Rita de Cássia Garcia Simão

Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.

New aspects on atrazine biodegradation

The world practice of using agrochemicals for long periods, in an indiscriminated and abusive way, has been a concern of the authorities involved in public health and sustainability of the natural resources, as a consequence of environmental contamination. Agrochemicals refer to a broad range of insecticides, fungicides and herbicides, and among them stands out atrazine, a herbicide intensively used in sugarcane, corn and sorghum cultures, among others. Researches have demonstrated that atrazine has toxic effects in algae, aquatic plants, aquatic insects, fishes and mammals. Due to the toxicity and persistence of atrazine in the environment, the search of microbial strains capable of degrading it is fundamental to the development of bioremediation processes, as corrective tools to solve the current problems of the irrational use of agrochemicals. This review relates the main microbial aspects and research on atrazine degradation by isolated microbial species and microbial consortia, as well as approaches on the development of techniques for microbial removal of atrazine in natural environments.

DnaK and GroEL are induced in response to antibiotic and heat shock in Acinetobacter baumannii

We studied the expression of DnaK and GroEL in Acinetobacter baumannii cells (strains ATCC 19606 and RS4) under stress caused by heat shock or antibiotics. A Western blot assay showed that DnaK and GroEL levels increased transiently more than 2-fold after exposure of bacterial cells to heat shock for 20 min at 50 degrees C. Heat induction of DnaK and GroEL was blocked completely when an inhibitor of transcription, rifampicin, was added 1 min before a temperature upshift to 50 degrees C, suggesting that the induction of these chaperones depends on transcription. A. baumannii cells pretreated at 45 degrees C for 30 min were better able to survive at 50 degrees C for 60 min than cells pretreated at 37 degrees C, indicating that A. baumannii is able to acquire thermotolerance. DnaK and GroEL were successfully induced in cells pre-incubated with a subinhibitory concentration of streptomycin. Moreover, bacterial cells pretreated for 30 min at 45 degrees C were better able to survive streptomycin exposure than cells pretreated at physiological temperatures. DnaK expression was upregulated in a multidrug-resistant strain of A. baumannii (RS4) in the presence of different antimicrobials (ampicillin+sulbactam, cefepime, meropenem and sulphamethoxazole+trimethoprim). This study is to the best of our knowledge the first to show that A. baumannii DnaK and GroEL could play an important role in the stress response induced by antibiotics.

Genotyping by RAPD-PCR analyses of Malassezia furfur strains from pityriasis versicolor and seborrhoeic dermatitis patients.

Malassezia furfur is lypophilic yeast commonly associate with dermatological disorders. In the present work, we described the isolation of 47 M. furfur strains from three groups of patients: pityriasis versicolor (21 isolates), seborrhoeic dermatitis (15 isolates) and seborrhoeic dermatitis of the HIV positive patients (11 isolates). To investigate the identity of the strains at molecular level, DNA genomic of M. furfur strains were prepared and used to RAPD-PCR analyses. RAPD assay were carried out using two decamer primers and bands pattern generated were analyzed by an Unweighted Pair-Group Method (UPGMA). Dendrogram established a distinct differentiation between M. furfur isolates from pityriasis versicolor and seborrhoeic dermatitis patients with or without AIDS. We concluded that RAPD typing presented a high discriminatory power between strains studied in this work and can be applied in epidemiological investigation of skin disease causing by M. furfur.

The accessory domain changes the accessibility and molecular topography of the catalytic interface in monomeric GH39 β-xylosidases

β-Xylosidases (EC 3.2.1.37) are among the principal glycosyl hydrolases involved in the breakdown of hemicelluloses, catalyzing the reduction of xylooligosaccharides to free xylose. All GH39 β-xylosidases structurally characterized to date display a modular multi-domain organization that assembles a tetrameric quaternary structure. In this work, the crystal structure and the SAXS molecular envelope of a new GH39 β-xylosidase from Caulobacter crescentus (CcXynB2) have been determined. Interestingly, CcXynB2 is a monomer in solution and comparative structural analyses suggest that the shortened C-terminus prevents the formation of a stable tetramer. Moreover, CcXynB2 has a longer loop from the auxiliary domain (the long α-helix-containing loop) which makes a number of polar and hydrophobic contacts with the parental (α/β)(8)-barrel domain, modifying the accessibility and the molecular topography of the catalytic interface. These interactions also maintain the accessory domain tightly linked to the catalytic core, which may be important for enzyme function and stability.

Xylanase from Fusarium heterosporum: Properties and influence of thiol compounds on xylanase activity

The properties of xylanase purified from Fusarium heterosporum that was grown in barley-brewing residue under solid-state fermentation and the effects of thiol compounds on the reactivation of the metal ion-inhibited xylanase were investigated. Xylanase was purified to homogeneity by ion exchange chromatography, and its molecular mass was estimated to be 19.5 kDa by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). The optimum pH for the xylanase was 5.0, and it was stable in acidic pH (4.5 to 5.5), where it retained more than 87% of its activity after 24 h. The optimum temperature was 50°C, and it had a half-life of 53 min at 45°C. The apparent Km and Vmax values for the xylanase were 5.63 mg/ml and 800 μmol/mg/min, respectively. Ba 2+ , Ca 2+ , Mg 2+ and the thiol compounds β-mercaptoethanol and dithiothreitol (DTT) enhanced xylanase activity, while Hg 2+ , Pb 2+ and Zn 2+ strongly inhibited enzyme activity. Furthermore, this xylanase had an alternative mode of regulation in the presence of thiol compounds because the enzyme was able to recover its catalytic activity after inhibition by heavy metal ions. Keywords: Hemicellulase, fungus, solid-state fermentation, barley brewing residue, thiol compounds African Journal of Biotechnology , Vol. 13(9), pp. 1047-1055, 26 February, 2014

