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Shabbir S, Wang W, Nawaz M, Boruah P, Kulyar MFEA, Chen M, Wu B, Liu P, Dai Y, Sun L, Gou Q, Liu R, Hu G, Younis T, He M. Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress. Microb Cell Fact 2023; 22:88. [PMID: 37127628 PMCID: PMC10152622 DOI: 10.1186/s12934-023-02095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Acetic acid and furfural (AF) are two major inhibitors of microorganisms during lignocellulosic ethanol production. In our previous study, we successfully engineered Zymomonas mobilis 532 (ZM532) strain by genome shuffling, but the molecular mechanisms of tolerance to inhibitors were still unknown. Therefore, this study investigated the responses of ZM532 and its wild-type Z. mobilis (ZM4) to AF using multi-omics approaches (transcriptomics, genomics, and label free quantitative proteomics). Based on RNA-Seq data, two differentially expressed genes, ZMO_RS02740 (up-regulated) and ZMO_RS06525 (down-regulated) were knocked out and over-expressed through CRISPR-Cas technology to investigate their roles in AF tolerance. Overall, we identified 1865 and 14 novel DEGs in ZM532 and wild-type ZM4. In contrast, 1532 proteins were identified in ZM532 and wild-type ZM4. Among these, we found 96 important genes in ZM532 involving acid resistance mechanisms and survival rates against stressors. Furthermore, our knockout results demonstrated that growth activity and glucose consumption of mutant strains ZM532∆ZMO_RS02740 and ZM4∆ZMO_RS02740 decreased with increased fermentation time from 42 to 55 h and ethanol production up to 58% in ZM532 than that in ZM532∆ZMO_RS02740. Hence, these findings suggest ZMO_RS02740 as a protective strategy for ZM ethanol production under stressful conditions.
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Affiliation(s)
- Samina Shabbir
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Department of Chemistry, The Women University Multan, Multan, Pakistan
| | - Weiting Wang
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Mohsin Nawaz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Prerona Boruah
- School of Biotechnology and Bioinformatics, DY PATIL Deemed to Be University, Navi Mumbai, India
| | | | - Mao Chen
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Panting Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Yonghua Dai
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Lingling Sun
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Qiyu Gou
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Renbin Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Guoquan Hu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Tahira Younis
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Pakistan
| | - Mingxiong He
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
- Chengdu National Agricultural Science and Technology Center, Chengdu, People's Republic of China.
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Zhang K, Zhang W, Qin M, Li Y, Wang H. Characterization and Application of the Sugar Transporter Zmo0293 from Zymomonas mobilis. Int J Mol Sci 2023; 24:ijms24065888. [PMID: 36982961 PMCID: PMC10055971 DOI: 10.3390/ijms24065888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for the commercial production of desirable bioproducts. Sugar transporters are responsible for the import of substrate sugars and the conversion of ethanol and other products. Glucose-facilitated diffusion protein Glf is responsible for facilitating the diffusion of glucose uptake in Z. mobilis. However, another sugar transporter-encoded gene, ZMO0293, is poorly characterized. We employed gene deletion and heterologous expression mediated by the CRISPR/Cas method to investigate the role of ZMO0293. The results showed that deletion of the ZMO0293 gene slowed growth and reduced ethanol production and the activities of key enzymes involved in glucose metabolism in the presence of high concentrations of glucose. Moreover, ZMO0293 deletion caused different transcriptional changes in some genes of the Entner Doudoroff (ED) pathway in the ZM4-ΔZM0293 strain but not in ZM4 cells. The integrated expression of ZMO0293 restored the growth of the glucose uptake-defective strain Escherichia coli BL21(DE3)-ΔptsG. This study reveals the function of the ZMO0293 gene in Z. mobilis in response to high concentrations of glucose and provides a new biological part for synthetic biology.
