Ming Chi; Guanglei Liu; Shoufeng Zhao; Jing Li; Ying Peng (pp. 1227-1241).

As some species of marine yeasts can colonize intestine of marine animals, they can be used as probiotics. It has been reported that β-glucans from marine yeast cells can be utilized as immuno-stimulants in marine animals. Some siderophores or killer toxins produced by marine yeasts have ability to inhibit growth of pathogenic bacteria or kill pathogenic yeasts in marine animals. The virulent factors from marine pathogens can be genetically displayed on marine yeast cells, and the yeast cells displaying the virulent factors can stimulate marine animals to produce specific antibody against the pathogens. Some marine yeast cells are rich in proteins and essential amino acids and can be used in nutrition for marine animals. The marine yeast cells rich in lipid can be used for biodiesel production. Recently, it has been reported that some strains of Yarrowia lipolytica isolated from marine environments can produce nanoparticles. Because many marine yeasts can remove organic pollutants and heavy metals, they can be applied to remediation of marine environments. It has been shown that the enzymes produced by some marine yeasts have many unique properties and many potential applications.

Keywords: Probiotics; Marine yeasts; Industrial enzymes; Vaccine; Siderophore; Bio-products

Metabolic flux distributions: genetic information, computational predictions, and experimental validation by Lars M. Blank; Lars Kuepfer (pp. 1243-1255).

Flux distributions in intracellular metabolic networks are of immense interest to fundamental and applied research, since they are quantitative descriptors of the phenotype and the operational mode of metabolism in the face of external growth conditions. In particular, fluxes are of relevance because they do not belong to the cellular inventory (e.g., transcriptome, proteome, metabolome), but are rather quantitative moieties, which link the phenotype of a cell to the specific metabolic mode of operation. A frequent application of measuring and redirecting intracellular fluxes is strain engineering, which ultimately aims at shifting metabolic activity toward a desired product to achieve a high yield and/or rate. In this article, we first review the assessment of intracellular flux distributions by either qualitative or rather quantitative computational methods and also discuss methods for experimental measurements. The tools at hand will then be exemplified on strain engineering projects from the literature. Finally, the achievements are discussed in the context of future developments in Metabolic Engineering and Synthetic Biology.

Keywords: Flux balance analysis; Metabolic network analysis; ¹³C-metabolic flux analysis; Synthetic biology; Metabolic engineering; Industrial biotechnology

Alcohol dehydrogenase of acetic acid bacteria: structure, mode of action, and applications in biotechnology by Toshiharu Yakushi; Kazunobu Matsushita (pp. 1257-1265).

Pyrroquinoline quinone-dependent alcohol dehydrogenase (PQQ-ADH) of acetic acid bacteria is a membrane-bound enzyme involved in the acetic acid fermentation by oxidizing ethanol to acetaldehyde coupling with reduction of membranous ubiquinone (Q), which is, in turn, re-oxidized by ubiquinol oxidase, reducing oxygen to water. PQQ-ADHs seem to have co-evolved with the organisms fitting to their own habitats. The enzyme consists of three subunits and has a pyrroloquinoline quinone, 4 heme c moieties, and a tightly bound Q as the electron transfer mediators. Biochemical, genetic, and electrochemical studies have revealed the unique properties of PQQ-ADH since it was purified in 1978. The enzyme is unique to have ubiquinol oxidation activity in addition to Q reduction. This mini-review focuses on the molecular properties of PQQ-ADH, such as the roles of the subunits and the cofactors, particularly in intramolecular electron transport of the enzyme from ethanol to Q. Also, we summarize biotechnological applications of PQQ-ADH as to enantiospecific oxidations for production of the valuable chemicals and bioelectrocatalysis for sensors and fuel cells using indirect and direct electron transfer technologies and discuss unsolved issues and future prospects related to this elaborate enzyme.

Keywords: Alcohol dehydrogenase; Acetic acid bacteria; Pyrroquinoline quinone; Ubiquinone; Bioelectrocatalysis

Applications of quorum sensing in biotechnology by Swati Choudhary; Claudia Schmidt-Dannert (pp. 1267-1279).

Many unicellular microorganisms use small signaling molecules to determine their local concentration. The processes involved in the production and recognition of these signals are collectively known as quorum sensing (QS). This form of cell–cell communication is used by unicellular microorganisms to co-ordinate their activities, which allows them to function as multi-cellular systems. Recently, several groups have demonstrated artificial intra-species and inter-species communication through synthetic circuits which incorporate components of bacterial QS systems. Engineered QS-based circuits have a wide range of applications such as production of biochemicals, tissue engineering, and mixed-species fermentations. They are also highly useful in designing microbial biosensors to identify bacterial species present in the environment and within living organisms. In this review, we first provide an overview of bacterial QS systems and the mechanisms developed by bacteria and higher organisms to obstruct QS communications. Next, we describe the different ways in which researchers have designed QS-based circuits and their applications in biotechnology. Finally, disruption of quorum sensing is discussed as a viable strategy for preventing the formation of harmful biofilms in membrane bioreactors and marine transportation.

Keywords: Quorum sensing; Biotechnology; Synthetic biology; Biofilm

Single-cell analysis and isolation for microbiology and biotechnology: methods and applications by Satoshi Ishii; Kanako Tago; Keishi Senoo (pp. 1281-1292).

Various single-cell isolation techniques, including dilution, micromanipulation, flow cytometry, microfluidics, and compartmentalization, have been developed. These techniques can be used to cultivate previously uncultured microbes, to assess and monitor cell physiology and function, and to screen for novel microbiological products. Various other techniques, such as viable staining, in situ hybridization, and those using autofluorescence proteins, are frequently combined with these single-cell isolation techniques depending on the purpose of the study. In this review article, we summarize currently available single-cell isolation techniques and their applications, when used in combination with other techniques, in microbiological and biotechnological studies.

Keywords: Single-cell isolation; Dilution-to-extinction; Micromanipulation; Flow cytometry; Microfluidics; Compartmentalization

Genetic and metabolic engineering of isoflavonoid biosynthesis by Hai Du; Yubi Huang; Yixiong Tang (pp. 1293-1312).

