The Journal of General and Applied Microbiology Vol. 60(2014) No. 6

A nitrilase gene cyc705 from Arthrobacter aurescens CYC705 for synthesis of iminodiacetic acid (IDA) was cloned. This gene contained a 930 bp ORF, which encoded a polypeptide of 310 amino acids. A recombinant Escherichia coli BL21(DE3)/pET28a-cyc705 was constructed to achieve the heterologous expression of cyc705. This recombinant nitrilase was purified to homogeneity with a molecular weight of 36.7 kDa on SDS-PAGE and mass spectrometry, and characterized to be an oligomer of 14 subunits by gel permeation chromatography. Using iminodiacetonitrile (IDAN) as the substrate, the V_max, K_m, k_cat and k_cat/K_m were 9.05 U mg⁻¹, 43.17 mM⁻¹, 94.1 min⁻¹ and 2.18×10³ min⁻¹ M⁻¹, respectively. The optimum temperature and pH were 25°C and 5.8. The suitable substrates for the purified nitrilase were short-chain aliphatic dinitriles. High concentration of IDAN could be hydrolyzed to IDA in a shorter time.

The objective of the present study was to isolate, identify and characterize new LAB strains with high probiotic potentials from Iranian (Isfahan) indigenous chickens. From 90 isolated LABs, 11 isolates had high growth rate under different stress conditions, including acid (pH 2.5), bile (0.5% oxgall), salt (6−15%) and temperatures 15 and 45°C, and their aggregation time was less than 120 min. Based on the molecular identification using 16S rDNA sequencing and phylogenetic analysis, the isolates belonged to two Lactobacillus salivarius and L. reuteri species. The isolates showed different tolerance to 16 clinically and veterinary relevant antibiotics, and most of them were resistant to or semi-tolerant of 7−15 different studied antibiotics. The Es11, Es12, Es3 and Es13 strains with resistance to or semi-tolerance of 15, 14 and 13 different antibiotics, respectively, were the most tolerant strains. The selected isolates showed a wide range of antimicrobial activity against 7 different pathogenic strains. All the isolates exhibited antagonistic activity against E. coli, Enterococcus hirae, Salmonella enterica and Staphylococcus aureus. The isolates Es6 and Es11 with high antagonistic activity and resistance against 6 of the studied pathogens were the most powerful antagonistic isolates. The values and types of adhesion to the Caco-2 cell cultures were significantly different (0−40 bacteria/Caco-2 cell), and the maximum adhesion was observed for the isolates Es6 and Es13 with 35 and 40 bacteria adhesion/cell, respectively. Finally, based on all the experiments, 7 strains, including Es1, Es6, Es7, Es11, Es12 and Es13, were selected for the further in vivo assays and possible use in the poultry industry.

Previously, we proposed a new method for production of RNA aptamers using the marine bacterium Rhodovulum sulfidophilum. A streptavidin RNA aptamer (an RNA which binds to streptavidin) was extracellularly produced by this bacterium containing engineered plasmid. The aptamer had full biological function. As a next step we attempted to produce another functional RNA, short hairpin RNAs (shRNAs) using this bacterial system. We have designed two types of shRNAs targeted to the luciferase gene. Here we report that shRNAs are successfully produced extracellularly by this system. Even if the shRNA has a long stem-loop structure which is thought to interfere with transcription in bacterial cells, the yield of the shRNA is almost the same as that of the streptavidin RNA aptamer. During the course of these experiments, we also found a new type of RNA processing for the double-stranded region of the shRNA.

We analyzed the bacterial community of Alaska pollock sikhae, a traditional Korean food made by natural fermentation with Alaska pollock, utilizing pyrosequencing. We fermented the Alaska pollock sikhae at two different temperatures (10°C and 20°C). Before fermentations, the bacterial community was varied. After fermentations, however, Lactobacillus sakei became dominant. The Alaska pollock sikhae sample before fermentations contained only 2% L. sakei, but the sample on day 6 of fermentation at 10°C comprised 74% L. sakei (90% at 20°C). In addition, we observed a reduction in the composition of unpreferred bacterial species for foods after fermentation. The composition of unpreferred bacterial species was more than 30% of total reads in samples before fermentation and decreased to less than 0.2% after fermentation. This result suggested that the fermentation of Alaska pollock sikhae can be beneficial for food safety. Alaska pollock sikhae might be a favorable habitat for L. sakei. Our study is the first report illustrating the alteration of the bacterial community of Alaska pollock sikhae during fermentation utilizing pyrosequencing analysis.