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Affiliation(s)
- Kun Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wenwen Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Mengxing Qin
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yi Li
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Hailei Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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Liu L, Li JT, Li SH, Liu LP, Wu B, Wang YW, Yang SH, Chen CH, Tan FR, He MX. The potential use of Zymomonas mobilis for the food industry. Crit Rev Food Sci Nutr 2022; 64:4134-4154. [PMID: 36345974 DOI: 10.1080/10408398.2022.2139221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Zymomonas mobilis is a gram-negative facultative anaerobic spore, which is generally recognized as a safe. As a promising ethanologenic organism for large-scale bio-ethanol production, Z. mobilis has also shown a good application prospect in food processing and food additive synthesis for its unique physiological characteristics and excellent industrial characteristics. It not only has obvious advantages in food processing and becomes the biorefinery chassis cell for food additives, but also has a certain healthcare effect on human health. Until to now, most of the research is still in theory and laboratory scale, and further research is also needed to achieve industrial production. This review summarized the physiological characteristics and advantages of Z. mobilis in food industry for the first time and further expounds its research status in food industry from three aspects of food additive synthesis, fermentation applications, and prebiotic efficacy, it will provide a theoretical basis for its development and applications in food industry. This review also discussed the shortcomings of its practical applications in the current food industry, and explored other ways to broaden the applications of Z. mobilis in the food industry, to promote its applications in food processing.
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Affiliation(s)
- Lu Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
- College of Food and Bioengineering, Chengdu University, Chengdu, P.R. China
| | - Jian-Ting Li
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
| | - Sheng-Hao Li
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
| | - Lin-Pei Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
| | - Yan-Wei Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
| | - Shi-Hui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, Hubei, P.R. China
| | - Cheng-Han Chen
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
| | - Fu-Rong Tan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
| | - Ming-Xiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, P.R. China
- College of Food and Bioengineering, Chengdu University, Chengdu, P.R. China
- Institute of Ecological Environment, Chengdu University of Technology, Chengdu, P.R. China
- Chengdu National Agricultural Science and Technology Center, Chengdu, P.R. China
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Martien JI, Trujillo EA, Jacobson TB, Tatli M, Hebert AS, Stevenson DM, Coon JJ, Amador-Noguez D. Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis. mSystems 2021; 6:e0098721. [PMID: 34783580 PMCID: PMC8594446 DOI: 10.1128/msystems.00987-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Zymomonas mobilis is an ethanologenic bacterium currently being developed for production of advanced biofuels. Recent studies have shown that Z. mobilis can fix dinitrogen gas (N2) as a sole nitrogen source. During N2 fixation, Z. mobilis exhibits increased biomass-specific rates of ethanol production. In order to better understand the physiology of Z. mobilis during N2 fixation and during changes in ammonium (NH4+) availability, we performed liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomics and shotgun proteomics under three regimes of nitrogen availability: continuous N2 fixation, gradual NH4+ depletion, and acute NH4+ addition to N2-fixing cells. We report dynamic changes in abundance of proteins and metabolites related to nitrogen fixation, motility, ammonium assimilation, amino acid biosynthesis, nucleotide biosynthesis, isoprenoid biosynthesis, and Entner-Doudoroff (ED) glycolysis, providing insight into the regulatory mechanisms that control these processes in Z. mobilis. Our analysis identified potential physiological mechanisms that may contribute to increased specific ethanol production during N2 fixation, including decreased activity of biosynthetic pathways, increased protein abundance of alcohol dehydrogenase (ADHI), and increased thermodynamic favorability of the ED pathway. Of particular relevance to advanced biofuel production, we found that intermediates in the methylerythritol phosphate (MEP) pathway for isoprenoid biosynthesis were depleted during N2 fixation, coinciding with decreased protein abundance of deoxyxylulose 5-phosphate synthase (DXS), the first enzyme in the pathway. This implies that DXS protein abundance serves as a native control point in regulating MEP pathway activity in Z. mobilis. The results of this study will inform metabolic engineering to further develop Z. mobilis as a platform organism for biofuel production. IMPORTANCE Biofuels and bioproducts have the potential to serve as environmentally sustainable replacements for petroleum-derived fuels and commodity molecules. Advanced fuels such as higher alcohols and isoprenoids are more suitable gasoline replacements than bioethanol. Developing microbial systems to generate advanced biofuels requires metabolic engineering to reroute carbon away from ethanol and other native products and toward desired pathways, such as the MEP pathway for isoprenoid biosynthesis. However, rational engineering of microbial metabolism relies on understanding metabolic control points, in terms of both enzyme activity and thermodynamic favorability. In Z. mobilis, the factors that control glycolytic rates, ethanol production, and isoprenoid production are still not fully understood. In this study, we performed metabolomic, proteomic, and thermodynamic analysis of Z. mobilis during N2 fixation. This analysis identified key changes in metabolite levels, enzyme abundance, and glycolytic thermodynamic favorability that occurred during changes in NH4+ availability, helping to inform future efforts in metabolic engineering.