Isoflavonoids are a diverse group of secondary metabolites derived from the phenylpropanoid pathway. These compounds are distributed predominantly in leguminous plants and play important roles in plant–environment interactions and human health. Consequently, the biosynthetic pathway of isoflavonoid compounds has been widely elucidated in the past decades. Up to now, most of the structural genes and some of the regulatory genes involved in this pathway have been isolated and well characterized. Nowadays, the protective effects of the legume isoflavonoids against hormone dependent cancers, cardiovascular disease, osteoporosis, and menopausal symptoms have generated considerable interest within the genetic and metabolic engineering fields to enhance the dietary intake of these compounds for disease prevention. Subsequently, there are some great progresses in genetic and metabolic engineering to improve their yields in leguminous and non-leguminous plants and/or microorganisms. Because of the field of flavonoid biosynthesis has been reviewed fairly extensively in the past, this review concentrates on the more recent development in the isoflavonoid branch of phenylpropanoid pathway, including gene isolation and characterization. In addition, we describe the state-of-the-art research with respect to genetic and metabolic engineering of isoflavonoid biosynthesis.

Keywords: Engineering; Isoflavonoid; Secondary metabolism; Legume

Carbohydrate metabolism in Corynebacterium glutamicum and applications for the metabolic engineering of l-lysine production strains by Bastian Blombach; Gerd M. Seibold (pp. 1313-1322).

Carbohydrates exclusively serve as feedstock for industrial amino acid production with Corynebacterium glutamicum. Due to the industrial interest, knowledge about the pathways for carbohydrate metabolization in C. glutamicum steadily increases, enabling the rational design of optimized strains and production processes. In this review, we provide an overview of the metabolic pathways for utilization of hexoses (glucose, fructose), disaccharides (sucrose, maltose), pentoses (d-ribose, l-arabinose, d-xylose), gluconate, and β-glucosides present in C. glutamicum. Recent approaches of metabolic engineering of l-lysine production strains based on the known pathways are described and evaluated with respect to l-lysine yields.

Keywords: Corynebacterium glutamicum ; Carbohydrates; Sugar; Metabolic engineering; Amino acid production; l-Lysine

Rhamnolipids: diversity of structures, microbial origins and roles by Ahmad Mohammad Abdel-Mawgoud; François Lépine; Eric Déziel (pp. 1323-1336).

Rhamnolipids are glycolipidic biosurfactants produced by various bacterial species. They were initially found as exoproducts of the opportunistic pathogen Pseudomonas aeruginosa and described as a mixture of four congeners: α-L-rhamnopyranosyl-α-L-rhamnopyranosyl-β-hydroxydecanoyl-β-hydroxydecanoate (Rha-Rha-C₁₀-C₁₀), α-L-rhamnopyranosyl-α-L-rhamnopyranosyl-β-hydroxydecanoate (Rha-Rha-C₁₀), as well as their mono-rhamnolipid congeners Rha-C₁₀-C₁₀ and Rha-C₁₀. The development of more sensitive analytical techniques has lead to the further discovery of a wide diversity of rhamnolipid congeners and homologues (about 60) that are produced at different concentrations by various Pseudomonas species and by bacteria belonging to other families, classes, or even phyla. For example, various Burkholderia species have been shown to produce rhamnolipids that have longer alkyl chains than those produced by P. aeruginosa. In P. aeruginosa, three genes, carried on two distinct operons, code for the enzymes responsible for the final steps of rhamnolipid synthesis: one operon carries the rhlAB genes and the other rhlC. Genes highly similar to rhlA, rhlB, and rhlC have also been found in various Burkholderia species but grouped within one putative operon, and they have been shown to be required for rhamnolipid production as well. The exact physiological function of these secondary metabolites is still unclear. Most identified activities are derived from the surface activity, wetting ability, detergency, and other amphipathic-related properties of these molecules. Indeed, rhamnolipids promote the uptake and biodegradation of poorly soluble substrates, act as immune modulators and virulence factors, have antimicrobial activities, and are involved in surface motility and in bacterial biofilm development.

Keywords: Biosurfactants; Pseudomonas ; Burkholderia

Production of pig liver esterase in batch fermentation of E. coli Origami by Elke Brüsehaber; Anja Schwiebs; Marlen Schmidt; Dominique Böttcher; Uwe T. Bornscheuer (pp. 1337-1344).

The establishment of a fermentation process for the production of pig liver esterase (PLE) in high yields is necessary for industrial applications. In our previous studies, we reported the recombinant expression of PLE in Escherichia coli Origami™ (DE3) in shake flask. Only a coexpression with chaperones GroEL/ES allowed the production of soluble and active enzyme. The optimization of the cultivation conditions, such as temperature, inducer concentrations, or media compositions to increase enzyme yield in a fermentation process is described here. Using fed-batch fermentation cell densities up to OD = 50 were obtained, but almost no active enzyme was expressed. Only batch fermentation was found suitable for production of active pig liver esterase and cell densities between OD = 7–13 and activities of 300–400 U L⁻¹ for isoenzyme PLE-1 (γPLE) and 1,400 U L⁻¹ for PLE-5 were obtained after 22 h total cultivation time or 18 h after induction of PLE expression, respectively.

Keywords: Fermentation; E. coli Origami; Pig liver esterase; Chaperones

Improved production of the tallysomycin H-1 in Streptoalloteichus hindustanus SB8005 strain by fermentation optimization by Ningning Zhang; Xiangcheng Zhu; Dong Yang; Jin Cai; Meifeng Tao; Liyan Wang; Yanwen Duan; Ben Shen; Zhinan Xu (pp. 1345-1353).

