Improving cellulosic ethanol fermentability of Zymomonas mobilis by overexpression of sodium ion tolerance gene ZMO0119

Probiotics for the Management of Sepsis: Advances in Animal Models and Intensive Care Unit Environments

Sepsis frequently leads to multiple organ failure and is a major cause of morbidity and mortality in critically ill patients. Although intensive care protocols and antibiotic therapy have improved sepsis treatment, specific management is lacking with respect to efficient protection from tissue damage and long-term outcomes. Probiotics are live microbes that modulate the immune system and inflammation and colonize the gut. In this narrative review, we have traced the evolution of the administration of probiotics in an animal model of sepsis and treatment alternatives in the intensive care unit setting. First, probiotics are categorized by species before describing their modulation of the microbiota, repair of tissue-specific damage, immune response, and molecular pathways to prevent complications. The impact on therapy for infant and adult patients is also addressed. Finally, we have emphasized the challenges and gaps in current studies as well as future perspectives for further investigation. The present review can open up avenues for new strategies that employ promising probiotic strains for the treatment of sepsis and discusses their ability to prevent disease-associated long-term complications.

Overexpression of Dioxygenase Encoding Gene Accelerates the Phenolic Aldehyde Conversion and Ethanol Fermentability of Zymomonas mobilis

NADH-dependent reductase enzyme catalyzes the phenolic aldehyde conversion and correspondingly improves the ethanol fermentability of the ethanologenic Zymomonas mobilis. This study constructed the transcriptional landscape of mono/dioxygenase genes in Z. mobilis ZM4 under the stress of the toxic phenolic aldehyde inhibitors of 4-hydroxybenzaldehyde, syringaldehyde, and vanillin. One specific dioxygenase encoding gene ZMO1721 was differentially expressed by 3.07-folds under the stress of 4-hydroxybenzaldehyde among the eleven mono/dioxygenase genes. The purified ZMO1721 shared 99.9% confidence and 48.0% identity with the oxidoreductase in Rhodoferax ferrireducens T118 was assayed and the NADH-dependent reduction activity was confirmed for phenolic aldehyde vanillin conversion. The ZMO1721 gene was then overexpressed in Z. mobilis ZM4 and the 4-hydroxybenzaldehyde conversion rate was accelerated. The cell growth, glucose consumption, and ethanol productivity of Z. mobilis ZM4 were also improved by ZMO1721 overexpression. The genes identified on improving phenolic aldehyde tolerance and ethanol fermentability in this study could be used as the synthetic biology tools for modification of ethanologenic strains.

Increasing sodium lactate production by enhancement of Na+ transmembrane transportation in Pediococcus acidilactici

Fermentative production of sodium lactate generally is a low efficient process because of the high Na⁺ osmatic stress on lactic acid bacterium cells. In this study, the homogeneous genes encoding Na⁺/H⁺ antiporters were screened and overexpressed in Pediococcus acidilactici for the enhancement of Na⁺ transmembrane transportation. The function of the gene RS02775 was identified and its overexpressing in P. acidilactici resulted in the significantly improved sodium lactate production. The recombinant not only accelerated the sugar consumption, but also achieved the record high titer of sodium lactate by 121.1 g/L using pure sugars and 132.4 g/L using wheat straw. The transcription analysis shows that the overexpression of Na⁺/H⁺ antiporter significantly upregulated the transcription of the sugar phosphorylation genes of P. acidilactici under high Na⁺ stress. This study provides an effective method for high titer production of sodium lactate using both pure sugars and lignocellulose feedstocks.

Sustainable environmental management and related biofuel technologies

Environmental sustainability criteria and rising energy demands, exhaustion of conventional resources of energy followed by environmental degradation due to abrupt climate changes have shifted the attention of scientists to seek renewable sources of green and clean energy for sustainable development. Bioenergy is an excellent alternative since it can be applied for several energy-requirements after utilizing suitable conversion methodology. This review elucidates all aspects of biofuels (bioethanol, biodiesel, and butanol) and their sustainability criteria. The principal focus is on the latest developments in biofuel production chiefly stressing on the role of nanotechnology. A plethora of investigations regarding the emerging techniques for process improvement like integration methods, less energy-intensive distillation techniques, and bioengineering of microorganisms are discussed. This can assist in making biofuel-production in a real-world market more economically and environmentally viable.

Increased salt tolerance in Zymomonas mobilis strain generated by adaptative evolution

BACKGROUND

Ethanologenic alphaproteobacterium Zymomonas mobilis has been acknowledged as a promising biofuel producer. There have been numerous efforts to engineer this species applicable for an industrial-scale bioethanol production. Although Z. mobilis is robustly resilient to certain abiotic stress such as ethanol, the species is known to be sensitive to saline stress at a mild concentration, which hampers its industrial use as an efficient biocatalyst. To overcome this issue, we implemented a laboratory adaptive evolution approach to obtain salt tolerant Z. mobilis strain.

RESULTS

During an adaptive evolution, we biased selection by cell morphology to exclude stressed cells. The evolved strains significantly improved growth and ethanol production in the medium supplemented with 0.225 M NaCl. Furthermore, comparative metabolomics revealed that the evolved strains did not accumulate prototypical osmolytes, such as proline, to counter the stress during their growth. The sequenced genomes of the studied strains suggest that the disruption of ZZ6_1149 encoding carboxyl-terminal protease was likely responsible for the improved phenotype.

CONCLUSIONS

The present work successfully generated strains able to grow and ferment glucose under the saline condition that severely perturbs parental strain physiology. Our approach to generate strains, cell shape-based diagnosis and selection, might be applicable to other kinds of strain engineering in Z. mobilis.