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Affiliation(s)
- Julia I. Martien
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Edna A. Trujillo
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Mehmet Tatli
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Alexander S. Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Joshua J. Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
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Yi X, Lin L, Mei J, Wang W. Transporter proteins in Zymomonas mobilis contribute to the tolerance of lignocellulose-derived phenolic aldehyde inhibitors. Bioprocess Biosyst Eng 2021; 44:1875-1882. [PMID: 33839896 DOI: 10.1007/s00449-021-02567-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/31/2021] [Indexed: 01/29/2023]
Abstract
Transporter proteins are of great importance for improving the tolerance of fermentation strains to lignocellulose-derived furans and phenolic inhibitors. Different from the documented transporter proteins responsible for the tolerance of furfural and 5-hydroxymethyl-furfural (HMF), transporters responsible for that of varied phenolic aldehyde inhibitors were less investigated and elucidated. Here, an interesting phenomenon was found that no phenolic alcohols were accumulated from phenolic aldehydes degradation in Zymomonas mobilis. A transcriptional profiling of transporter genes was established in Z. mobilis ZM4 under phenolic aldehydes stress using DNA microarray. Six transporter proteins were identified as the potential candidates responsible for the tolerance of phenolic aldehydes including ABC transporter (ZMO0799 and ZMO0800), MFS transporter (ZMO1288 and ZMO1856), and RND transporter (ZMO0282 and ZMO0798). Furthermore, the analysis showed that the key transporters were significantly correlated with oxidoreductases and transcriptional regulators. This work would provide several important transporter genes serving as synthetic biology tools for improving the robustness of biorefinery strains.
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Affiliation(s)
- Xia Yi
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China.
| | - Ling Lin
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
| | - Jun Mei
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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Han R, Haning K, Gonzalez-Rivera JC, Yang Y, Li R, Cho SH, Huang J, Simonsen BA, Yang S, Contreras LM. Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis. Front Bioeng Biotechnol 2020; 8:155. [PMID: 32195236 PMCID: PMC7064620 DOI: 10.3389/fbioe.2020.00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/14/2020] [Indexed: 01/18/2023] Open
Abstract
sRNAs represent a powerful class of regulators that influences multiple mRNA targets in response to environmental changes. However, very few direct sRNA-sRNA interactions have been deeply studied in any organism. Zymomonas mobilis is a bacterium with unique ethanol-producing metabolic pathways in which multiple small RNAs (sRNAs) have recently been identified, some of which show differential expression in ethanol stress. In this study, we show that two sRNAs (Zms4 and Zms6) are upregulated under ethanol stress and have significant impacts on ethanol tolerance and production in Z. mobilis. We conducted multi-omics analysis (combining transcriptomics and sRNA-immunoprecipitation) to map gene networks under the influence of their regulation. We confirmed that Zms4 and Zms6 bind multiple RNA targets and regulate their expressions, influencing many downstream pathways important to ethanol tolerance and production. In particular, Zms4 and Zms6 interact with each other as well as many other sRNAs, forming a novel sRNA-sRNA direct interaction network. This study thus uncovers a sRNA network that co-orchestrates multiple ethanol related pathways through a diverse set of mRNA targets and a large number of sRNAs. To our knowledge, this study represents one of the largest sRNA-sRNA direct interactions uncovered so far.