Tallysomycin (TLM) H-1, a novel TLM analog, is the major product isolated from Streptoalloteichus hindustanus SB8005, a genetically engineered strain from S. hindustanus E465-94 ATCC 31158. Based on the structural comparison and experimental assays, TLM H-1 represents a novel bleomycin (BLM) analog displaying DNA cleavage activity similar to its parent compounds TLM and BLM, both representatives of the glycopeptide anticancer antibiotics. The low titer of TLM H-1 in the engineered SB8005 strain has greatly limited its further study. In this paper, fermentation optimization for TLM H-1 production in the SB8005 strain is described; single-factor optimization and response surface methodology proved invaluable. The results indicated that three variables including distiller’s grains and solubles, copper sulfate, and maltose out of eight parameters could significantly influence the TLM H-1 production. With systematic comparison and evaluation, the final optimized fermentation medium was determined. The optimized yield of TLM H-1 in the bench-top fermentor was 249.9 mg/L, which is 26.8 times higher than reported using the original medium, and 12.9-fold higher than that of the parent compound TLM produced by the wild-type strain. This work provides important parameters for TLM H-1 production by fermentation and should facilitate further mechanistic studies and clinical developments of TLM H-1 as an anticancer agent.

Keywords: Tallysomycin; Bleomycin; Fermentation optimization; Streptoalloteichus hindustanus ; Plackett–Burman design; Response surface methodology

Ethanol production from SPORL-pretreated lodgepole pine: preliminary evaluation of mass balance and process energy efficiency by J. Y. Zhu; Wenyuan Zhu; Patricia OBryan; Bruce S. Dien; Shen Tian; Rolland Gleisner; X. J. Pan (pp. 1355-1365).

Lodgepole pine from forest thinnings is a potential feedstock for ethanol production. In this study, lodgepole pine was converted to ethanol with a yield of 276 L per metric ton of wood or 72% of theoretical yield. The lodgepole pine chips were directly subjected to sulfite pretreatment to overcome recalcitrance of lignocellulose (SPORL) pretreatment and then disk-milled; the recovered cellulose substrate was quais-simultaneously saccharified enzymatically and fermented to ethanol using commercial cellulases and Saccharomyces cerevisiae D5A. The liquor stream from the pretreatment containing hydrolyzed sugars mainly from hemicelluloses was fermented by the same yeast strain after detoxification using an XAD resin column. The SPORL pretreatment was conducted at 180°C for a period of 25 min with a liquor-to-wood ratio of 3:1 (v/w) in a laboratory digester. Three levels of sulfuric acid charge (0.0%, 1.4%, and 2.2% on an oven dried wood basis in w/w) and three levels of sodium bisulfite charge (0.0%, 4.0%, and 8.0% in w/w) were applied. Mechanical and thermal energy consumption for milling and pretreatment were determined. These data were used to determine the efficiency of sugar recoveries and net ethanol energy production values and to formulate a preliminary mass and energy balance.

Keywords: Cellulosic ethanol; SPORL; Fermentation/saccharification; Woody biomass; Pretreatment; Ethanol yield

Enhanced biosynthetic gene expressions and production of ganoderic acids in static liquid culture of Ganoderma lucidum under phenobarbital induction by Cui-Xia Liang; Ying-Bo Li; Jun-Wei Xu; Jia-Le Wang; Xiao-Ling Miao; Ya-Jie Tang; Tingyue Gu; Jian-Jiang Zhong (pp. 1367-1374).

Static liquid culture of Ganoderma lucidum, a traditional Chinese medicinal mushroom, is a proven technology for producing ganoderic acids, which are secondary metabolites that possess antitumor properties. In this work, the addition of phenobarbital, a P450 inducer, was used to enhance the production of total and individual ganoderic acids in a two-stage cultivation involving a period of initial shake flask culture followed by static liquid culture of G. lucidum. The dosage and time of phenobarbital induction were critical for the enhanced production of ganoderic acids. The addition of 100 μM (final concentration) phenobarbital on day 5 after the shake flask culture was converted to the static liquid culture was found to be optimal, resulting in a maximal amount of total ganoderic acids of 41.4 ± 0.6 mg/g cell dry weight and increases in the levels of ganoderic acid-Mk, -T, -S, and -Me in the treated cells by 47%, 28%, 36%, and 64%, respectively. Meanwhile, the accumulation of lanosterol, a key intermediate, was found to decrease and transcriptions of three key genes encoding 3-hydroxy-3-methylglutaryl coenzyme A reductase, squalene synthase, and lanosterol synthase in the triterpene biosynthetic pathway were up-regulated under phenobarbital induction. This work demonstrated a useful strategy for the enhanced production of ganoderic acids by G. lucidum.

Keywords: Ganoderma lucidum ; Ganoderic acid; Phenobarbital induction; Gene expression; Mushroom fermentation technology

Conversion of rice straw to bio-based chemicals: an integrated process using Lactobacillus brevis by Jae-Han Kim; David E. Block; Sharon P. Shoemaker; David A. Mills (pp. 1375-1385).

Commercialization of lignocellulosic biomass as a feedstock for bio-based chemical production is problematic due to the high processing costs of pretreatment and saccharifying enzymes combined with low product yields. Such low product yield can be attributed, in large part, to the incomplete utilization of the various carbohydrate sugars found in the lignocellulosic biomass. In this study, we demonstrate that Lactobacillus brevis is able to simultaneously metabolize all fermentable carbohydrates in acid pre-processed rice straw hydrolysate, thereby allowing complete utilization of all released sugars. Inhibitors present in rice straw hydrolysate did not affect lactic acid production. Moreover, the activity of exogenously added cellulases was not reduced in the presence of growing cultures of L. brevis. These factors enabled the use of L. brevis in a process termed simultaneous saccharification and mixed sugar fermentation (SSMSF). In SSMSF with L. brevis, sugars present in rice straw hydrolysate were completely utilized while the cellulase maintained its maximum activity due to the lack of feedback inhibition from glucose and/or cellobiose. By comparison to a sequential hydrolysis and fermentation process, SSMSF reduced operation time and the amount of cellulase enzyme necessary to produce the same amount of lactic acid.

Keywords: Lactobacillus brevis ; Carbon catabolite repression; Simultaneous carbohydrate utilization; Lignocellulosic biomass; SSMSF

Use of sustainable chemistry to produce an acyl amino acid surfactant by Gabriel O. Reznik; Prashanth Vishwanath; Michelle A. Pynn; Joy M. Sitnik; Jeffrey J. Todd; Jun Wu; Yan Jiang; Brendan G. Keenan; Andrew B. Castle; Richard F. Haskell; Temple F. Smith; Ponisseril Somasundaran; Kevin A. Jarrell (pp. 1387-1397).