Perspectives and new directions for bioprocess optimization using Zymomonas mobilis in the ethanol production

Zymomonas mobilis is an ethanologenic microbe that has a demonstrated potential for use in lignocellulosic biorefineries for bioethanol production. Z. mobilis exhibits a number of desirable characteristics for use as an ethanologenic microbe, with capabilities for metabolic engineering and bioprocess modification. Many advanced genetic tools, including mutation techniques, screening methods and genome editing have been successively performed to improve various Z. mobilis strains as potential consolidated ethanologenic microbes. Many bioprocess strategies have also been applied to this organism for bioethanol production. Z. mobilis biofilm reactors have been modified with various benefits, including high bacterial populations, less fermentation times, high productivity, high cell stability, resistance to the high concentration of substrates and toxicity, and higher product recovery. We suggest that Z. mobilis biofilm reactors could be used in bioethanol production using lignocellulosic substrates under batch, continuous and repeated batch processes.

Simultaneous nitrogen fixation and ethanol production by Zymomonas mobilis

This work reports on production of ethanol with simultaneous fixing of nitrogen (N₂) using the anaerobic bacterium Zymomonas mobilis DSM 473. A batch fermentation with an initial glucose concentration of 50 g L^-1, an initial pH of ∼5.5, an inoculum size of 10% by volume and a N₂ feeding rate of 50 mL min^-1 without mechanical agitation was found to provide the highest ethanol productivity (0.401 g L^-1 h^-1). Ethanol yield on glucose exceeded 97% of the theoretical maximum. The nitrogen content of the microbial biomass was 10.4% w/w at 65 h and all of it was derived by fixation of dinitrogen. Repeated-batch fermentations were investigated for ethanol production using simultaneous nitrogen fixation. A 2-cycle repeated-batch fermentation lasting 71 h gave a maximum ethanol yield on glucose of 0.475 g g^-1 and an ethanol productivity of 0.675 g L^-1 h^-1. The yield (0.415 g g^-1) and productivity (0.638 g L^-1 h^-1) were reduced in a 3-cycle repeated batch operation lasting 94 h. The need to fix nitrogen did not reduce the final achievable ethanol concentration, or the ethanol yield on glucose, relative to fermentations provided with fixed nitrogen, but did reduce the ethanol productivity by ∼82% because less cell mass was produced.

Identification and characterization of ethanol-inducible promoters of Zymomonas mobilis based on omics data and dual reporter-gene system

Zymomonas mobilis is a model bacterial ethanologen and has been engineered to produce lignocellulosic biofuels and biochemicals such as 2,3-butanediol. We have previously identified promoters of different strengths using systems biology datasets and characterized them using the flow cytometry-based dual reporter-gene system. Here, we further demonstrated the capability of applying the dual reporter-gene system and omics datasets on discovering inducible promoters. Ten candidate ethanol-inducible promoters were identified through omics datasets mining and clustering. Using the dual reporter-gene system, these promoters were characterized under natural growth, ethanol stress, and ethanol-induced condition to investigate the transcriptional strength and ethanol inducibility. The results demonstrated that three promoters of P0405, P0435, and P0038 driving the expression of native genes of ZMO0405, ZMO0435, and ZMO0038, correspondingly, are potential ethanol-responsive promoters and may be growth related. This study not only identified and verified three ethanol-inducible promoters as biological parts, which can be used to synchronize the expression of heterologous pathway genes with the ethanol production process of Z. mobilis, but also demonstrated the power of combining omics datasets and dual reporter-gene system to identify biological parts for metabolic engineering and synthetic biology applications in Z. mobilis and related microorganisms.

Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era

BACKGROUND

Zymomonas mobilis is a model bacterial ethanologen with many systems biology studies reported. Besides lignocellulosic ethanol production, Z. mobilis has been developed as a platform for biochemical production through metabolic engineering. However, identification and rigorous understanding of the genetic origins of cellular function, especially those based in non-coding region of DNA, such as promoters and ribosomal binding sites (RBSs), are still in its infancy. This knowledge is crucial for the effective application of Z. mobilis to new industrial applications of biotechnology for fuels and chemicals production.

RESULTS

In this study, we explored the possibility to systematically predict the strength of promoters based on systems biology datasets. The promoter strength was clustered based on the expression values of downstream genes (or proteins) from systems biology studies including microarray, RNA-Seq and proteomics. Candidate promoters with different strengths were selected for further characterization, which include 19 strong, nine medium, and ten weak ones. A dual reporter-gene system was developed which included appropriate reporter genes. These are the opmCherry reporter gene driven by the constitutive PlacUV5 promoter for calibration, and EGFP reporter gene driven by candidate promoters for quantification. This dual reporter-gene system was confirmed using the inducible promoter, Ptet, which was used to determine the strength of these predicted promoters with different strengths. In addition, the dual reporter-gene system was applied to determine four synthetic RBSs with different translation initiation rates based on the prediction from bioinformatics server RBS calculator. Our results showed that the correlations between the prediction and experimental results for the promoter and RBS strength are relatively high, with R ² values more than 0.7 and 0.9, respectively.

CONCLUSIONS

This study not only identified and characterized 38 promoters and four RBSs with different strengths for future metabolic engineering in Z. mobilis, but also established a flow cytometry-based dual reporter-gene system to characterize genetic elements including, but not limited to the promoters and RBSs studied in this work. This study also suggested the feasibility of predicting and selecting candidate genetic elements based on omics datasets and bioinformatics tools. Moreover, the dual reporter-gene system developed in this study can be utilized to characterize other genetic elements of Z. mobilis, which can also be applied to other microorganisms.