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Affiliation(s)
- Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Katie Haning
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Juan C Gonzalez-Rivera
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Runxia Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Seung Hee Cho
- Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
| | - Ju Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Bobi A Simonsen
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
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Physiological effects of overexpressed sigma factors on fermentative stress response of Zymomonas mobilis. Braz J Microbiol 2019; 51:65-75. [PMID: 31701383 DOI: 10.1007/s42770-019-00158-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/11/2019] [Indexed: 01/04/2023] Open
Abstract
Zymomonas mobilis is a bacterium of industrial interest due to its high ethanol productivity and high tolerance to stresses. Although the physiological parameters of fermentation are well characterized, there are few studies on the molecular mechanisms that regulate the response to fermentative stress. Z. mobilis ZM4 presents five different sigma factors identified in the genome annotation, but the absence of sigma 38 leads to the questioning of which sigma factors are responsible for its mechanism of fermentative stress response. Thus, in this study, factors sigma 32 and sigma 24, traditionally related to heat shock, were tested for their influence on the response to osmotic and ethanol stress. The overexpression of these sigma factors in Z. mobilis ZM4 strain confirmed that both are associated with heat shock response, as described in other bacteria. Moreover, sigma 32 has also a role in the adaptation to osmotic stress, increasing both growth rate and glucose influx rate. The same strain that overexpresses sigma 32 also showed a decrease in ethanol tolerance, suggesting an antagonism between these two mechanisms. It was not possible to conclude if sigma 24 really affects ethanol tolerance in Z. mobilis, but the overexpression of this sigma factor led to a decrease in ethanol productivity.
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Zhang K, Lu X, Li Y, Jiang X, Liu L, Wang H. New technologies provide more metabolic engineering strategies for bioethanol production in Zymomonas mobilis. Appl Microbiol Biotechnol 2019; 103:2087-2099. [PMID: 30661108 DOI: 10.1007/s00253-019-09620-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 02/06/2023]
Abstract
Bioethanol has been considered as a potentially renewable energy source, and metabolic engineering plays an important role in the production of biofuels. As an efficient ethanol-producing bacterium, Zymomonas mobilis has garnered special attention due to its high sugar uptake, ethanol yield, and tolerance. Different metabolic engineering strategies have been used to establish new metabolic pathways for Z. mobilis to broaden its substrate range, remove competing pathways, and enhance its tolerance to ethanol and lignocellulosic hydrolysate inhibitors. Recent advances in omics technology, computational modeling and simulation, system biology, and synthetic biology contribute to the efficient re-design and manipulation of microbes via metabolic engineering at the whole-cell level. In this review, we summarize the progress of some new technologies used for metabolic engineering to improve bioethanol production and tolerance in Z. mobilis. Some successful examples of metabolic engineering used to develop strains for ethanol production are described in detail. Lastly, some important strategies for future metabolic engineering efforts are also highlighted.
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Affiliation(s)
- Kun Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xinxin Lu
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yi Li
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xiaobing Jiang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Lei Liu
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Hailei Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.
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Yang Y, Shen W, Huang J, Li R, Xiao Y, Wei H, Chou YC, Zhang M, Himmel ME, Chen S, Yi L, Ma L, Yang S. Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:52. [PMID: 30911332 PMCID: PMC6417218 DOI: 10.1186/s13068-019-1399-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/08/2019] [Indexed: 05/09/2023]
Abstract
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.