Surfactants find wide commercial use as foaming agents, emulsifiers, and dispersants. Currently, surfactants are produced from petroleum, or from seed oils such as palm or coconut oil. Due to concerns with CO₂ emissions and the need to protect rainforests, there is a growing necessity to manufacture these chemicals using sustainable resources In this report, we describe the engineering of a native nonribosomal peptide synthetase pathway (i.e., surfactin synthetase), to generate a Bacillus strain that synthesizes a highly water-soluble acyl amino acid surfactant, rather than the water insoluble lipopeptide surfactin. This novel product has a lower CMC and higher water solubility than myristoyl glutamate, a commercial surfactant. This surfactant is produced by fermentation of cellulosic carbohydrate as feedstock. This method of surfactant production provides an approach to sustainable manufacturing of new surfactants.

Keywords: Surfactant; NRPS engineering; Sustainable chemistry; Acyl amino acid; Combinatorial synthesis

Performance and microbial ecology of air-cathode microbial fuel cells with layered electrode assemblies by Caitlyn S. Butler; Robert Nerenberg (pp. 1399-1408).

Microbial fuel cells (MFCs) can be built with layered electrode assemblies, where the anode, proton exchange membrane (PEM), and cathode are pressed into a single unit. We studied the performance and microbial community structure of MFCs with layered assemblies, addressing the effect of materials and oxygen crossover on the community structure. Four MFCs with layered assemblies were constructed using Nafion or Ultrex PEMs and a plain carbon cloth electrode or a cathode with an oxygen-resistant polytetrafluoroethylene diffusion layer. The MFC with Nafion PEM and cathode diffusion layer achieved the highest power density, 381 mW/m² (20 W/m³). The rates of oxygen diffusion from cathode to anode were three times higher in the MFCs with plain cathodes compared to those with diffusion-layer cathodes. Microsensor studies revealed little accumulation of oxygen within the anode cloth. However, the abundance of bacteria known to use oxygen as an electron acceptor, but not known to have exoelectrogenic activity, was greater in MFCs with plain cathodes. The MFCs with diffusion-layer cathodes had high abundance of exoelectrogenic bacteria within the genus Geobacter. This work suggests that cathode materials can significantly influence oxygen crossover and the relative abundance of exoelectrogenic bacteria on the anode, while PEM materials have little influence on anode community structure. Our results show that oxygen crossover can significantly decrease the performance of air-cathode MFCs with layered assemblies, and therefore limiting crossover may be of particular importance for these types of MFCs.

Keywords: Microbial fuel cells; Air cathode; Oxygen crossover; Diffusion layer; Geobacter

A novel lectin with highly potent antiproliferative and HIV-1 reverse transcriptase inhibitory activities from cicada (Cicada flammata) by Xiu Juan Ye; Tzi Bun Ng (pp. 1409-1418).

A dimeric lectin with a molecular weight of 60 kDa and high hemagglutinating activity was isolated from dried cicadas. It was adsorbed on Q-Sepharose and unadsorbed on Affi-Gel Blue gel. Its hemagglutinating activity was stable up to 55 °C and between pH 2 and 13. The activity was inhibited by glucuronic acid and raffinose, K⁺ ions, and Mg²⁺ ions. Cicada lectin potently inhibited proliferation of HepG2 hepatoma and MCF 7 breast cancer cells, with an IC₅₀ value of 0.76 and 0.49 µM, respectively. It potently inhibited HIV-1 reverse transcriptase activity with an IC₅₀ of 0.36 μM but was devoid of mitogenic activity on spleen cells. Its N-terminal sequence exhibited slight similarity to a conserved hypothetical protein from Culex quinquefasciatus and a gene product from transcript GH19834-RA of Drosophila grimshawi, but there was no resemblance to lectins from other insects, including Drosophila, Sarcophaga, Glossina, and Aedes species.

Keywords: Cicada; Lectin; Antiproliferative; HIV-1 reverse transcriptase

A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily by Edwin van Bloois; Daniel E. Torres Pazmiño; Remko T. Winter; Marco W. Fraaije (pp. 1419-1430).

DyP-type peroxidases comprise a novel superfamily of heme-containing peroxidases which is unrelated to the superfamilies of known peroxidases and of which only a few members have been characterized in some detail. Here, we report the identification and characterization of a DyP-type peroxidase (TfuDyP) from the thermophilic actinomycete Thermobifida fusca. Biochemical characterization of the recombinant enzyme showed that it is a monomeric, heme-containing, thermostable, and Tat-dependently exported peroxidase. TfuDyP is not only active as dye-decolorizing peroxidase as it also accepts phenolic compounds and aromatic sulfides. In fact, it is able to catalyze enantioselective sulfoxidations, a type of reaction that has not been reported before for DyP-type peroxidases. Site-directed mutagenesis was used to determine the role of two conserved residues. D242 is crucial for catalysis while H338 represents the proximal heme ligand and is essential for heme incorporation. A genome database analysis revealed that DyP-type peroxidases are frequently found in bacterial genomes while they are extremely rare in other organisms. Most of the bacterial homologs are potential cytosolic enzymes, suggesting metabolic roles different from dye degradation. In conclusion, the detailed biochemical characterization reported here contributes significantly to our understanding of these enzymes and further emphasizes their biotechnological potential.

Keywords: Peroxidase; Heme; Sulfoxidation; Enantioselective; Dye decolorizing

Characterization of thermostable FMN-dependent NADH azoreductase from the moderate thermophile Geobacillus stearothermophilus by Ken’ichiro Matsumoto; Yuichi Mukai; Daiki Ogata; Fumi Shozui; John Masani Nduko; Seiichi Taguchi; Toshihiko Ooi (pp. 1431-1438).

The gene encoding an FMN-dependent NADH azoreductase, AzrG, from thermophilic Geobacillus stearothermophilus was cloned and functionally expressed in recombinant Escherichia coli. Purified recombinant AzrG is a homodimer of 23 kDa and bore FMN as a flavin cofactor. The optimal temperature of AzrG was 85 °C for the degradation of Methyl Red (MR). AzrG remained active for 1 h at 65 °C and for 1 month at 30 °C, demonstrating both superior thermostability and long-term stability of the enzyme. AzrG efficiently decolorized MR, Ethyl Red at 30 °C. Furthermore, the enzyme exhibited a wide-range of degrading activity towards several tenacious azo dyes, such as Acid Red 88, Orange I, and Congo Red. These results suggested the sustainable utilization of G. stearothermophilus as an azo-degrading strain for AzrG carrying whole-cell wastewater treatments for azo pollutants under high temperature conditions.