High levels of β-xylosidase in Thermomyces lanuginosus: potential use for saccharification

A new strain of Thermomyces lanuginosus was isolated from the Atlantic Forest biome, and its β-xylosidases optimization in response to agro-industrial residues was performed. Using statistical approach as a strategy for optimization, the induction of β-xylosidases activity was evaluated in residual corn straw, and improved so that the optimum condition achieved high β-xylosidases activities 1003 U/mL. According our known, this study is the first to show so high levels of β-xylosidases activities induction. In addition, the application of an experimental design with this microorganism to induce β-xylosidases has not been reported until the present work. The optimal conditions for the crude enzyme extract were pH 5.5 and 60 °C showing better thermostability at 55 °C. The saccharification ability of β-xylosidase in the presence of hemicellulose obtained from corn straw raw and xylan from beechwood substrates showed a xylo-oligosaccharide to xylose conversion yield of 80 and 50%, respectively, at 50 °C. Our data strongly indicated that the β-xylosidases activities was not subjected to the effects of potential enzyme inhibitors often produced during fermentation process. These data suggest the application of this enzyme studied for saccharification of hemicellulose, an abundant residue in the American continents, thus providing an interesting alternative for future tests for energy production.

Characterization of a novel Aspergillus niger beta-glucosidase tolerant to saccharification of lignocellulosic biomass products and fermentation inhibitors

Properties of beta-glucosidase produced by Aspergillus niger URM 6642 recently isolated from the Atlantic rainforest biome and its potential tolerance to saccharification of lignocellulosic biomass products and fermentation inhibitors was evaluated. The fungus was cultivated under solid state culture conditions at 37°C with different agro-industrial wastes. High levels of beta-glucosidase (3778.9 U g−1)from A. niger were obtained with rice meal as substrate under solid state culture conditions after ten days. Optimum pH for this particular beta-glucosidase activity was 4.0 although it was stable in the range of 4.0 to 7.0. The half-life (T½) of beta-glucosidase at 55°C is 3 h. However, at the optimum temperature of the enzyme, 65°C, T½ is 20 min. The enzyme showed tolerance to various compounds such as glucose, xylose, 5-hydroxymethyl furfural, furfural, coumarin, ethanol and acetic acid. Therefore, beta-glucosidase from the novel A. niger species may be of potential use in the saccharification of lignocellulosic biomass, as well as an additional enzyme supplement in cellulase cocktails used to increase the yield of fermentable sugars.

Depletion of the xynB2 Gene Upregulates β-Xylosidase Expression in C . crescentus

Caulobacter crescentus is able to express several enzymes involved in the utilization of lignocellulosic biomasses. Five genes, xynB1–5, that encode β-xylosidases are present in the genome of this bacterium. In this study, the xynB2 gene, which encodes β-xylosidase II (CCNA_02442), was cloned under the control of the PxylX promoter to generate the O-xynB2 strain, which overexpresses the enzyme in the presence of xylose. In addition, a null mutant strain, Δ-xynB2, was created by two homologous recombination events where the chromosomal xynB2 gene was replaced by a copy that was disrupted by the spectinomycin-resistant cassette. We demonstrated that C. crescentus cells lacking β-xylosidase II upregulates the xynB genes inducing β-xylosidase activity. Transcriptional analysis revealed that xynB1 (RT-PCR analysis) and xynB2 (lacZ transcription fusion) gene expression was induced in the Δ-xynB2 cells, and high β-xylosidase activity was observed in the presence of different agro-industrial residues in the null mutant strain, a characteristic that can be explored and applied in biotechnological processes. In contrast, overexpression of the xynB2 gene caused downregulation of the expression and activity of the β-xylosidase. For example, the β-xylosidase activity that was obtained in the presence of sugarcane bagasse was 7-fold and 16-fold higher than the activity measured in the C. crescentus parental and O-xynB2 cells, respectively. Our results suggest that β-xylosidase II may have a role in controlling the expression of the xynB1 and xynB2 genes in C. crescentus.

β-(1→3)-Glucan of the Southern Bracket Mushroom, Ganoderma australe (Agaricomycetes), Stimulates Phagocytosis and Interleukin-6 Production in Mouse Peritoneal Macrophages

Ganoderma australe was studied to determine the composition of the cell wall, and polysaccharide fraction SK5 was obtained after freeze-thawing an aqueous 5% potassium hydroxide extraction. The monosaccharide composition of the SK5 fraction revealed by gas chromatography-mass spectrometry showed 81.3% glucose, and analyses by 13C nuclear magnetic resonance spectroscopy confirmed a β-glucan with glycosidic links of the (1→3)-β type and most likely 4-O substituted. In addition, the biological effect of the β-glucan from G. australe was evaluated via in vitro cell cultures of peritoneal macrophages isolated from Swiss mice. Biological assays were assessed for toxicity and cell activation, interleukin-6 cytokine concentrations, and the ability to stimulate phagocytic activity. There was an increase in interleukin-6 by approximately 111% with 1.0 µg/mL of polysaccharide, and phagocyte activity was increased in all concentrations examined, obtaining 52.3% with 0.25 µg/mL polysaccharide. The results indicate that a β-(1→3)-glucan isolated from G. australe can be classified as a biological response modifier.