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Yang X, Wang H, Ding D, Fang H, Dong H, Zhang D. A hybrid RNA-protein biosensor for high-throughput screening of adenosylcobalamin biosynthesis. Synth Syst Biotechnol 2024; 9:513-521. [PMID: 38680948 PMCID: PMC11047186 DOI: 10.1016/j.synbio.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 05/01/2024] Open
Abstract
Genetically encoded circuits have been successfully utilized to assess and characterize target variants with desirable traits from large mutant libraries. Adenosylcobalamin is an essential coenzyme that is required in many intracellular physiological reactions and is widely used in the pharmaceutical and food industries. High-throughput screening techniques capable of detecting adenosylcobalamin productivity and selecting superior adenosylcobalamin biosynthesis strains are critical for the creation of an effective microbial cell factory for the production of adenosylcobalamin at an industrial level. In this study, we developed an RNA-protein hybrid biosensor whose input part was an endogenous RNA riboswitch to specifically respond to adenosylcobalamin, the inverter part was an orthogonal transcriptional repressor to obtain signal inversion, and the output part was a fluorescent protein to be easily detected. The hybrid biosensor could specifically and positively correlate adenosylcobalamin concentrations to green fluorescent protein expression levels in vivo. This study also improved the operating concentration and dynamic range of the hybrid biosensor by systematic optimization. An individual cell harboring the hybrid biosensor presented over 20-fold higher fluorescence intensity than the negative control. Then, using such a biosensor combined with fluorescence-activated cell sorting, we established a high-throughput screening platform for screening adenosylcobalamin overproducers. This study demonstrates that this platform has significant potential to quickly isolate high-productive strains to meet industrial demand and that the framework is acceptable for various metabolites.
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Affiliation(s)
- Xia Yang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dongqin Ding
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Meier D, Rauch C, Wagner M, Klemm P, Blumenkamp P, Müller R, Ellenberger E, Karia KM, Vecchione S, Serrania J, Lechner M, Fritz G, Goesmann A, Becker A. A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis. BIODESIGN RESEARCH 2024; 6:0025. [PMID: 38384496 PMCID: PMC10880074 DOI: 10.34133/bdr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024] Open
Abstract
The construction of complex synthetic gene circuits with predetermined and reliable output depends on orthogonal regulatory parts that do not inadvertently interfere with the host machinery or with other circuit components. Previously, extracytoplasmic function sigma factors (ECFs), a diverse group of alternative sigma factors with distinct promoter specificities, were shown to have great potential as context-independent regulators, but so far, they have only been used in a few model species. Here, we show that the alphaproteobacterium Sinorhizobium meliloti, which has been proposed as a plant-associated bacterial chassis for synthetic biology, has a similar phylogenetic ECF acceptance range as the gammaproteobacterium Escherichia coli. A common set of orthogonal ECF-based regulators that can be used in both bacterial hosts was identified and used to create 2-step delay circuits. The genetic circuits were implemented in single copy in E. coli by chromosomal integration using an established method that utilizes bacteriophage integrases. In S. meliloti, we demonstrated the usability of single-copy pABC plasmids as equivalent carriers of the synthetic circuits. The circuits were either implemented on a single pABC or modularly distributed on 3 such plasmids. In addition, we provide a toolbox containing pABC plasmids compatible with the Golden Gate (MoClo) cloning standard and a library of basic parts that enable the construction of ECF-based circuits in S. meliloti and in E. coli. This work contributes to building a context-independent and species-overarching ECF-based toolbox for synthetic biology applications.