Keywords: Flavoprotein; Oxidoreductase; Thermal stability; Circular dichroism

Antibacterial and biofilm removal activity of a podoviridae Staphylococcus aureus bacteriophage SAP-2 and a derived recombinant cell-wall-degrading enzyme by Jee-Soo Son; Se-Jung Lee; Soo Youn Jun; Seong Jun Yoon; Sang Hyeon Kang; Hyoung Rok Paik; Jung Ok Kang; Yun-Jaie Choi (pp. 1439-1449).

Antibacterial and biofilm removal activity of a new podoviridae Staphylococcus aureus bacteriophage (SAP-2), which belongs to the φ29-like phage genus of the Podoviridae family, and a cell-wall-degrading enzyme (SAL-2), which is derived from bacteriophage SAP-2, have been characterized. The cell-wall-degrading enzyme SAL-2 was expressed in Escherichia coli in a soluble form using a low-temperature culture. The cell-wall-degrading enzyme SAL-2 had specific lytic activity against S. aureus, including methicillin-resistant strains, and showed a minimum inhibitory concentration of about 1 μg/ml. In addition, this enzyme showed a broader spectrum of activity within the Staphylococcus genus compared with bacteriophage SAP-2 in its ability to remove the S. aureus biofilms. Thus, the cell-wall-degrading enzyme SAL-2 can be used to prevent and treat biofilm-associated S. aureus infections either on its own or in combination with other cell-wall-degrading enzymes with anti-S. aureus activity.

Keywords: Cell-wall-degrading enzyme; Podoviridae; Bacteriophage; Biofilm; Staphylococcus aureus

Location of flavone B-ring controls regioselectivity and stereoselectivity of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4 by Jiyoung Seo; Su-Il Kang; Ji-Young Ryu; Young-Ju Lee; Ki Deok Park; Mihyang Kim; Dongho Won; Hye-Yeon Park; Joong-Hoon Ahn; Youhoon Chong; Robert A. Kanaly; Jaehong Han; Hor-Gil Hur (pp. 1451-1462).

Naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 incorporated dioxygen at the C7 and C8 positions on the A-rings of flavone and isoflavone with different stereoselectivity, resulting in the formation of (7S,8S)-dihydroxy-2-phenyl-7,8-dihydro-4H-chromen-4-one (flavone-cis-(7S,8S)-dihydrodiol) and (7R,8R)-dihydroxy-3-phenyl-7,8-dihydro-4H-chromen-4-one (isoflavone-cis-(7R,8R)-dihydrodiol), respectively. In addition, NDO was shown to incorporate dioxygen at the C5 and C6 positions on the A-ring and the C2′ and C3′ positions on the B-ring of isoflavone, resulting in the production of (5S,6R)-dihydroxy-3-phenyl-5,6-dihydro-4H-chromen-4-one (isoflavone-cis-(5S,6R)-dihydrodiol) and 3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]-4H-chromen-4-one (isoflavone-cis-(2′R,3′S)-dihydrodiol), respectively. The metabolites were identified by LC/MS, ¹H, and ¹³C NMR analyses and TD-SCF calculations combined with CD spectroscopy. In the case of flavone biotransformation, formation of flavone-(7S,8S)-dihydrodiol is likely to be the result of hydrogen bond interactions between the substrate and the active site of the dioxygenase. On the contrary, regioselective dioxygenation of isoflavone was found not to occur, and this may be due to the fact that the same hydrogen bonds that occur in the case of the flavone reaction cannot be established due to steric hindrance caused by the position of the B-ring. It is therefore proposed that the regioselectivity and stereoselectivity of NDO from strain NCIB 9816-4 are controlled by the position of the phenyl ring on flavone molecules.

Keywords: Dihydrodiol; Flavone; Naphthalene dioxygenase; Regioselectivity; Stereoselectivity

A novel xyloglucan-specific endo-β-1,4-glucanase: biochemical properties and inhibition studies by Dominic D. W. S. Wong; Victor J. Chan; Amanda A. McCormack; Sarah B. Batt (pp. 1463-1471).

A novel xyloglucan-specific endo-β-1,4-glucanase gene (xeg5A) was isolated, cloned, and expressed in Esherichia coli. The enzyme XEG5A consisted of a C-terminal catalytic domain and N-terminal sequence of ~90 amino acid residues with unknown function. The catalytic domain assumed an (α/β)₈-fold typical of glycoside hydrolase (GH) family 5, with the two catalytic residues Glu240 and Glu362 located on opposite sides of the surface groove of the molecule. The recombinant enzyme showed high specificity towards tamarind xyloglucan and decreasing activity towards xyloglucan oligosaccharide (HDP-XGO), carboxymethyl cellulose, and lichenan. Tamarind xyloglucan was hydrolyzed to three major fragments, XXXG, XXLG/XLXG, and XLLG. The hydrolysis followed the Michaelis–Menten kinetics, yielding K _m and V _max of 3.61 ± 0.23 mg/ml and 0.30 ± 0.01 mg/ml/min, respectively. However, the hydrolysis of HDP-XGO showed a decrease in the rate at high concentrations suggesting appearance of excess substrate inhibition. The addition of XXXG resulted in linear noncompetitive inhibition on the hydrolysis of tamarind xyloglucan giving a K _i of 1.46 ± 0.13 mM. The enzyme was devoid of transglycosylase activities.

Keywords: Xyloglucan-specific endo-β-1,4-glucanase; Endo-xyloglucanase; Xyloglucanase gene; Xyloglucanase characterization

Characterization of β-glucosidase from a strain of Penicillium purpurogenum KJS506 by Marimuthu Jeya; Ah-Reum Joo; Kyoung-Mi Lee; Manish Kumar Tiwari; Kyoung-Min Lee; Sang-Hwan Kim; Jung-Kul Lee (pp. 1473-1484).

