1
|
Behrendt G, Vlachonikolou M, Tietgens H, Bettenbrock K. Construction and comparison of different vehicles for heterologous gene expression in Zymomonas mobilis. Microb Biotechnol 2024; 17:e14381. [PMID: 38264843 PMCID: PMC10832546 DOI: 10.1111/1751-7915.14381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/08/2023] [Accepted: 11/12/2023] [Indexed: 01/25/2024] Open
Abstract
Zymomonas mobilis has the potential to be an optimal chassis for the production of bulk chemicals derived from pyruvate. However, a lack of available standardized and characterized genetic tools hinders both efficient engineering of Z. mobilis and progress in basic research on this organism. In this study, a series of different shuttle vectors were constructed based on the replication mechanisms of the native Z. mobilis plasmids pZMO1, pZMOB04, pZMOB05, pZMOB06, pZMO7 and p29191_2 and on the broad host range replication origin of pBBR1. These plasmids as well as genomic integration sites were characterized for efficiency of heterologous gene expression, stability without selection and compatibility. We were able to show that a wide range of expression levels could be achieved by using different plasmid replicons. The expression levels of the constructs were consistent with the relative copy numbers, as determined by quantitative PCR. In addition, most plasmids are compatible and could be combined. To avoid plasmid loss, antibiotic selection is required for all plasmids except the pZMO7-based plasmid, which is stable also without selection pressure. Stable expression of reporter genes without the need for selection was also achieved by genomic integration. All modules were adapted to the modular cloning toolbox Zymo-Parts, allowing easy reuse and combination of elements. This work provides an overview of heterologous gene expression in Z. mobilis and adds a rich set of standardized genetic elements to an efficient cloning system, laying the foundation for future engineering and research in this area.
Collapse
Affiliation(s)
- Gerrich Behrendt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Maria Vlachonikolou
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Helga Tietgens
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Katja Bettenbrock
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Song H, Yang Y, Li H, Du J, Hu Z, Chen Y, Yang N, Mei M, Xiong Z, Tang K, Yi L, Zhang Y, Yang S. Determination of Nucleotide Sequences within Promoter Regions Affecting Promoter Compatibility between Zymomonas mobilis and Escherichia coli. ACS Synth Biol 2022; 11:2811-2819. [PMID: 35771099 DOI: 10.1021/acssynbio.2c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A promoter plays a crucial role in controlling the expression of the target gene in cells, thus being one of the key biological parts for synthetic biology practices. Although significant efforts have been made to identify and characterize promoters with different strengths in various microorganisms, the compatibility of promoters within different hosts still lacks investigation. In this study, we chose the native Pgap promoter of Zymomonas mobilis to investigate nucleotide sequences within promoter regions affecting promoter compatibility between Escherichia coli and Z. mobilis. Pgap is one of the strongest promotors in Z. mobilis that has many excellent characteristics to be developed as microbial cell factories. Using EGFP as a reporter, a Z. mobilis-derived Pgap mutant library was constructed and sorted in E. coli, with candidate promoters exhibiting high fluorescence intensity collected. A total of 53 variants were finally selected and sequenced by Sanger sequencing. The sequencing results grouped these variants into 12 different Pgap variant types, among which seven types presented higher promoter strength than native Pgap in E. coli. The next-generation sequencing technique was then employed to identify key mutations within the Pgap promoter region that affect the promoter compatibility. Finally, six important sites were identified and confirmed to help increase Pgap strength in E. coli while keeping similar strength of native Pgap in Z. mobilis. Compared to native Pgap, synthetic promoters combining these sites had enhanced strength; especially, Pgap-6M combining all six sites exhibited 20-fold greater strength than native Pgap in E. coli. This study thus not only determined six important sites affecting promoter compatibility but also confirmed a series of Pgap promoter variants with strong promoter activity in both E. coli and Z. mobilis. In addition, a strategy was established in this study to investigate and determine nucleotide sequences in promoter regions affecting promoter compatibility, which can be applied in other microorganisms to help reveal universal factors affecting promoter compatibility and design promoters with desired strengths among different microbial cell factories.
