Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories

Kim, Donghyuk; Woo, Han Min

doi:10.1007/s00253-018-9353-2

Cited by 23 publications

(17 citation statements)

References 63 publications

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“…Since xylose reductase and xylitol dehydrogenase are usually cofactor dependent, overexpression of these genes will result in the imbalance of cofactors in Z. mobilis and lead to the accumulation of the deleterious intermediate xylitol [ 31 ]. Therefore, in the present study, we evaluated the effect of overexpression of xylose isomerase (XI) and xylulokinase in xylose-utilization recombinant strain Z. mobilis 8b to avoid this problem, which can convert xylose to xylulose-5-phosphate without cofactors.…”

Section: Introductionmentioning

confidence: 99%

Development and characterization of efficient xylose utilization strains of Zymomonas mobilis

Lou

Wang

Yang

et al. 2021

Biotechnol Biofuels

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Background Efficient use of glucose and xylose is a key for the economic production of lignocellulosic biofuels and biochemicals, and different recombinant strains have been constructed for xylose utilization including those using Zymomonas mobilis as the host. However, the xylose utilization efficiency still needs to be improved. In this work, the strategy of combining metabolic engineering and adaptive laboratory evolution (ALE) was employed to develop recombinant Z. mobilis strains that can utilize xylose efficiently at high concentrations, and NGS-based genome resequencing and RNA-Seq transcriptomics were performed for strains evolved after serial transfers in different media to understand the impact of xylose and differences among strains with different xylose-utilization capabilities at molecular level. Results Heterologous genes encoding xylose isomerase and xylulokinase were evaluated, which were then introduced into xylose-utilizing strain Z. mobilis 8b to enhance its capacity of xylose utilization. The results demonstrated that the effect of three xylose isomerases on xylose utilization was different, and the increase of copy number of xylose metabolism genes can improve xylose utilization. Among various recombinant strains constructed, the xylose utilization capacity of the recombinant strain 8b-RsXI-xylB was the best, which was further improved through continuous adaption with 38 transfers over 100 days in 50 g/L xylose media. The fermentation performances of the parental strain 8b, the evolved 8b-S38 strain with the best xylose utilization capability, and the intermediate strain 8b-S8 in different media were compared, and the results showed that only 8b-S38 could completely consume xylose at 50 g/L and 100 g/L concentrations. In addition, the xylose consumption rate of 8b-S38 was faster than that of 8b at different xylose concentrations from 50 to 150 g/L, and the ethanol yield increased by 16 ~ 40%, respectively. The results of the mixed-sugar fermentation also demonstrated that 8b-S38 had a higher xylose consumption rate than 8b, and its maximum ethanol productivity was 1.2 ~ 1.4 times higher than that of 8b and 8b-S8. Whole-genome resequencing identified three common genetic changes in 8b-S38 compared with 8b and 8b-S8. RNA-Seq study demonstrated that the expression levels of genes encoding chaperone proteins, ATP-dependent proteases, phage shock proteins, ribosomal proteins, flagellar operons, and transcriptional regulators were significantly increased in xylose media in 8b-S38. The up-regulated expression of these genes may therefore contribute to the efficient xylose utilization of 8b-S38 by maintaining the normal cell metabolism and growth, repairing cellular damages, and rebalancing cellular energy to help cells resist the stressful environment. Conclusions This study provides gene candidates to improve xylose utilization, and the result of expressing an extra copy of xylose isomerase and xylulokinase improved xylose utilization also provides a direction for efficient xylose-utilization strain development in other microorganisms. In addition, this study demonstrated the necessity to combine metabolic engineering and ALE for industrial strain development. The recombinant strain 8b-S38 can efficiently metabolize xylose for ethanol fermentation at high xylose concentrations as well as in mixed sugars of glucose and xylose, which could be further developed as the microbial biocatalyst for the production of lignocellulosic biofuels and biochemicals.

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Section: Introductionmentioning

confidence: 99%

Development and characterization of efficient xylose utilization strains of Zymomonas mobilis

Lou

Wang

Yang

et al. 2021

Biotechnol Biofuels

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“…Contemporary synthetic biology and metabolic engineering offer the possibility of expanding the substrate range of microbial cell factories beyond the sugars typically used as carbon sources (Calero and Nikel, ; Prather, ). Examples of this sort of metabolic manipulation for broadening substrate ‘palatability’ of bacteria include several chemical species, ranging from simple C1 compounds such as CO 2 or HCOOH (Antonovsky et al., ; Yishai et al., ) to structurally complex substrates such as lignocellulosic materials derived from biomass (Beckham et al., ; Barton et al., ; Kim and Woo, ). Alcohols conform a special category of alternative substrates for biotechnology, and they are currently being discussed as promising renewables for sustainable bioproduction (Stowell et al., ; Smith, ; Dahod et al., ; Hoffmann et al., ).…”

Section: Introductionmentioning

confidence: 99%

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

Poblete‐Castro

Wittmann

Nikel

2019

Microbial Biotechnology

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Summary The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.

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“…A genome analysis of 492 bacteria strains of Bacillus, Bifidobacterium, Caulobacter, Corynebacterium, Escherichia, Lactobacillus, and Xanthomonas and the search for genes involved in xylose metabolism have been performed. The analysis revealed that the pathways of XI and Weimberg were the prevalent routes, with the XI pathway being the best preserved (Figure 1) [100].…”

Section: Xylose Metabolic Network In Bacteriamentioning

confidence: 99%

Xylose Metabolism in Bacteria—Opportunities and Challenges towards Efficient Lignocellulosic Biomass-Based Biorefineries

et al. 2021

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In a sustainable society based on circular economy, the use of waste lignocellulosic biomass (LB) as feedstock for biorefineries is a promising solution, since LB is the world’s most abundant renewable and non-edible raw material. LB is available as a by-product from agricultural and forestry processes, and its main components are cellulose, hemicellulose, and lignin. Following suitable physical, enzymatic, and chemical steps, the different fractions can be processed and/or converted to value-added products such as fuels and biochemicals used in several branches of industry through the implementation of the biorefinery concept. Upon hydrolysis, the carbohydrate-rich fraction may comprise several simple sugars (e.g., glucose, xylose, arabinose, and mannose) that can then be fed to fermentation units. Unlike pentoses, glucose and other hexoses are readily processed by microorganisms. Some wild-type and genetically modified bacteria can metabolize xylose through three different main pathways of metabolism: xylose isomerase pathway, oxidoreductase pathway, and non-phosphorylative pathway (including Weimberg and Dahms pathways). Two of the commercially interesting intermediates of these pathways are xylitol and xylonic acid, which can accumulate in the medium either through manipulation of the culture conditions or through genetic modification of the bacteria. This paper provides a state-of-the art perspective regarding the current knowledge on xylose transport and metabolism in bacteria as well as envisaged strategies to further increase xylose conversion into valuable products.

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Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories

Cited by 23 publications

References 63 publications

Development and characterization of efficient xylose utilization strains of Zymomonas mobilis

Development and characterization of efficient xylose utilization strains of Zymomonas mobilis

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

Xylose Metabolism in Bacteria—Opportunities and Challenges towards Efficient Lignocellulosic Biomass-Based Biorefineries

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