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Affiliation(s)
- Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Wei Shen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Ju Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Runxia Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yubei Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Yat-Chen Chou
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
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10
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Chang D, Yu Z, Ul Islam Z, French WT, Zhang Y, Zhang H. Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:283. [PMID: 30356850 PMCID: PMC6190654 DOI: 10.1186/s13068-018-1287-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Toxic compounds present in both the hydrolysate and pyrolysate of lignocellulosic biomass severely hinder the further conversion of lignocellulose-derived fermentable sugars into useful chemicals by common biocatalysts like Zymomonas mobilis, which has remarkable advantages over yeast. Although the extra detoxification treatment prior to fermentation process can help biocatalysts to eliminate the inhibitory environment, it is not environment friendly and cost effective for industrial application. As also reported by previous studies, an ideal and holistic approach to solve this issue is to develop microbial strains with inhibitor tolerance. However, previously engineered strains had the limitation that they could not cope well with the synergistic effect of multiple inhibitors as they are resistant only to a single inhibitor. Hence, understanding the universal cellular responses of Z. mobilis to various inhibitors may guide the designing of rational strategies to obtain more robust engineered strains for biofuel production from lignocellulosic biomass. RESULTS Quantitative proteomics and metabolomics approaches were used to determine the cellular responses of Z. mobilis ZM4 to representative biomass-derived inhibitors like formic acid, acetic acid, furfural, 5-hydroxymethylfurfural, and phenol. The differentially expressed proteins identified under the challenge of single and combined inhibitors were involved in cell wall/membrane biogenesis, energy production, DNA replication, DNA recombination, DNA repair, DNA transcription, RNA translation, posttranslational modification, biosynthesis of amino acids, central carbon metabolism, etc. Metabolomics analysis showed that the up- or down-regulation pattern of metabolites was changed consistently with that of relevant proteins. CONCLUSION Fifteen up-regulated proteins (e.g., Isopropylmalate isomerase LeuC, transcription-repair-coupling factor Mfd, and phosphoglucose isomerase PGI) and thirteen down-regulated proteins (e.g., TonB-dependent transporter ZMO1522, transcription termination factor Rho, and S1/P1 nuclease ZMO0127) were identified as candidate proteins related to all the stress conditions, implying that these proteins are potential biomarkers for the improvement of Z. mobilis ZM4 to resist complex biomass-derived inhibitors. These data can be used to generate a database of inhibitor-tolerance biomarkers, which could provide a basis for engineering Z. mobilis that would be able to grow in the presence of multiple inhibitors and directly ferment the biomass-derived sugars into biofuels.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049 People’s Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049 People’s Republic of China
| | - Zia Ul Islam
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049 People’s Republic of China
- Department of Sustainable Bioproducts, Mississippi State University, Mississippi State, MS 39762 USA
| | - W. Todd French
- Dave C. Swalm School of Chemical Engineering, Mississippi State University, P.O. Box 9595, Mississippi State, MS 39762 USA
| | - Yiming Zhang
- Environmental Protection Bureau, Shunyi District, Beijing, 101300 People’s Republic of China
| | - Hongxun Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049 People’s Republic of China
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11
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Xia J, Liu CG, Zhao XQ, Xiao Y, Xia XX, Bai FW. Contribution of cellulose synthesis, formation of fibrils and their entanglement to the self-flocculation of Zymomonas mobilis. Biotechnol Bioeng 2018; 115:2714-2725. [PMID: 30063083 DOI: 10.1002/bit.26806] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/21/2018] [Accepted: 07/23/2018] [Indexed: 11/09/2022]
Abstract
Due to the unique Entner-Doudoroff pathway, Zymomonas mobilis has been acknowledged as a potential host to be engineered for biorefinery to produce biofuels and biobased chemicals. The self-flocculation of Z. mobilis can make the bacterial cells self-immobilized within bioreactors for high density to improve product productivities, and in the meantime enhance their tolerance to stresses, particularly product inhibition and the toxicity of byproducts released during the pretreatment of lignocellulosic biomass. In this work, we explored mechanism underlying such a phenotype with the self-flocculating strain ZM401 developed from the regular non-flocculating strain ZM4. Cellulase de-flocculation and the restoration of the self-flocculating phenotype for the de-flocculated bacterial cells subjected to culture confirmed the essential role of cellulose biosynthesis in the self-flocculation of ZM401. Furthermore, the deactivation of both Type I and Type IV restriction-modification systems was performed for ZM4 and ZM401 to improve their transformation efficiencies. Comparative genome analysis detected the deletion of a thymine from ZMO1082 in ZM401, leading to a frame-shift mutation for the putative gene to be integrated into the neighboring downstream gene ZMO1083 encoding the catalytic subunit A of cellulose synthase, and consequently created a new gene to encode a larger transmembrane protein BcsA_401 for more efficient synthesis of cellulose as well as the development of cellulose fibrils and their entanglement for the self-flocculation of the mutant. These speculations were confirmed by the morphological observation of the bacterial cells under scanning electron microscopy, the impact of the gene deletion on the self-flocculation of ZM401, and the restoration of the self-flocculating phenotype of ZM401 ΔbcsA by the gene complementation. The progress will lay a foundation not only for fundamental research in deciphering molecular mechanisms underlying the self-flocculation of Z. mobilis and stress tolerance associated with the morphological change but also for technological innovations in engineering non-flocculating Z. mobilis and other bacterial species with the self-flocculating phenotype.
