Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering.

Nowadays, biofuels, especially bioethanol, are becoming increasingly popular as an alternative to fossil fuels. Zymomonas mobilis is a desirable species for bioethanol production due to its unique characteristics, such as low biomass production and high-rate glucose metabolism. However, several factors can interfere with the fermentation process and hinder microbial activity, including lignocellulosic hydrolysate inhibitors, high temperatures, an osmotic environment, and high ethanol concentration. Overcoming these limitations is critical for effective bioethanol production. In this review, the stress response mechanisms of Z. mobilis are discussed in comparison to other ethanol-producing microbes. The mechanism of stress response is divided into physiological (changes in growth, metabolism, intracellular components, and cell membrane structures) and molecular (up and down-regulation of specific genes and elements of the regulatory system and their role in expression of specific proteins and control of metabolic fluxes) changes. Systemic metabolic engineering approaches, such as gene manipulation, overexpression, and silencing, are successful methods for building new metabolic pathways. Therefore, this review discusses systems metabolic engineering in conjunction with systems biology and synthetic biology as an important method for developing new strains with an effective response mechanism to fermentation stresses during bioethanol production. Overall, understanding the stress response mechanisms of Z. mobilis can lead to more efficient and effective bioethanol production.

In-vivo and in-vitro wound healing and tissue repair effect of Trametes versicolor polysaccharide extract.

Regarding different medical benefits of fungi, using the medical mushroom extracts as wound-healing agents is gaining popularity. This study, evaluated the wound healing characteristics of Trametes versicolor. Anti-oxidant activity addressed by employing the DPPH (2,2-diphenyl-1-picrylhydrazyl) assay resulting 53.7% inhibitory effect. Besides, for anti-microbial ability determination, the MIC (Minimum Inhibitory Concentration) of extract measured which Escherichia coli growth was inhibited at 1.1 mg/ml, and Staphylococcus aureus did not grow at 4.38 mg/ml of extract. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) method indicated dose dependence of the extract with 63 ± 3% and 28 ± 3% viability at 1250 µg/ml and 156.25 µg/ml of extract, which higher concentration caused higher cell viability. The outcome of gene expression analysis determined that overall expression of FGF2 (Fibroblast Growth Factor 2), IL-1ß (Interleukin-1ß), and TGF-ß1 (Transforming Growth Factor-ß1) was 4 times higher at 48 h than at 24 h in treated cells, suggesting a stimulating effect on cell growth. An in-vivo animal model suggested enhanced wound healing process after treatment with 0.01 g of extract. Furthermore, the number of fibroblasts, epidermal thickness, and collagen fiber was respectively 2, 3, and threefold higher in treated mice when compared to untreated mice. The treated wounds of mice showed 100% and 60% of untreated mice of healing within 14 days. The results of this research show promise for the fungus-based wound healing treatments, which may help with tissue regeneration and the healing of cutaneous wounds.

Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective.

Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.

Impact of hfq and sigE on the tolerance of Zymomonas mobilis ZM4 to furfural and acetic acid stresses.

Zymomonas mobilis, as an ethanologenic microorganism with many desirable industrial features, faces crucial obstacles in the lignocellulosic ethanol production process. A significant hindrance occurs during the pretreatment procedure that not only produces fermentable sugars but also releases severe toxic compounds. As diverse parts of regulation networks are involved in different aspects of complicated tolerance to inhibitors, we developed ZM4-hfq and ZM4-sigE strains, in which hfq and sigE genes were overexpressed, respectively. ZM4-hfq is a transcription regulator and ZM4-sigE is a transcription factor that are involved in multiple stress responses. In the present work, by overexpressing these two genes, we evaluated their impact on the Z. mobilis tolerance to furfural, acetic acid, and sugarcane bagasse hydrolysates. Both recombinant strains showed increased growth rates and ethanol production levels compared to the parental strain. Under a high concentration of furfural, the growth rate of ZM4-hfq was more inhibited compared to ZM4-sigE. More precisely, fermentation performance of ZM4-hfq revealed that the yield of ethanol production was less than that of ZM4-sigE, because more unused sugar had remained in the medium. In the case of acetic acid, ZM4-sigE was the superior strain and produced four and two-fold more ethanol compared to the parental strain and ZM4-hfq, respectively. Comparison of inhibitor tolerance between single and multiple toxic inhibitors in the fermentation of sugarcane bagasse hydrolysate by ZM4-sigE strain showed similar results. In addition, ethanol production performance was considerably higher in ZM4-sigE as well. Finally, the results of the qPCR analysis suggested that under both furfural and acetic acid treatment experiments, overproduction of both hfq and sigE improves the Z. mobilis tolerance and its ethanol production capability. Overall, our study showed the vital role of the regulatory elements to overcome the obstacles in lignocellulosic biomass-derived ethanol and provide a platform for further improvement by directed evolution or systems metabolic engineering tools.

A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4.

