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Hu Z, Liu Q, Ouyang B, Wang G, Wei C, Zhao X. Recent advances in genetic engineering to enhance plant-polysaccharide-degrading enzyme expression in Penicillium oxalicum: A brief review. Int J Biol Macromol 2024; 278:134775. [PMID: 39153674 DOI: 10.1016/j.ijbiomac.2024.134775] [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] [Received: 07/12/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
With the depletion of non-renewable fossil fuels, there has been an increasing emphasis on renewable biomass. Penicillium oxalicum is notable for its exceptional capacity to secrete a diverse array of enzymes that degrade plant polysaccharides into monosaccharides. These valuable monosaccharides can be harnessed in the production of bioethanol and other sustainable forms of energy. By enhancing the production of plant-polysaccharide-degrading enzymes (PPDEs) in P. oxalicum, we can optimize the utilization of plant biomass. This paper presents recent advances in augmenting PPDE expression in P. oxalicum through genetic engineering strategies involving protoplast preparation, transformation, and factors influencing PPDE gene expression.
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Affiliation(s)
- Ziyan Hu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Qiling Liu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Bei Ouyang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Guoping Wang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Chenyang Wei
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China.
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2
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Sun X, Shang Y, Zhang B, Guo P, Luo Y, Wu H. Engineering of fast-growing Vibrio natriegens for biosynthesis of poly(3-hydroxybutyrate-co-lactate). BIORESOUR BIOPROCESS 2024; 11:86. [PMID: 39249183 PMCID: PMC11383894 DOI: 10.1186/s40643-024-00801-4] [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: 07/10/2024] [Accepted: 08/25/2024] [Indexed: 09/10/2024] Open
Abstract
Poly(3-hydroxybutyrate-co-lactate) [P(3HB-co-LA)] is a highly promising valuable biodegradable material with good biocompatibility and degradability. Vibrio natriegens, owing to its fast-growth, wide substrate spectrum characteristics, was selected to produce P(3HB-co-LA). Herein, the crucial role of acetyltransferase PN96-18060 for PHB synthesis in V. natriegens was identified. Heterologous pathway of P(3HB-co-LA) was introduced into V. natriegens successfully, in addition, overexpression of the dldh gene led to 1.84 fold enhancement of the lactate content in P(3HB-co-LA). Finally, the production of P(3HB-co-LA) was characterized under different carbon sources. The lactate fraction in P(3HB-co-LA) was increased to 28.3 mol% by the modification, about 1.84 times of that of the control. This is the first successful case of producing the P(3HB-co-LA) in V. natriegens. Collectively, this study showed that V. natriegens is an attractive host organism for producing P(3HB-co-LA) and has great potential to produce other co-polymers.
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Affiliation(s)
- Xinye Sun
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yanzhe Shang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Binghao Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Pengye Guo
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
- Key Laboratory of Bio-based Material Engineering of China, National Light Industry Council, 130 Meilong Road, Shanghai, 200237, China.
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3
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Wagner M, Döhlemann J, Geisel D, Sobetzko P, Serrania J, Lenz P, Becker A. Engineering a Sinorhizobium meliloti Chassis with Monopartite, Single Replicon Genome Configuration. ACS Synth Biol 2024; 13:2515-2532. [PMID: 39109796 DOI: 10.1021/acssynbio.4c00281] [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: 08/17/2024]
Abstract
Multipartite bacterial genomes pose challenges for genome engineering and the establishment of additional replicons. We simplified the tripartite genome structure (3.65 Mbp chromosome, 1.35 Mbp megaplasmid pSymA, 1.68 Mbp chromid pSymB) of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Strains with bi- and monopartite genome configurations were generated by targeted replicon fusions. Our design preserved key genomic features such as replichore ratios, GC skew, KOPS, and coding sequence distribution. Under standard culture conditions, the growth rates of these strains and the wild type were nearly comparable, and the ability for symbiotic nitrogen fixation was maintained. Spatiotemporal replicon organization and segregation were maintained in the triple replicon fusion strain. Deletion of the replication initiator-encoding genes, including the oriVs of pSymA and pSymB from this strain, resulted in a monopartite genome with oriC as the sole origin of replication, a strongly unbalanced replichore ratio, slow growth, aberrant cellular localization of oriC, and deficiency in symbiosis. Suppressor mutation R436H in the cell cycle histidine kinase CckA and a 3.2 Mbp inversion, both individually, largely restored growth, but only the genomic rearrangement recovered the symbiotic capacity. These strains will facilitate the integration of secondary replicons in S. meliloti and thus be useful for genome engineering applications, such as generating hybrid genomes.