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Affiliation(s)
- Juan Xia
- State Key Laboratory of Microbial Metabolism, Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Xiao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Xia Xia
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Feng-Wu Bai
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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12
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Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, Contreras LM, Yang S. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng 2018; 50:57-73. [PMID: 29627506 DOI: 10.1016/j.ymben.2018.04.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/31/2018] [Accepted: 04/01/2018] [Indexed: 12/22/2022]
Abstract
Biorefinery of biomass-based biofuels and biochemicals by microorganisms is a competitive alternative of traditional petroleum refineries. Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for commercial production of desirable bioproducts through metabolic engineering. In this review, we summarize the metabolic engineering progress achieved in Z. mobilis to expand its substrate and product ranges as well as to enhance its robustness against stressful conditions such as inhibitory compounds within the lignocellulosic hydrolysates and slurries. We also discuss a few metabolic engineering strategies that can be applied in Z. mobilis to further develop it as a robust workhorse for economic lignocellulosic bioproducts. In addition, we briefly review the progress of metabolic engineering in Z. mobilis related to the classical synthetic biology cycle of "Design-Build-Test-Learn", as well as the progress and potential to develop Z. mobilis as a model chassis for biorefinery practices in the synthetic biology era.
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Affiliation(s)
- Xia Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Qiaoning He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Yongfu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jingwen Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Katie Haning
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Yun Hu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI, United States.
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
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13
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de Araújo LCA, de Cássia Dias Mendes T, Dos Santos BS, da Mota Silveira Filho V, de Souza Lima GM, de Araújo JM, Dos Santos Correia MT, de Oliveira MBM, Morais Júnior MA, da Silva MV. Molecular identification and physiological characterization of Zymomonas mobilis strains from fuel-ethanol production plants in north-east Brazil. Lett Appl Microbiol 2018; 67:54-63. [PMID: 29603295 DOI: 10.1111/lam.12888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 11/28/2022]
Abstract
Zymomonas mobilis has long attracted attention owing to its capacity to ferment hexose to ethanol. From a taxonomic viewpoint, Z. mobilis is a unique species of the genus Zymomonas, separated into three subspecies, Z. mobilis subsp. mobilis, Z. mobilis subsp. pomaceae and Z. mobilis subsp. francensis on the basis of physiological tests, which are often unreliable owing to the genetic proximity among these species. Currently, the use of molecular techniques is more appropriate for identification of these bacterial subspecies. In this study, the 32 strains of Z. mobilis present in the UFPEDA bacterial collection were characterized using molecular techniques, such as sequencing of the 16S rDNA gene and its theoretical restriction profile, classifying them as members of the subspecies, Z. mobilis subsp. mobilis. In addition, anaerobic cultivations were performed, which showed the biological diversity of the strains in terms of growth, sugar consumption and ethanol production. From these results, it was possible to identify the strain Z-2-80 as a promising bacterium for use in the fermentation process. SIGNIFICANCE AND IMPACT OF THE STUDY Zymomonas mobilis is a bacterium of great relevance to biotechnology, owing to its capacity to ferment hexose to ethanol. On a molecular basis, 32 isolates were identified as Z. mobilis subsp. mobilis. However, intraspecific diversity was identified when these were grown under strictly anaerobic conditions. The results obtained from this study suggest a strain of Z. mobilis as an alternative for use in the fermentation process.