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Affiliation(s)
- Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Christian Rauch
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcel Wagner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Raphael Müller
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Eric Ellenberger
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Kinnari M. Karia
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Stefano Vecchione
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Georg Fritz
- The University of Western Australia, School of Molecular Sciences, Perth, Australia
| | - Alexander Goesmann
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
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3
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Liu Y, Huang W, Wang Q, Ma C, Chang Y, Su J. Research on the targeted improvement of the yield of a new VB 12-producing strain, Ensifer adhaerens S305, based on genomic and transcriptomic analysis. BMC Biotechnol 2023; 23:53. [PMID: 38082291 PMCID: PMC10712150 DOI: 10.1186/s12896-023-00824-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Vitamin B12 (VB12) has a wide range of applications and high economic value. In this study, a new strain with high VB12 production potential, Ensifer adhaerens S305, was identified in sewage. Because E. adhaerens strains have become the main strains for VB12 production via fermentation in recent years, the directional modification of the S305 strain to obtain a strain suitable for the industrial production of VB12 has great potential and commercial value. RESULTS 16S rRNA and genome-wide phylogenetic tree analysis combined with average nucleotide identity (ANI) analysis showed that the high-yielding VB12 strain was a E. adhaerens strain and that its VB12 synthesis pathway genes were highly similar to related genes of strains of this and other species, including E. adhaerens Casida A, Pseudomonas denitrificans SC 510, and E. adhaerens Corn53. High-pressure liquid chromatography (HPLC) results indicated that the VB12 yields of the S305 strain were more than double those of the Casida A strain under different medium components. Multiple genes with significantly upregulated and downregulated transcription were identified by comparing the transcription intensity of different genes through transcriptome sequencing. KEGG enrichment analysis of the porphyrin metabolism pathway identified 9 significantly upregulated and downregulated differentially expressed genes (DEGs) in the VB12 synthesis pathway, including 7 transcriptionally upregulated genes (cobA, cobT, hemA, cobJ, cobN, cobR, and cobP) that were episomally overexpressed in the Casida A strain. The results showed that the VB12 yield of the overexpressed strain was higher than that of the wild-type strain. Notably, the strains overexpressing the cobA and cobT genes exhibited the most significant increases in VB12 yield, i.e., 31.4% and 24.8%, respectively. The VB12 yield of the S305 strain in shake-flask culture was improved from 176.6 ± 8.21 mg/L to 245.6 ± 4.36 mg/L by integrating the cobA and cobT genes into the strain. CONCLUSION Phylogenetic tree and ANI analysis showed that the Ensifer and Sinorhizobium strains were quite different at the genome level; the overexpression and integrated expression of significantly upregulated genes in the VB12 synthesis pathway could increase the yield of VB12, further improving the VB12 yield of the E. adhaerens S305 strain.
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Affiliation(s)
- Yongheng Liu
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Wei Huang
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Qi Wang
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Cilang Ma
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Yongyong Chang
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Jianyu Su
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China.
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4
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Kang Q, Fang H, Xiang M, Xiao K, Jiang P, You C, Lee SY, Zhang D. A synthetic cell-free 36-enzyme reaction system for vitamin B 12 production. Nat Commun 2023; 14:5177. [PMID: 37620358 PMCID: PMC10449867 DOI: 10.1038/s41467-023-40932-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Adenosylcobalamin (AdoCbl), a biologically active form of vitamin B12 (coenzyme B12), is one of the most complex metal-containing natural compounds and an essential vitamin for animals. However, AdoCbl can only be de novo synthesized by prokaryotes, and its industrial manufacturing to date was limited to bacterial fermentation. Here, we report a method for the synthesis of AdoCbl based on a cell-free reaction system performing a cascade of catalytic reactions from 5-aminolevulinic acid (5-ALA), an inexpensive compound. More than 30 biocatalytic reactions are integrated and optimized to achieve the complete cell-free synthesis of AdoCbl, after overcoming feedback inhibition, the complicated detection, instability of intermediate products, as well as imbalance and competition of cofactors. In the end, this cell-free system produces 417.41 μg/L and 5.78 mg/L of AdoCbl using 5-ALA and the purified intermediate product hydrogenobyrate as substrates, respectively. The strategies of coordinating synthetic modules of complex cell-free system describe here will be generally useful for developing cell-free platforms to produce complex natural compounds with long and complicated biosynthetic pathways.
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Affiliation(s)
- Qian Kang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Huan Fang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Mengjie Xiang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
| | - Kaixing Xiao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Pingtao Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Chun You
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 four program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Dawei Zhang
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, 300308, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.
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5
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Liu G, Wang H, Tong B, Cui Y, Vonesch SC, Dong H, Zhang D. An Efficient CRISPR/Cas12e System for Genome Editing in Sinorhizobium meliloti. ACS Synth Biol 2023; 12:898-903. [PMID: 36795971 DOI: 10.1021/acssynbio.2c00629] [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: 02/18/2023]
Abstract
CRISPR/Cas systems have been widely used in the precise and traceless genetic engineering of bacteria. Sinorhizobium meliloti 320 (SM320) is a Gram-negative bacterium with a low efficiency of homologous recombination but a strong ability to produce vitamin B12. Here, a CRISPR/Cas12e-based genome engineering toolkit, CRISPR/Cas12eGET, was constructed in SM320. The expression level of CRISPR/Cas12e was tuned through promoter optimization and the use of a low copy plasmid to adjust Cas12e cutting activity to the low homologous recombination efficiency of SM320, resulting in improved transformation and precision editing efficiencies. Furthermore, the accuracy of CRISPR/Cas12eGET was improved by deleting the ku gene involved in NHEJ repair in SM320. This advance will be useful for metabolic engineering and basic research on SM320, and it further provides a platform to develop the CRISPR/Cas system in strains where the efficiency of homologous recombination is low.