A new xylanase gene (xyn43A) from Aspergillus niger XZ-3S was cloned and expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL. The coding region of the gene was separated by only one intron 86 bp in length. It encoded 318 amino acid residues of a protein with a calculated molecular weight (MW) of 33.47 kDa plus a signal peptide of 19 amino acids. The amino acid sequence of the xyn43A gene showed 77.56% amino acid identity to A. nidulans xylanase, and the phylogenetic tree analysis revealed that xyn43A had close relationships with those of family 43 of glycosyl hydrolases reported from other microorganisms. Three-dimensional structure modeling showed that Xyn43A had a typical five-blade β-propeller fold. The mature peptide encoding cDNA was subcloned into pET-28a (+) expression vector. The resultant recombinant plasmid pET-28a-xyn43A was transformed into Escherichia coli BL21-CodonPlus (DE3)-RIL, and xylanase activity was measured. A maximum activity of 61.43 U/mg was obtained from the cellular extract of E. coli BL21-CodonPlus (DE3)-RIL harboring pET-28a-xyn43A. The recombinant xylanase had optimal activity at pH5.0 and 45°C. Fe³⁺, Cu²⁺ and EDTA had an obvious active effect on the enzyme.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), derived from the outer-membrane protein (OMP) fraction, has been used as a potential candidate for vaccine development. The gene-encoding 37 kDa GAPDH outer membrane protein (OMP) from Edwardsiella ictaluri was amplified using polymerase chain reaction (PCR) and was cloned and expressed in Escherichia coli BL21 (DE3). Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting, and nucleotide and amino acid sequencing were used to analyze the expressed antigenic protein and gene encoding this protein. Comparative DNA and protein sequence analysis of GAPDH from E. ictaluri GAPDHs from several Gram-negative bacterial species within the Enterobacteriaceae family revealed that the GAPDHs within this group are highly conserved and share a sequence similarity of 75−100% with E. ictaluri GDPDH. Rabbit antiserum raised against the E. ictaluri recombinant GAPDH (rGAPDH) protein recognized purified GADPH, indicating that it has a strong immunogenicity. Tilapia fish were intraperitoneally immunized with formalin-killed E. ictaluri whole cells, and rGAPDH (30 μg fish⁻¹) from E. ictaluri, both of which were emulsified in ISA 763A adjuvant. At 3 months after immunization, fish were challenged with the E. tarda strain to assess vaccine efficacy; the relative percent survival (RPS) values were found to exceed 71.4%. The specific mean antibody titer log₂ level of groups vaccinated with rGAPDH at 3 months was significantly higher than that of non-vaccinated fish (control group). Therefore, this recombinant protein can be considered a multi-purpose candidate vaccine against several pathogenic bacteria.

The antimicrobial activities of isolated compounds from seed extracts of Moringa oleifera and synergistic antimicrobial efficacy through hybridized complex of organic-inorganic composite materials were studied. The two main components of the Moringa oleifera seed were isolated and determined to be niazimicin and 4-(α-L-rhamnosyloxy)-benzyl isothiocyanate (RBI). The antimicrobial activity of the separated compounds of the Moringa oleifera seed were tested in vitro against 3 bacterial species and 2 fungal species by the paper disc diffusion assay and broth dilution methods. Both compounds showed antimicrobial activity against tested species and RBI was more effective than niazimicin. The MIC of RBI on S. aureus, E. coli, P. aeruginosa, C. albicans, and A. niger was 0.005%, 0.1%, 0.5%, 0.5%, and 0.5%, respectively, while the MIC of niazimicin on S. aureus was 0.1%. Next, we investigated the combined antimicrobial action of mesoporous ZnO and RBI by incorporating the compound within the pore of mesoporous ZnO. The MIC of mesoporous ZnO with RBI on S. aureus, E. coli, P. aeruginosa, C. albicans, and A. niger was 0.001%, 0.01%, 0.5%, 0.1%, and 0.1%, respectively. A synergistic effect of RBI with mesoporous ZnO was shown. From these results, the mesoporous ZnO could act as a reservoir for RBI and mesoporous ZnO with RBI could be used for cosmetic preservatives.

Tobramycin is an important broad spectrum aminoglycoside antibiotic widely used against severe Gram-negative bacterial infections. It is produced by base-catalyzed hydrolysis of carbamoyltobramycin (CTB) generated by S. tenebrarius. We herein report the construction of a genetically engineered S. tenebrarius for direct fermentative production of tobramycin by disruption of aprK and tobZ. A unique putative NDP-octodiose synthase gene aprK was disrupted to optimize the production of CTB, resulting in the blocking of apramycin biosynthesis and the obvious increase in CTB production of aprK disruption mutant S. tenebrarius ST316. Additional mutation on the carbamoyltransferase gene tobZ in S. tenebrarius ST316 generated a strain ST318 that produces tobramycin as a single metabolite. ST318 could be used for industrial fermentative production of tobramycin.

The production of glucose oxidase (GOX) and catalase (CAT) by submerged fermentation of the free and immobilized xerophytic fungus Aspergillus niger under equal conditions was compared. To immobilize fungal spores, entrapment in PVA/alginate beads treated with NaNO₃/CaCl₂ was performed. The yield of immobilization in the beads with a diameter less than 1mm was equal to 100%. Fungus growth and substrate consumption were evaluated in both fermentation systems, demonstrating the lag-period presence in the case of the first cycle of immobilized fungus use. The enzyme production by immobilized fungus reuse was carried out. In these cases, greater enzymatic GOX activity was detected, while CAT activity decreased. SEM micrographs for the beads with immobilized fungus applied in the first and second fermentation cycles were obtained, presenting fungus spreading inside the sphere, spore presence and branching hyphae. Immobilization of A. niger on PVA/alginate beads is effective for GOX and CAT production at least on 2−3 repeated fermentative cycles. Thus, immobilization enables repeated use of microbial cells.

Lactic acid bacteria that grow under alkaline conditions (pH 10) were isolated from various sources in Okinawa (Japan). These alkali-tolerant and alkaliphilic bacteria were classified as follows: Microbacterium sp. (1 strain), Enterococcus spp. (9 strains), Alkalibacterium spp. (3 strains), Exiguobacterium spp. (5 strains), Oceanobacillus spp. (3 strains) and Bacillus spp. (7 strains) by 16S rRNA gene sequencing. By fermentation, many strains were able to convert glucose into mainly L-(+)-lactic acid of high optical purity in alkaline broth. This result indicated that valuable L-(+)-lactic acid-producing bacteria could be isolated efficiently by screening under alkaline conditions. Six strains were selected and their ability to produce lactic acid at different initial pH was compared. Enterococcus casseliflavus strain 79w3 gave the highest lactic acid concentration. Lactic acid concentration and productivity were 103 g L⁻¹ (optical purity of 99.5% as L-isomer) and 2.2 g L⁻¹ h⁻¹, respectively when 129 g L⁻¹ of glucose was used by batch fermentation.