A novel β-glucosidase (BGL)-producing strain was isolated and identified as Penicillium purpurogenum KJS506 based on its morphology and internal transcribed spacer (ITS) rDNA gene sequence. When rice straw and corn steep powder were used as carbon and nitrogen sources, respectively, the maximal BGL activity of 12.3 U ml⁻¹, one of the highest levels among BGL-producing microorganisms was observed. The optimum temperature and pH for BGL production were 32 °C and 4, respectively. An extracellular BGL was purified to homogeneity by sequential chromatography of P. purpurogenum culture supernatants, and the purified BGL showed higher activity (V _max = 934 U mg protein^–1) than most BGLs from other sources. The complete ORF of bgl3 was cloned from P. purpurogenum by a modified thermal asymmetric interlaced polymerase chain reaction. The bgl3 gene consists of a 2,571-bp ORF and encodes a putative protein containing 856 amino acids with a calculated molecular mass of 89,624 Da. The putative gene product was identified as a member of glycoside hydrolase family 3. The present results should contribute to improved industrial production of BGL by P. purpurogenum KJS506.

Keywords: Cloning; β-Glucosidase; Homology modeling; Penicillium purpurogenum ; TAIL-PCR

Loss of phosphomannomutase activity enhances actinorhodin production in Streptomyces coelicolor by Yung-Hun Yang; Eunjung Song; Sung-Hee Park; Ji-Nu Kim; Kwangwon Lee; Eunjung Kim; Yun-Gon Kim; Byung-Gee Kim (pp. 1485-1492).

Phosphomannomutase (ManB), whose main function is the conversion of mannose-6-phosphate to mannose-1-phosphate, is involved in biosynthesis of GDP-mannose for numerous processes such as synthesis of structural carbohydrates, production of alginates and ascorbic acid, and post-translational modification of proteins in prokaryotes and eukaryotes. ManB isolated from Streptomyces coelicolor was shown to have both phosphomannomutase and phosphoglucomutase activities. Deletion of manB in S. coelicolor caused a dramatic increase in actinorhodin (ACT) production in the low-glucose Difco nutrient (DN) medium, whereas the wild-type strain did not produce ACT on this medium. Experiments involving complementation of the manB deletion showed that increased ACT production in DN media was due to blockage of phosphomannomutase activity rather than phosphoglucomutase activity. This result therefore provides useful information for the design of strategies that enhance antibiotic production through the control of carbon flux.

Keywords: Streptomyces coelicolor ; Phosphomannomutase; Phosphoglucomutase; manB; Antibiotic production; Glycogen

Display of Candida antarctica lipase B on Pichia pastoris and its application to flavor ester synthesis by Guo-Dong Su; Deng-Feng Huang; Shuang-Yan Han; Sui-Ping Zheng; Ying Lin (pp. 1493-1501).

Two alternative cell-surface display systems were developed in Pichia pastoris using the α-agglutinin and Flo1p (FS) anchor systems, respectively. Both the anchor cell wall proteins were obtained originally from Saccharomyces cerevisiae. Candida antarctica lipase B (CALB) was displayed functionally on the cell surface of P. pastoris using the anchor proteins α-agglutinin and FS. The activity of CALB displayed on P. pastoris was tenfold higher than that of S. cerevisiae. The hydrolytic and synthetic activities of CALB fused with α-agglutinin and FS anchored on P. pastoris were investigated. The hydrolytic activities of both lipases displayed on yeast cells surface were more than 200 U/g dry cell after 120 h of culture (200 and 270 U/g dry cell, respectively). However, the synthetic activity of CALB fused with α-agglutinin on P. pastoris was threefold higher than that of the FS fusion protein when applied to the synthesis of ethyl caproate. Similarly, the CALB displayed on P. pastoris using α-agglutinin had a higher catalytic efficiency with respect to the synthesis of other short-chain flavor esters than that displayed using the FS anchor. Interestingly, for some short-chain esters, the synthetic activity of displaying CALB fused with α-agglutinin on P. pastoris was even higher than that of the commercial CALB Novozyme 435.

Keywords: Yeast surface display; Pichia pastoris ; Candida antarctica lipase B; Flavor ester synthesis

Exploring improved endoglucanase expression in Saccharomyces cerevisiae strains by Lisa du Plessis; Shaunita H. Rose; Willem H. van Zyl (pp. 1503-1511).

The endoglucanase I and II genes (egI or Cel7B and egII or Cel5A) of Trichoderma reesei QM6a were successfully cloned and expressed in Saccharomyces cerevisiae under the transcriptional control of the yeast ENO1 promoter and terminator sequences. Random mutagenesis of the egI-bearing plasmid resulted in a twofold increase in extracellular EGI activity. Both endoglucanase genes were co-expressed with the synthetic, codon-optimised cellobiohydrolase gene (s-cbhI) from T. reesei as well as the β-glucosidase gene (bgl1) from Saccharomycopsis fibuligera in S. cerevisiae. Extracellular endoglucanase activity was lower when co-expressed with s-cbhI or bgl1. Recombinant strains were able to hydrolyse phosphoric acid swollen cellulose, generating mainly cellotriose, cellobiose and glucose. Cellobiose accumulated, suggesting the β-glucosidase activity to be the rate-limiting factor. As a consequence, the recombinant strains were unable to produce enough glucose for growth on amorphous cellulose. The results of this study provide insight into further optimisation of recombinantly expressed cellulase combinations for saccharification and fermentation of cellulose to ethanol.

Keywords: Cellulose degradation; Bioethanol; S. cerevisiae ; Endoglucanase

Comparative analysis of membranous proteomics of Shewanella decolorationis S12 grown with azo compound or Fe (III) citrate as sole terminal electron acceptor by Bo Wang; Meiying Xu; Guoping Sun (pp. 1513-1523).