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Affiliation(s)
- Guangqing Liu
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, No.1 Qinggongyuan, Dalian 116034, PR China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Baisong Tong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Sibylle C Vonesch
- VIB-KU Leuven Center for Microbiology, Leuven 3001, Belgium.,KU Leuven Centre of Microbial and Plant Genetics, KU Leuven, Leuven 3001, Belgium
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Dawei Zhang
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, No.1 Qinggongyuan, Dalian 116034, PR China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
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6
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Berihu M, Somera TS, Malik A, Medina S, Piombo E, Tal O, Cohen M, Ginatt A, Ofek-Lalzar M, Doron-Faigenboim A, Mazzola M, Freilich S. A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data. MICROBIOME 2023; 11:8. [PMID: 36635724 PMCID: PMC9835355 DOI: 10.1186/s40168-022-01438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment. RESULTS This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from 'sick' vs 'healthy/recovered' rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant's potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2 . CONCLUSIONS This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. Video Abstract.
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Affiliation(s)
- Maria Berihu
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Tracey S. Somera
- United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | | | - Shlomit Medina
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden
| | - Ofir Tal
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), P.O. Box 447, 49500 Migdal, Israel
| | - Matan Cohen
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Alon Ginatt
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | | | - Adi Doron-Faigenboim
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Mark Mazzola
- United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, Wenatchee, WA 98801 USA
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600 South Africa
| | - Shiri Freilich
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
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7
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Cui Y, Dong H, Tong B, Wang H, Chen X, Liu G, Zhang D. A versatile Cas12k-based genetic engineering toolkit (C12KGET) for metabolic engineering in genetic manipulation-deprived strains. Nucleic Acids Res 2022; 50:8961-8973. [PMID: 35920322 PMCID: PMC9410911 DOI: 10.1093/nar/gkac655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022] Open
Abstract
The genetic modification of microorganisms is conducive to the selection of high-yield producers of high-value-added chemicals, but a lack of genetic tools hinders the industrialization of most wild species. Therefore, it is crucial to develop host-independent gene editing tools that can be used for genetic manipulation-deprived strains. The Tn7-like transposon from Scytonema hofmanni has been shown to mediate homologous recombination-independent genomic integration after heterologous expression in Escherichia coli, but the integration efficiency of heterologous sequences larger than 5 kb remains suboptimal. Here, we constructed a versatile Cas12k-based genetic engineering toolkit (C12KGET) that can achieve genomic integration of fragments up to 10 kb in size with up to 100% efficiency in challenging strains. Using C12KGET, we achieved the first example of highly efficient genome editing in Sinorhizobium meliloti, which successfully solved the problem that industrial strains are difficult to genetically modify, and increased vitamin B12 production by 25%. In addition, Cas12k can be directly used for transcriptional regulation of genes with up to 92% efficiency due to its naturally inactivated nuclease domain. The C12KGET established in this study is a versatile and efficient marker-free tool for gene integration as well as transcriptional regulation that can be used for challenging strains with underdeveloped genetic toolkits.
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Affiliation(s)
- Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Baisong Tong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xipeng Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Guangqing Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Xu S, Xiao Z, Yu S, Zeng W, Zhu Y, Zhou J. Enhanced cobalamin biosynthesis in Ensifer adhaerens by regulation of key genes with gradient promoters. Synth Syst Biotechnol 2022; 7:941-948. [PMID: 35664931 PMCID: PMC9157374 DOI: 10.1016/j.synbio.2022.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 10/28/2022] Open
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9
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Efficient ex-situ biosynthesis of vitamin B12 by Propionibacterium freudenreichii using membrane separation coupling technology. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Liu Z, Dong H, Wu X, Fang H, Cong L, Zhu B, Zhang D. Identification of a xylose-inducible promoter and its application for improving vitamin B 12 production in Sinorhizobium meliloti. Biotechnol Appl Biochem 2020; 68:856-864. [PMID: 32770805 DOI: 10.1002/bab.2002] [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: 03/13/2020] [Accepted: 07/03/2020] [Indexed: 11/11/2022]
Abstract
Sinorhizobium meliloti 320 is a vitamin B12 (VB12 ) high-producing strain that has been isolated and identified in our previous study. Because the regulatory toolbox for S. meliloti is limited, we searched for new genetic components and identified the two xylose-inducible promoters PA and PB based on a promoter-probe vector with a green fluorescent protein (GFP) as reporter. Compared with the ParaA promoter from S. meliloti, both promoters exhibited higher induced expression and lower basal expression. Subsequently, the influence of glucose or sucrose on the expression of GFP driven by these three promoters was assayed. Glucose repressed all three promoters, and the expression of ParaA was the lowest in the presence of glucose. Although sucrose repressed the expression of PA by 35% and improved the expression of ParaA by 16%, the expression level of PA was the highest and was 13% higher than that of ParaA . Lastly, we overexpressed the hemA gene in the C4 pathway using the PA promoter in S. meliloti 320, and the VB12 production of the engineered strain increased by 11%. The VB12 production was further increased by 11% by adding 0.1% sodium succinate to the culture medium.