Zymomonas mobilis ZM4 has recently been used for a variety of biotechnological purposes. To rationally enhance its metabolic performance, a reliable genome-scale metabolic network model (GEM) of this organism is required. To this end, we reconstructed a genome-scale metabolic model (iHN446) for Z. mobilis, which involves 446 genes, 859 reactions, and 894 metabolites. We started by first reconciling the existing GEMs previously constructed for Z. mobilis to obtain a draft network. Next, recent gene annotations, up-to-date literature, physiological data and biochemical databases were used to upgrade the network. Afterward, the draft network went through a curative and iterative process of gap-filling by computational tools and manual refinement. The final model was evaluated using experimental data and literature information. We next applied this model as a platform for analyzing the links between transcriptome-flux and transcriptome-metabolome. We found that experimental observations were in agreement with the predicted results from our final GEM. Taken together, this comprehensive model (iHN446) can be utilized for studying metabolism in Z. mobilis and finding rational targets for metabolic engineering applications.

Detoxification impact of Trichosporon cutaneum in saline condition for efficient reduction of phenol co-contaminated with cadmium.

Treatment strategies applied for co-contaminated environments may not work due to a mixture of organic and inorganic contaminants. Here, we study the efficiency of simultaneous phenol and cadmium removal by Trichosporon cutaneum in saline condition. Initially, phenol degradation and cadmium removal were analyzed separately. The results showed the high potential of T. cutaneum for phenol degradation and almost all the phenol (1250 mg/L) was degraded in the presence of 5% NaCl. Cadmium removal by T. cutaneum indicated a direct relation to NaCl concentration. Increasing salt concentration from 0 to 5% caused an increase in cadmium adsorption from 57.3 to 80.2%. In the simultaneous remediation of phenol and cadmium, T. cutaneum showed a delay in the growth curve and phenol degradation, probably because of toxicity effect of cadmium, but at the end of a week, almost the same amount of phenol was removed (> 99% in 1250 mg/L phenol). T. cutaneum showed good efficiency in cadmium removal in simultaneous remediation and removed 90, 89, and 75% of cadmium in the existence of 5% NaCl in 750, 1000, and 1250 mg/L initial concentration of phenol, respectively. Our findings support the high activity of T. cutaneum in the bioremediation of polluted saline areas that phenol coexists with cadmium.

Blastobotrys persicus sp. nov., an ascomycetous yeast species isolated from cave soil.

Two strains (AHD129-1T and AHD129-2) of a new anamorphic yeast species were isolated from Mejare cave soil samples of Abdanan, Ilam, Iran. Nucleotide divergence in the D1/D2 domain of the large subunit (LSU) rRNA, and internal transcribed spacer (ITS) genes suggest that the two strains can be assigned to the Trichomonascus/Blastobotrys clade. A maximum likelihood tree based on sequences of the D1/D2 domain revealed that the new species is closely related to the species Trichomonascus ciferrii, Candida allociferrii, and Candida mucifera. The new species could be distinguished from the closely related species by its ability to grow at 42 °C and the inability to assimilate D-arabinose and D-mannitol. The name B. persicus sp. nov. is proposed for the new anamorphic species. The type strain of B. persicus is AHD129-1T = IBRC-M30238T = CBS 14259T, and the Mycobank number is MB 819148.

Synergistic Effect of Sarocladium sp. and Cryptococcus sp. Co-Culture on Crude Oil Biodegradation and Biosurfactant Production.

This study was conducted to evaluate the co-culture ability of two yeast (Sarocladium sp. and Cryptococcus sp.) isolates as compared to their individual cultures in surfactant production and oil degradation. The results showed that individual culture of each strain was capable of producing surfactant, degrading oil, and pyrene; also, a synergistic effect was observed when a co-culture was applied. Oil removal and biomass production were 28 and 35% higher in the co-culture than in individual cultures, respectively. To investigate the synergistic effects of mix culture on oil degradation, the surface tension, emulsification activity (EA), and cell surface hydrophobicity of individual and co-culture were studied. A comparison between the produced biosurfactant and chemical surfactants showed that individual culture of each yeast strain could reduce the surface tension like SDS and about 10% better than Tween 80. The results showed that the microbial consortium could reduce the surface tension more, by 10 and 20%, than SDS and Tween 80, respectively. Both individual cultures of Sarocladium sp. and Cryptococcus sp. showed good emulsification activity (0.329 and 0.412, respectively) when compared with a non-inoculated medium. Emulsification activity measurement for the two yeast mix cultures showed an excellent 33 and 67% increase as compared to the individual culture of Sarocladium sp. and Cryptococcus sp., respectively. The cell surface hydrophobicity of Sarocladium sp. and Cryptococcus sp. increased (38 and 85%) when the cells were treated with pyrene as a hydrophobic substrate for four generations. Finally, a 40% increase for pyrene degradation was measured in a co-culture of the two yeast mix culture. According to the results of the present study, the co-culture system exhibited better performance and this study will enhance the understanding of the synergistic effects of yeast co-culture on oil degradation.