Shewanella decolorationis S12 is capable of carrying out anaerobic respiration using azo dyes and Fe (III) citrate as electron acceptors. In the present study, proteomic techniques including two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry were used to analyze the similarity and the dissimilarity of the membrane proteins isolated from strain S12 cells grown in amaranth or Fe (III) citrate with defined inorganic salt medium. The cells of strain S12 grown under a saturated dissolved oxygen condition served as controls. This is the first work that made the comparative analysis of cell membranous proteomics of strain S12 grown with azo compound or Fe (III) citrate as a sole terminal electron acceptor. The results showed that most of the membrane proteins of strain S12 under azo respiration are similar to those under Fe (III) respiration, but dissimilar from those of oxygen-grown cells. FdnH and FrdB were expressed specifically in azo respiration. NqrA-2, DctP, and hypothetical protein SO_4719 showed relative overexpression in azo respiration compared with Fe (III) respiration. OmpA family protein SO_3545 was detected to be specific to Fe (III) respiration. Furthermore, ArgF, SdhA, and HoxK were expressed markedly in both amaranth- and Fe (III) citrate-grown cultures compared with oxygen-grown cultures.

Keywords: Shewanella decolorationis S12; Azo respiration; Fe (III) respiration; Membrane proteins; 2-DE; MALDI-TOF/TOF/MS

A preliminary investigation on the growth requirement for monovalent cations, divalent cations and medium ionic strength of marine actinomycete Salinispora by Ginger Tsueng; Kin Sing Lam (pp. 1525-1534).

In this paper, we report that three species of Salinispora, S. arenicola, S. tropica, and S. pacifica, require magnesium and calcium, for growth, with S. pacifica having the most stringent growth requirement for these ions. Interaction between these ions in supporting the growth of Salinispora was observed. We also demonstrated that the absolute requirement of sodium to support the growth of Salinispora has not been established as all three species of Salinispora can use either potassium or lithium to replace sodium to support maximum growth. While lithium can replace sodium to support maximum growth of Salinispora, it is more toxic to S. arenicola than S. tropica and S. pacifica, inhibiting the growth of S. arenicola at 189 mM but without effect on the growth of S. tropica and S. pacifica. Using both sodium chloride-based and lithium chloride-based media, we showed that Salinispora has a growth requirement for divalent ions, magnesium and calcium as well as growth requirement for ionic strength (8.29 to 15.2 mS/cm). S. arenicola has a lower growth requirement for ionic strength than S. tropica and S. pacifica.

Keywords: Salinispora arenicola ; Salinispora tropica ; Salinispora pacifica ; Monovalent cations; Divalent cations; Medium ionic strength

Poly-β-hydroxybutyrate (PHB) increases growth performance and intestinal bacterial range-weighted richness in juvenile European sea bass, Dicentrarchus labrax by Peter De Schryver; Amit Kumar Sinha; Prabesh Singh Kunwar; Kartik Baruah; Willy Verstraete; Nico Boon; Gudrun De Boeck; Peter Bossier (pp. 1535-1541).

The bacterial storage polymer poly-β-hydroxybutyrate (PHB) has the potential to be used as an alternative anti-infective strategy for aquaculture rearing. In this research, the effects of (partially) replacing the feed of European sea bass juveniles with PHB were investigated. During a 6-week trial period, the PHB showed the ability to act as an energy source for the fish. This indicated that PHB was degraded and used during gastrointestinal passage. The gut pH decreased from 7.7 to 7.2 suggesting that the presence of PHB in the gut led to the increased production of (short-chain fatty) acids. The diets supplemented with 2% and 5% PHB (w/w) induced a gain of the initial fish weight with a factor 2.4 and 2.7, respectively, relative to a factor 2.2 in the normal feed treatment. Simultaneously, these treatments showed the highest bacterial range-weighted richness in the fish intestine. Based on molecular analysis, higher dietary PHB levels induced larger changes in the bacterial community composition. From our results, it seems that PHB can have a beneficial effect on fish growth performance and that the intestinal bacterial community structure may be closely related to this phenomenon.

Keywords: Prebiotics; Antibiotics; Infection; Growth promoting agent; Host–microbe interactions

A new manganese superoxide dismutase identified from Beauveria bassiana enhances virulence and stress tolerance when overexpressed in the fungal pathogen by Xue-Qin Xie; Jie Wang; Bao-Fu Huang; Sheng-Hua Ying; Ming-Guang Feng (pp. 1543-1553).

A superoxide dismutase (SOD) was characterized from Beauveria bassiana, a fungal entomopathogen widely applied to insect control. This 209-aa enzyme (BbSod2) showed no more than 71% sequence identity to other fungal Mn-SODs, sharing all conserved residues with the Mn-SOD family and lacking a mitochondrial signal. The SOD activity of purified BbSod2 was significantly elevated by Mn²⁺, suppressed by Cu²⁺ and Zn²⁺ but inhibited by Fe³⁺. Overexpressing the enzyme in a BbSod2-absent B. bassiana strain enhanced its SOD activity (107.2 ± 6.1 U mg⁻¹ protein) by 4–10-fold in different transformants analyzed. The best BbSod2-transformed strain with the SOD activity of 1,157.9 ± 74.7 U mg⁻¹ was 93% and 61% more tolerant to superoxide-generating menadione in both colony growth (EC₅₀ = 2.41 ± 0.03 versus 1.25 ± 0.01 mM) and conidial germination (EC₅₀ = 0.89 ± 0.06 versus 0.55 ± 0.07 mM), and 23% more tolerant to UV-B irradiation (LD₅₀ = 0.49 ± 0.02 versus 0.39 ± 0.01 J cm⁻²). Its virulence to Spodoptera litura larvae was enhanced by 26% [LT₅₀ = 4.5 (4.2–4.8) versus 5.7 (5.2–6.4) days]. Our study highlights for the first time that the Mn²⁺-cofactored, cytosolic BbSod2 contributes significantly to the virulence and stress tolerance of B. bassiana and reveals possible means to improving field persistence and efficacy of a fungal formulation by manipulating the antioxidant enzymes of a candidate strain.

Keywords: Beauveria bassiana ; Manganese superoxide dismutase; Enzyme overexpression; Antioxidative activity; Stress tolerance; Virulence

Bacterial biodiversity and dynamics during malolactic fermentation of Tempranillo wines as determined by a culture-independent method (PCR-DGGE) by Patricia Ruiz; Susana Seseña; Pedro Miguel Izquierdo; María Llanos Palop (pp. 1555-1562).