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Affiliation(s)
- Zhenquan Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Xiangying Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Lina Cong
- School of Biological Engineering, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Beiwei Zhu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, People's Republic of China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
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11
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Optimization of hydrogenobyrinic acid biosynthesis in Escherichia coli using multi-level metabolic engineering strategies. Microb Cell Fact 2020; 19:118. [PMID: 32487216 PMCID: PMC7268678 DOI: 10.1186/s12934-020-01377-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hydrogenobyrinic acid is a key intermediate of the de-novo aerobic biosynthesis pathway of vitamin B12. The introduction of a heterologous de novo vitamin B12 biosynthesis pathway in Escherichia coli offers an alternative approach for its production. Although E. coli avoids major limitations that currently faced by industrial producers of vitamin B12, such as long growth cycles, the insufficient supply of hydrogenobyrinic acid restricts industrial vitamin B12 production. RESULTS By designing combinatorial ribosomal binding site libraries of the hemABCD genes in vivo, we found that their optimal relative translational initiation rates are 10:1:1:5. The transcriptional coordination of the uroporphyrinogen III biosynthetic module was realized by promoter engineering of the hemABCD operon. Knockdown of competitive heme and siroheme biosynthesis pathways by RBS engineering enhanced the hydrogenobyrinic acid titer to 20.54 and 15.85 mg L-1, respectively. Combined fine-tuning of the heme and siroheme biosynthetic pathways enhanced the hydrogenobyrinic acid titer to 22.57 mg L-1, representing a remarkable increase of 1356.13% compared with the original strain FH215-HBA. CONCLUSIONS Through multi-level metabolic engineering strategies, we achieved the metabolic balance of the uroporphyrinogen III biosynthesis pathway, eliminated toxicity due to by-product accumulation, and finally achieved a high HBA titer of 22.57 mg L-1 in E. coli. This lays the foundation for high-yield production of vitamin B12 in E. coli and will hopefully accelerate its industrial production.
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12
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Metabolic engineering of Escherichia coli for de novo biosynthesis of vitamin B 12. Nat Commun 2018; 9:4917. [PMID: 30464241 PMCID: PMC6249242 DOI: 10.1038/s41467-018-07412-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/01/2018] [Indexed: 11/30/2022] Open
Abstract
The only known source of vitamin B12 (adenosylcobalamin) is from bacteria and archaea. Here, using genetic and metabolic engineering, we generate an Escherichia coli strain that produces vitamin B12 via an engineered de novo aerobic biosynthetic pathway. In vitro and/or in vivo analysis of genes involved in adenosylcobinamide phosphate biosynthesis from Rhodobacter capsulatus suggest that the biosynthetic steps from co(II)byrinic acid a,c-diamide to adocobalamin are the same in both the aerobic and anaerobic pathways. Finally, we increase the vitamin B12 yield of a recombinant E. coli strain by more than ∼250-fold to 307.00 µg g−1 DCW via metabolic engineering and optimization of fermentation conditions. Beyond our demonstration of E. coli as a microbial biosynthetic platform for vitamin B12 production, our study offers an encouraging example of how the several dozen proteins of a complex biosynthetic pathway can be transferred between organisms to facilitate industrial production. Vitamin B12 is an essential nutrient with limited natural sources. Here the authors transfer 28 pathway synthesis genes from several bacteria including R. capsulatus to E. coli and, using metabolic engineering and optimised fermentation conditions, achieve high yields.