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Affiliation(s)
- Marcel Wagner
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Johannes Döhlemann
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - David Geisel
- Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Patrick Sobetzko
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Peter Lenz
- Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany
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Barnum CR, Paviani B, Couture G, Masarweh C, Chen Y, Huang YP, Markel K, Mills DA, Lebrilla CB, Barile D, Yang M, Shih PM. Engineered plants provide a photosynthetic platform for the production of diverse human milk oligosaccharides. NATURE FOOD 2024; 5:480-490. [PMID: 38872016 PMCID: PMC11199141 DOI: 10.1038/s43016-024-00996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Human milk oligosaccharides (HMOs) are a diverse class of carbohydrates which support the health and development of infants. The vast health benefits of HMOs have made them a commercial target for microbial production; however, producing the approximately 200 structurally diverse HMOs at scale has proved difficult. Here we produce a diversity of HMOs by leveraging the robust carbohydrate anabolism of plants. This diversity includes high-value and complex HMOs, such as lacto-N-fucopentaose I. HMOs produced in transgenic plants provided strong bifidogenic properties, indicating their ability to serve as a prebiotic supplement with potential applications in adult and infant health. Technoeconomic analyses demonstrate that producing HMOs in plants provides a path to the large-scale production of specific HMOs at lower prices than microbial production platforms. Our work demonstrates the promise in leveraging plants for the low-cost and sustainable production of HMOs.
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Affiliation(s)
- Collin R Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA, USA
| | - Bruna Paviani
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
| | - Garret Couture
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Chad Masarweh
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
| | - Ye Chen
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Yu-Ping Huang
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
| | - Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Mills
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, Davis, CA, USA
| | - Minliang Yang
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
- Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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5
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Fizikova A, Subcheva E, Kozlov N, Tvorogova V, Samarina L, Lutova L, Khlestkina E. Agrobacterium Transformation of Tea Plants ( Camellia sinensis (L.) KUNTZE): A Small Experiment with Great Prospects. PLANTS (BASEL, SWITZERLAND) 2024; 13:675. [PMID: 38475520 DOI: 10.3390/plants13050675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024]
Abstract
Tea has historically been one of the most popular beverages, and it is currently an economically significant crop cultivated in over 50 countries. The Northwestern Caucasus is one of the northernmost regions for industrial tea cultivation worldwide. The domestication of the tea plant in this region took approximately 150 years, during which plantations spreading from the Ozurgeti region in northern Georgia to the southern city of Maykop in Russia. Consequently, tea plantations in the Northern Caucasus can serve as a source of unique genotypes with exceptional cold tolerance. Tea plants are known to be recalcitrant to Agrobacterium-mediated transfection. Research into optimal transfection and regeneration methodologies, as well as the identification of tea varieties with enhanced transformation efficiency, is an advanced strategy for improving tea plant culture. The aim of this study was to search for the optimal Agrobacterium tumefaciens-mediated transfection protocol for the Kolkhida tea variety. As a result of optimizing the transfection medium with potassium phosphate buffer at the stages of pre-inoculation, inoculation and co-cultivation, the restoration of normal morphology and improvement in the attachment of Agrobacterium cells to the surface of tea explants were observed by scanning electron microscopy. And an effective method of high-efficiency Agrobacteria tumefaciens-mediated transfection of the best local tea cultivar, Kolkhida, was demonstrated for the first time.