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Affiliation(s)
- L C A de Araújo
- Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - B S Dos Santos
- Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | | | - G M de Souza Lima
- Department of Antibiotics, Federal University of Pernambuco, Recife, Brazil
| | - J M de Araújo
- Department of Antibiotics, Federal University of Pernambuco, Recife, Brazil
| | | | - M B M de Oliveira
- Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
| | - M A Morais Júnior
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - M V da Silva
- Department of Biochemistry, Federal University of Pernambuco, Recife, Brazil
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14
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Huang S, Xue T, Wang Z, Ma Y, He X, Hong J, Zou S, Song H, Zhang M. Furfural-tolerant Zymomonas mobilis derived from error-prone PCR-based whole genome shuffling and their tolerant mechanism. Appl Microbiol Biotechnol 2018; 102:3337-3347. [PMID: 29464326 DOI: 10.1007/s00253-018-8817-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/22/2018] [Accepted: 01/27/2018] [Indexed: 11/29/2022]
Abstract
Furfural-tolerant strain is essential for the fermentative production of biofuels or chemicals from lignocellulosic biomass. In this study, Zymomonas mobilis CP4 was for the first time subjected to error-prone PCR-based whole genome shuffling, and the resulting mutants F211 and F27 that could tolerate 3 g/L furfural were obtained. The mutant F211 under various furfural stress conditions could rapidly grow when the furfural concentration reduced to 1 g/L. Meanwhile, the two mutants also showed higher tolerance to high concentration of glucose than the control strain CP4. Genome resequencing revealed that the F211 and F27 had 12 and 13 single-nucleotide polymorphisms. The activity assay demonstrated that the activity of NADH-dependent furfural reductase in mutant F211 and CP4 was all increased under furfural stress, and the activity peaked earlier in mutant than in control. Also, furfural level in the culture of F211 was also more rapidly decreased. These indicate that the increase in furfural tolerance of the mutants may be resulted from the enhanced NADH-dependent furfural reductase activity during early log phase, which could lead to an accelerated furfural detoxification process in mutants. In all, we obtained Z. mobilis mutants with enhanced furfural and high concentration of glucose tolerance, and provided valuable clues for the mechanism of furfural tolerance and strain development.
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Affiliation(s)
- Suzhen Huang
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Tingli Xue
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhiquan Wang
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yuanyuan Ma
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China. .,Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, China.
| | - Xueting He
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jiefang Hong
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China
| | - Shaolan Zou
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China
| | - Hao Song
- Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
| | - Minhua Zhang
- R&D Center for Petrochemical Technology, Tianjin University, Weijin Road No. 92, Nankai District, Tianjin, 300072, China.,Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin, China
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15
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Yang S, Vera JM, Grass J, Savvakis G, Moskvin OV, Yang Y, McIlwain SJ, Lyu Y, Zinonos I, Hebert AS, Coon JJ, Bates DM, Sato TK, Brown SD, Himmel ME, Zhang M, Landick R, Pappas KM, Zhang Y. Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:125. [PMID: 29743953 PMCID: PMC5930841 DOI: 10.1186/s13068-018-1116-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/11/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2-8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain. RESULTS In this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1-2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion. CONCLUSIONS The complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.