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13
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Cai Y, Xia M, Dong H, Qian Y, Zhang T, Zhu B, Wu J, Zhang D. Engineering a vitamin B 12 high-throughput screening system by riboswitch sensor in Sinorhizobium meliloti. BMC Biotechnol 2018; 18:27. [PMID: 29751749 PMCID: PMC5948670 DOI: 10.1186/s12896-018-0441-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 04/30/2018] [Indexed: 12/23/2022] Open
Abstract
Background As a very important coenzyme in the cell metabolism, Vitamin B12 (cobalamin, VB12) has been widely used in food and medicine fields. The complete biosynthesis of VB12 requires approximately 30 genes, but overexpression of these genes did not result in expected increase of VB12 production. High-yield VB12-producing strains are usually obtained by mutagenesis treatments, thus developing an efficient screening approach is urgently needed. Result By the help of engineered strains with varied capacities of VB12 production, a riboswitch library was constructed and screened, and the btuB element from Salmonella typhimurium was identified as the best regulatory device. A flow cytometry high-throughput screening system was developed based on the btuB riboswitch with high efficiency to identify positive mutants. Mutation of Sinorhizobium meliloti (S. meliloti) was optimized using the novel mutation technique of atmospheric and room temperature plasma (ARTP). Finally, the mutant S. meliloti MC5–2 was obtained and considered as a candidate for industrial applications. After 7 d’s cultivation on a rotary shaker at 30 °C, the VB12 titer of S. meliloti MC5–2 reached 156 ± 4.2 mg/L, which was 21.9% higher than that of the wild type strain S. meliloti 320 (128 ± 3.2 mg/L). The genome of S. meliloti MC5–2 was sequenced, and gene mutations were identified and analyzed. Conclusion To our knowledge, it is the first time that a riboswitch element was used in S. meliloti. The flow cytometry high-throughput screening system was successfully developed and a high-yield VB12 producing strain was obtained. The identified and analyzed gene mutations gave useful information for developing high-yield strains by metabolic engineering. Overall, this work provides a useful high-throughput screening method for developing high VB12-yield strains. Electronic supplementary material The online version of this article (10.1186/s12896-018-0441-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, No. 29, thirteenth Avenue Binhai District, Tianjin, 300457, China
| | - Miaomiao Xia
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yuan Qian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science & Technology, No. 29, thirteenth Avenue Binhai District, Tianjin, 300457, China
| | - Beiwei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, 116034, People's Republic of China
| | - Jinchuan Wu
- Industrial Biotechnology Division, Institute of Chemical and Engineering Sciences, 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China. .,School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian, 116034, People's Republic of China.
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14
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Döhlemann J, Wagner M, Happel C, Carrillo M, Sobetzko P, Erb TJ, Thanbichler M, Becker A. A Family of Single Copy repABC-Type Shuttle Vectors Stably Maintained in the Alpha-Proteobacterium Sinorhizobium meliloti. ACS Synth Biol 2017; 6:968-984. [PMID: 28264559 PMCID: PMC7610768 DOI: 10.1021/acssynbio.6b00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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A considerable
share of bacterial species maintains segmented genomes.
Plant symbiotic α-proteobacterial rhizobia contain up to six repABC-type replicons in addition to the primary chromosome.
These low or unit-copy replicons, classified as secondary chromosomes,
chromids, or megaplasmids, are exclusively found in α-proteobacteria.
Replication and faithful partitioning of these replicons to the daughter
cells is mediated by the repABC region. The importance
of α-rhizobial symbiotic nitrogen fixation for sustainable agriculture
and Agrobacterium-mediated plant transformation as
a tool in plant sciences has increasingly moved biological engineering
of these organisms into focus. Plasmids are ideal DNA-carrying vectors
for these engineering efforts. On the basis of repABC regions collected from α-rhizobial secondary replicons, and
origins of replication derived from traditional cloning vectors, we
devised the versatile family of pABC shuttle vectors propagating in Sinorhizobium meliloti, related members of the Rhizobiales, and Escherichia coli. A modular plasmid library
providing the elemental parts for pABC vector assembly was founded.
The standardized design of these vectors involves five basic modules:
(1) repABC cassette, (2) plasmid-derived origin of
replication, (3) RK2/RP4 mobilization site (optional), (4) antibiotic
resistance gene, and (5) multiple cloning site flanked by transcription
terminators. In S. meliloti, pABC vectors showed
high propagation stability and unit-copy number. We demonstrated stable
coexistence of three pABC vectors in addition to the two indigenous
megaplasmids in S. meliloti, suggesting combinability
of multiple compatible pABC plasmids. We further devised an in vivo cloning strategy involving Cre/lox-mediated translocation of large DNA fragments to an autonomously
replicating repABC-based vector, followed by conjugation-mediated
transfer either to compatible rhizobia or E. coli.
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Affiliation(s)
- Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Marcel Wagner
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Carina Happel
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Martina Carrillo
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Tobias J. Erb
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Martin Thanbichler
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
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