Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics

Yang, Shihui; Pan, Chongle; Hurst, Gregory B.; Dice, Lezlee; Davison, Brian H.; Brown, Steven D.

doi:10.3389/fmicb.2014.00246

Cited by 44 publications

(45 citation statements)

References 60 publications

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“…2 Mb, Seo et al ., ). The genome annotation has been improved recently (Yang et al ., ), which greatly assists in the accumulation of Z. mobilis systems biology data, especially the microarray‐based transcriptomic datasets of different strains grown under different conditions (Yang et al ., , , , ,b; Hayashi et al ., ; He et al ., ,b; Jeon et al ., ; Skerker et al ., ; Yi et al ., ; Zhang et al ., ). The availability of several other Z. mobilis genomes, such as CP4, NCIMB 11163, ATCC 29191, ATCC 29192, ATCC 10988 and ZM4 mutants of ATCC 31822 and ATCC 31823 (Kouvelis et al ., , , , ; Peralta‐Yahya and Keasling, ; Pappas et al ., ; Smith and Liao, ; Desiniotis et al ., ; Zhao et al ., , ) and other strains in the sequencing pipeline makes comparative genomics research practical.…”

Section: Classical Genetics Tools and Emerging Technologymentioning

confidence: 99%

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Yang

Fei

Zhang

et al. 2016

Microbial Biotechnology

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172

110

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Summary Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.

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Section: Classical Genetics Tools and Emerging Technologymentioning

confidence: 99%

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Yang

Fei

Zhang

et al. 2016

Microbial Biotechnology

Self Cite

172

110

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“…For example, transcriptomic profiles of Z. mobilis wild-type strain ZM4 or its xyloseutilizing derivative 8b in response to furfural, acetate, or phenolic aldehyde inhibitors (4-hydroxybenzaldehyde, syringaldehyde, and vanillin) have been investigated (He et al 2012;Yang et al 2014a;Yi et al 2015). In addition, integrated proteomic and transcriptomic approaches were used to understand the molecular mechanism of an acetate-tolerant strain (Yang et al 2014c). All these studies demonstrated that multiple-gene regulation is responsive for the inhibitor tolerance in Z. mobilis involving in carbohydrate metabolism, DNA replication, recombination and repair, transcriptional regulation, and universal stress responses.…”

Section: Robustness Improvement By Reverse Genetics Approachesmentioning

confidence: 99%

Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis

Yang

Tang

et al. 2018

Bioresour. Bioprocess.

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Pretreatment is the key step to overcome the recalcitrance of lignocellulosic biomass making sugars available for subsequent enzymatic hydrolysis and microbial fermentation. During the process of pretreatment and enzymatic hydrolysis as well as fermentation, various toxic compounds may be generated with strong inhibition on cell growth and the metabolic capacity of fermenting strains. Zymomonas mobilis is a natural ethanologenic bacterium with many desirable industrial characteristics, but it can also be severely affected by lignocellulosic hydrolysate inhibitors. In this review, analytical methods to identify and quantify potential inhibitory compounds generated during lignocellulose pretreatment and enzymatic hydrolysis were discussed. The effect of hydrolysate inhibitors on Z. mobilis was also summarized as well as corresponding approaches especially the high-throughput ones for the evaluation. Then the strategies to enhance inhibitor tolerance of Z. mobilis were presented, which include both forward and reverse genetics approaches such as classical and novel mutagenesis approaches, adaptive laboratory evolution, as well as genetic and metabolic engineering. Moreover, this review provided perspectives and guidelines for future developments of robust strains for efficient bioethanol or biochemical production from lignocellulosic materials.

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“…Cells were resuspended with test medium. Bioscreen C assays were carried out as described previously [16,[27][28][29][30][31]…”

Section: Resultsmentioning

confidence: 99%

Underlying Mechanism of Uncoupled Cell Growth and Ethanol Fermentation of Zymomonas mobilis using Different Nitrogen Sources

Li¹,

Jin²,

Du³

et al. 2020

Preprint

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Background: Microbial growth needs C, N, P, S as well as metal ions such as magnesium, which is a major cofactor for enzymes involved in various metabolic activities. Yeast extract is widely used as nitrogen supply as well as vitamins and growth factors to sustain microbial growth in the culture medium. Zymomonas mobilis is a model ethanologenic bacterium for ethanol production, and has been developing as a chassis for diverse biochemical production. Although yeast extract is routinely used to prepare rich medium (RM) for Z. mobilis, the glucose consumption and ethanol production of Z. mobilis in RM were not coupled with cell growth in some studies. Results: In this study, the effects of different nitrogen sources as well as the supplementation of additional nitrogen source into RM and minimum medium (MM) on cell growth and ethanol fermentation of Z. mobilis were investigated to understand the uncoupled cell growth and ethanol fermentation for efficient carbon utilization and optimal ethanol productivity of Z. mobilis. Our results indicated that nitrogen sources such as yeast extract from different companies affected cell growth, glucose utilization, and the corresponding ethanol production. We also quantified the concentrations of major ion elements in different organic nitrogen sources using the quantitative analytic approach of Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES), and demonstrated that metal ions such as magnesium in the media affected glucose consumption, cell growth, and ethanol fermentation. The effect of magnesium on gene expression was further investigated using RNA-Seq transcriptomics, and our result indicated that the lack of Mg2+ triggered stress responses while decreasing energy-consuming metabolism. Conclusions: Our work demonstrated that concentrations of metal ions such as magnesium and molybdenum in nitrogen sources are essential for vigorous cell growth, and the difference of Mg2+concentration in different yeast extract was one of the major factors affecting the coupling of cell growth and ethanol fermentation in Z. mobilis. We also revealed that genes responsive for Mg2+ deficiency in the medium were majorly related to stress responses and energy conservation. The importance of metal ions on cell growth and ethanol fermentation suggested that metal ions should become one of the parameters for monitoring the quality of commercial nitrogen sources and optimizing microbial culture medium for economic biochemical production.

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Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics

Cited by 44 publications

References 60 publications

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis

Underlying Mechanism of Uncoupled Cell Growth and Ethanol Fermentation of Zymomonas mobilis using Different Nitrogen Sources

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