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Affiliation(s)
- Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
- DOE-National Bioenergy Center, National Renewable Energy Laboratory (NREL), Golden, CO 80401 USA
| | - Jessica M. Vera
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Jeff Grass
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Giannis Savvakis
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15701 Athens, Greece
| | - Oleg V. Moskvin
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Yongfu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Sean J. McIlwain
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Yucai Lyu
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
- Present Address: China Three Gorges University, Yichang, 443002 Hubei China
| | - Irene Zinonos
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15701 Athens, Greece
| | - Alexander S. Hebert
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Joshua J. Coon
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Donna M. Bates
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Trey K. Sato
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Steven D. Brown
- DOE-BioEnergy Science Center, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831 USA
- DOE-Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37831 USA
- Present Address: LanzaTech, Inc., Skokie, IL 60077 USA
| | - Michael E. Himmel
- DOE-Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO 80401 USA
| | - Min Zhang
- DOE-National Bioenergy Center, National Renewable Energy Laboratory (NREL), Golden, CO 80401 USA
| | - Robert Landick
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
| | - Katherine M. Pappas
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis, 15701 Athens, Greece
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI USA
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16
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Vyrides I, Stuckey DC. Compatible solute addition to biological systems treating waste/wastewater to counteract osmotic and other environmental stresses: a review. Crit Rev Biotechnol 2017; 37:865-879. [DOI: 10.1080/07388551.2016.1266460] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ioannis Vyrides
- Department of Environmental Science and Technology, Cyprus University of Technology, Lemesos, Cyprus
| | - David C. Stuckey
- Department of Chemical Engineering, Imperial College London, London, UK
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17
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Yang S, Fei Q, Zhang Y, Contreras LM, Utturkar SM, Brown SD, Himmel ME, Zhang M. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb Biotechnol 2016; 9:699-717. [PMID: 27629544 PMCID: PMC5072187 DOI: 10.1111/1751-7915.12408] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 12/04/2022] Open
Abstract
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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Affiliation(s)
- Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Qiang Fei
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - Sagar M Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA
| | - Steven D Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Dong G, He M, Feng H. Functional Characterization of CRISPR-Cas System in the Ethanologenic Bacterium <i>Zymomonas mobilis</i> ZM4. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/aim.2016.63018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Yang S, Mohagheghi A, Franden MA, Chou YC, Chen X, Dowe N, Himmel ME, Zhang M. Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:189. [PMID: 27594916 PMCID: PMC5010730 DOI: 10.1186/s13068-016-0606-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/26/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND To develop pathways for advanced biofuel production, and to understand the impact of host metabolism and environmental conditions on heterologous pathway engineering for economic advanced biofuels production from biomass, we seek to redirect the carbon flow of the model ethanologen Zymomonas mobilis to produce desirable hydrocarbon intermediate 2,3-butanediol (2,3-BDO). 2,3-BDO is a bulk chemical building block, and can be upgraded in high yields to gasoline, diesel, and jet fuel. RESULTS 2,3-BDO biosynthesis pathways from various bacterial species were examined, which include three genes encoding acetolactate synthase, acetolactate decarboxylase, and butanediol dehydrogenase. Bioinformatics analysis was carried out to pinpoint potential bottlenecks for high 2,3-BDO production. Different combinations of 2,3-BDO biosynthesis metabolic pathways using genes from different bacterial species have been constructed. Our results demonstrated that carbon flux can be deviated from ethanol production into 2,3-BDO biosynthesis, and all three heterologous genes are essential to efficiently redirect pyruvate from ethanol production for high 2,3-BDO production in Z. mobilis. The down-selection of best gene combinations up to now enabled Z. mobilis to reach the 2,3-BDO production of more than 10 g/L from glucose and xylose, as well as mixed C6/C5 sugar streams derived from the deacetylation and mechanical refining process. CONCLUSIONS This study confirms the value of integrating bioinformatics analysis and systems biology data during metabolic engineering endeavors, provides guidance for value-added chemical production in Z. mobilis, and reveals the interactions between host metabolism, oxygen levels, and a heterologous 2,3-BDO biosynthesis pathway. Taken together, this work provides guidance for future metabolic engineering efforts aimed at boosting 2,3-BDO titer anaerobically.
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Affiliation(s)
- Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Ali Mohagheghi
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Mary Ann Franden
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Yat-Chen Chou
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Xiaowen Chen
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Nancy Dowe
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
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