The bacterial population during malolactic fermentation of Tempranillo wine was studied using the polymerase chain reaction-denaturing gradient gel electrophoresis, a culture-independent method successfully used for identification and monitoring of bacterial population in different habitats included food fermentations. The results showed that Oenococcus oeni was the predominant species in the malolactic fermentation of Tempranillo wines, although the presence of Gluconobacter oxydans, Asaia siamensis, Serratia sp., and Enterobacter sp. was also observed. These results were partly coincidental with those obtained from a culture-dependent method, using a selective medium. Therefore, it may be concluded that for a more complete knowledge of the bacterial community present during malolactic fermentation of Tempranillo wine, an approach that combines a culture-independent method and a culture-dependent method would be advisable.

Keywords: Malolactic fermentation; Tempranillo wine; RAPD-PCR; PCR-DGGE

The role of salicylate and biosurfactant in inducing phenanthrene degradation in batch soil slurries by Avery Gottfried; Naresh Singhal; Roy Elliot; Simon Swift (pp. 1563-1571).

The majority of polycyclic aromatic hydrocarbons (PAHs) sorb strongly to soil organic matter posing a complex barrier to biodegradation. Biosurfactants can increase soil-sorbed PAHs desorption, solubilisation, and dissolution into the aqueous phase, which increases the bioavailability of PAHs for microbial metabolism. In this study, biosurfactants, carbon sources, and metabolic pathway inducers were tested as stimulators of microorganism degradation. Phenanthrene served as a model PAH and Pseudomonas putida ATCC 17484 was used as the phenanthrene degrading microorganism for the liquid solutions and soil used in this investigation. Bench-scale trials demonstrated that the addition of rhamnolipid biosurfactant increases the apparent aqueous solubility of phenanthrene, and overall degradation by at least 20% when combined with salicylate or glucose in liquid solution, when compared to solutions that contained salicylate or glucose with no biosurfactant. However, salicylate addition, with no biosurfactant addition, increased the total degradation of phenanthrene 30% more than liquid systems with only biosurfactant addition. In soil slurries, small amounts of biosurfactant (0.25 g/L) showed a significant increase in total removal when only biosurfactant was added. In soil slurries containing salicylate, the effects of biosurfactant additions were negligible as there was greater than 90% removal, regardless of the biosurfactant concentration. The results of experiments performed in this study provide further evidence that an in situ enhancement strategy for phenanthrene degradation could focus on providing additional carbon substrates to induce metabolic pathway catabolic enzyme production, if degradation pathway intermediates are known.

Keywords: Bioremediation; Biosurfactant; Salicylate; Polycyclic aromatic hydrocarbons; Pseudomonas putida

Efficient treatment of garbage slurry in methanogenic bioreactor packed by fibrous sponge with high porosity by Kengo Sasaki; Daisuke Sasaki; Masahiko Morita; Shin-ichi Hirano; Norio Matsumoto; Naoya Ohmura; Yasuo Igarashi (pp. 1573-1583).

Adding a supporting material to a methanogenic bioreactor treating garbage slurry can improve efficiency of methane production. However, little is known on how characteristics (e.g., porosity and hydrophobicity) of the supporting material affect the bioreactor degrading garbage slurry. We describe the reactor performances and microbial communities in bioreactors containing hydrophilic or hydrophobic sheets, or fibrous hydrophilic or hydrophobic sponges. The porosity affected the efficiency of methane production and solid waste removal more than the hydrophilic or hydrophobic nature of the supporting material. When the terminal restriction fragment length polymorphism technique was used at a lower organic loading rate (OLR), microbial diversities in the suspended fraction were retained on the hydrophobic, but not the hydrophilic, sheets. Moreover, real-time quantitative polymerase chain reaction (PCR) performed at a higher OLR revealed that the excellent performance of reactors containing fibrous sponges with high porosity (98%) was supported by a clear increase in the numbers of methanogens on these sponges, resulting in larger total numbers of methanogens in the reactors. In addition, the bacterial communities in fractions retained on both the hydrophobic and hydrophilic fibrous sponges differed from those in the suspended fraction, thus increasing bacterial diversity in the reactor. Thus, higher porosity of the supporting material improves the bioreactor performance by increasing the amount of methanogens and bacterial diversity; surface hydrophobicity contributes to maintaining the suspended microbial community.

Keywords: Supporting material; Methane fermentation; Garbage; Porosity; Hydrophobicity

Mineralization of s-triazine herbicides by a newly isolated Nocardioides species strain DN36 by Koji Satsuma (pp. 1585-1592).

A novel s-triazine-mineralizing bacterium—Nocardioides sp. strain DN36—was isolated from paddy field soil treated with ring-U-¹⁴C-labeled simetryn ([¹⁴C]simetryn) in a model paddy ecosystem (microcosm). In a tenfold-diluted R2A medium, strain DN36 liberated ¹⁴CO₂ from not only [¹⁴C]simetryn but also three ring-U-¹⁴C-labeled s-triazines: atrazine, simazine, and propazine. We found that DN36 mineralized ring-U-¹⁴C–cyanuric acid added as an initial substrate, indicating that the bacterium mineralized s-triazine herbicides via a common metabolite, namely, cyanuric acid. Strain DN36 harbored a set of genes encoding previously reported s-triazine-degrading enzymes (TrzN-AtzB-AtzC), and it also transformed ametryn, prometryn, dimethametryn, atraton, simeton, and prometon. The findings suggest that strain DN36 can mineralize a diverse range of s-triazine herbicides. To our knowledge, strain DN36 is the first Nocardioides strain that can individually mineralize s-triazine herbicides via the ring cleavage of cyanuric acid. Further, DN36 could not grow on cyanuric acid, and the degradation seemed to occur cometabolically.

Keywords: s-Triazine herbicides; Atrazine; Cyanuric acid; s-Triazine ring mineralization; Gram-positive strains; Nocardioides

Erratum to: In vivo Tn5-based transposon mutagenesis of Streptomycetes by Lutz Petzke; Andriy Luzhetskyy (pp. 1593-1593).

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Applied Microbiology and Biotechnology (v.86, #5)

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Applied Microbiology and Biotechnology (v.86, #5)