Collapse
Affiliation(s)
- Haoyue Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Han Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jun Du
- Beijing Tsingke Biotechnology Co., Ltd., Beijing 101111, China
| | - Zhousheng Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ning Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiqiang Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ke Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| |
Collapse
|
4
|
Braga A, Gomes D, Rainha J, Cardoso BB, Amorim C, Silvério SC, Fernández-Lobato M, Rodrigues JL, Rodrigues LR. Tailoring fructooligosaccharides composition with engineered Zymomonas mobilis ZM4. Appl Microbiol Biotechnol 2022; 106:4617-4626. [PMID: 35739346 DOI: 10.1007/s00253-022-12037-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/05/2022] [Accepted: 06/18/2022] [Indexed: 11/02/2022]
Abstract
Zymomonas mobilis ZM4 is an attractive host for the development of microbial cell factories to synthesize high-value compounds, including prebiotics. In this study, a straightforward process to produce fructooligosaccharides (FOS) from sucrose was established. To control the relative FOS composition, recombinant Z. mobilis strains secreting a native levansucrase (encoded by sacB) or a mutated β-fructofuranosidase (Ffase-Leu196) from Schwanniomyces occidentalis were constructed. Both strains were able to produce a FOS mixture with high concentration of 6-kestose. The best results were obtained with Z. mobilis ZM4 pB1-sacB that was able to produce 73.4 ± 1.6 g L-1 of FOS, with a productivity of 1.53 ± 0.03 g L-1 h-1 and a yield of 0.31 ± 0.03 gFOS gsucrose-1. This is the first report on the FOS production using a mutant Z. mobilis ZM4 strain in a one-step process. KEY POINTS: • Zymomonas mobilis was engineered to produce FOS in a one-step fermentation process. • Mutant strains produced FOS mixtures with high concentration of 6-kestose. • A new route to produce tailor-made FOS mixtures was presented.
Collapse
Affiliation(s)
- Adelaide Braga
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniela Gomes
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - João Rainha
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Beatriz B Cardoso
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Cláudia Amorim
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Sara C Silvério
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - María Fernández-Lobato
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry-Rocasolano (CSIC), 28006, Madrid, Spain
| | - Joana L Rodrigues
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Lígia R Rodrigues
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal. .,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.
| |
Collapse
|
5
|
Trichez D, Carneiro CVGC, Braga M, Almeida JRM. Recent progress in the microbial production of xylonic acid. World J Microbiol Biotechnol 2022; 38:127. [PMID: 35668329 DOI: 10.1007/s11274-022-03313-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/19/2022] [Indexed: 01/03/2023]
Abstract
Interest in the production of renewable chemicals from biomass has increased in the past years. Among these chemicals, carboxylic acids represent a significant part of the most desirable bio-based products. Xylonic acid is a five-carbon sugar-acid obtained from xylose oxidation that can be used in several industrial applications, including food, pharmaceutical, and construction industries. So far, the production of xylonic acid has not yet been available at an industrial scale; however, several microbial bio-based production processes are under development. This review summarizes the recent advances in pathway characterization, genetic engineering, and fermentative strategies to improve xylonic acid production by microorganisms from xylose or lignocellulosic hydrolysates. In addition, the strengths of the available microbial strains and processes and the major requirements for achieving biotechnological production of xylonic acid at a commercial scale are discussed. Efficient native and engineered microbial strains have been reported. Xylonic acid titers as high as 586 and 171 g L-1 were obtained from bacterial and yeast strains, respectively, in a laboratory medium. Furthermore, relevant academic and industrial players associated with xylonic acid production will be presented.
Collapse
Affiliation(s)
- Débora Trichez
- Laboratory of Genetics and Biotechnology, EMBRAPA Agroenergia, Brasília, Brazil
| | - Clara Vida G C Carneiro
- Laboratory of Genetics and Biotechnology, EMBRAPA Agroenergia, Brasília, Brazil.,Graduate Program of Microbial Biology, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - Melissa Braga
- Innovation and Business Office, EMBRAPA Agroenergia, Brasília, Brazil
| | - João Ricardo M Almeida
- Laboratory of Genetics and Biotechnology, EMBRAPA Agroenergia, Brasília, Brazil. .,Graduate Program of Microbial Biology, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil.
| |
Collapse
|
6
|
Lekshmi Sundar MS, Madhavan Nampoothiri K. An overview of the metabolically engineered strains and innovative processes used for the value addition of biomass derived xylose to xylitol and xylonic acid. BIORESOURCE TECHNOLOGY 2022; 345:126548. [PMID: 34906704 DOI: 10.1016/j.biortech.2021.126548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Xylose, the most abundant pentose sugar of the hemicellulosic fraction of lignocellulosic biomass, has to be utilized rationally for the commercial viability of biorefineries. An effective pre-treatment strategy for the release of xylose from the biomass and an appropriate microbe of the status of an Industrial strain for the utilization of this pentose sugar are key challenges which need special attention for the economic success of the biomass value addition to chemicals. Xylitol and xylonic acid, the alcohol and acid derivatives of xylose are highly demanded commodity chemicals globally with plenty of applications in the food and pharma industries. This review emphasis on the natural and metabolically engineered strains utilizing xylose and the progressive and innovative fermentation strategies for the production and subsequent recovery of the above said chemicals from pre-treated biomass medium.
Collapse
Affiliation(s)
- M S Lekshmi Sundar
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG Campus, Ghaziabad, Uttar Pradesh 201002, India
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695019, Kerala, India.
| |
Collapse
|