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Affiliation(s)
- Anastasia Fizikova
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 2/28, Yana Fabritsiusa Street, 354002 Sochi, Russia
| | - Elena Subcheva
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia
| | - Nikolay Kozlov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb 7/9, 199034 Saint-Petersburg, Russia
| | - Varvara Tvorogova
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb 7/9, 199034 Saint-Petersburg, Russia
| | - Lidia Samarina
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 2/28, Yana Fabritsiusa Street, 354002 Sochi, Russia
| | - Ludmila Lutova
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb 7/9, 199034 Saint-Petersburg, Russia
| | - Elena Khlestkina
- Plant Biology and Biotechnology Department, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), B. Morskaya Street, 42-44, 190000 St. Petersburg, Russia
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6
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Barnum CR, Paviani B, Couture G, Masarweh C, Chen Y, Huang YP, Mills DA, Lebrilla CB, Barile D, Yang M, Shih PM. Plant-based production of diverse human milk oligosaccharides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558286. [PMID: 37786679 PMCID: PMC10541580 DOI: 10.1101/2023.09.18.558286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Human milk oligosaccharides (HMOs) are a diverse class of carbohydrates that aid in the health and development of infants. The vast health benefits of HMOs have made them a commercial target for microbial production; however, producing the ∼130 structurally diverse HMOs at scale has proven difficult. Here, we produce a vast diversity of HMOs by leveraging the robust carbohydrate anabolism of plants. This diversity includes high value HMOs, such as lacto-N-fucopentaose I, that have not yet been commercially produced using state-of-the-art microbial fermentative processes. HMOs produced in transgenic plants provided strong bifidogenic properties, indicating their ability to serve as a prebiotic supplement. Technoeconomic analyses demonstrate that producing HMOs in plants provides a path to the large-scale production of specific HMOs at lower prices than microbial production platforms. Our work demonstrates the promise in leveraging plants for the cheap and sustainable production of HMOs.
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7
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Waldburger L, Thompson MG, Weisberg AJ, Lee N, Chang JH, Keasling JD, Shih PM. Transcriptome architecture of the three main lineages of agrobacteria. mSystems 2023; 8:e0033323. [PMID: 37477440 PMCID: PMC10469942 DOI: 10.1128/msystems.00333-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.
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Affiliation(s)
- Lucas Waldburger
- Department of Bioengineering, University of California, Berkeley, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Namil Lee
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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Etminani F, Harighi B, Mozafari AA. Effect of volatile compounds produced by endophytic bacteria on virulence traits of grapevine crown gall pathogen, Agrobacterium tumefaciens. Sci Rep 2022; 12:10510. [PMID: 35732688 PMCID: PMC9217936 DOI: 10.1038/s41598-022-14864-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
The volatile organic compounds (VOCs) produced by endophytic bacteria have a significant role in the control of phytopathogens. In this research, the VOCs produced by endophytic bacteria including Serratia sp. Ba10, Pantoea sp. Sa14, Enterobacter sp. Ou80, Pseudomonas sp. Ou22, Pseudomonas sp. Sn48 and Pseudomonas sp. Ba35, which were previously isolated from healthy domesticated and wild-growing grapevine were evaluated in terms of their effects on the virulence traits of Agrobacterium tumefaciens Gh1, the causal agent of crown gall disease. Based on the gas chromatography-mass spectrometry analysis, 16, 15, 14, 7, 16, and 15 VOCs have been identified with high quality in strains of Ba10, Sa14, Ou80, Ou22, Sn48, and Ba35, respectively. All endophytic bacteria produced VOCs that significantly reduced crown gall symptoms and inhibited the populations of A. tumefaciens Gh1 at different levels. Moreover, scanning electron microscopy analysis revealed various morphological abnormalities in the A. tumefaciens cells exposed to the VOCs produced by Ba35, Ou80, and Sn48 strains. The VOCs significantly reduced swarming-, swimming-, twitching motility and biofilm formation by A. tumefaciens Gh1. Our results revealed that VOCs could reduce the attachment of A. tumefaciens Gh1 cells to root tissues of grapevine cultivars Rashe and Bidane sefid, as well as chemotaxis motility towards root extract of both cultivars. Based on our results, it was shown that the antibacterial VOCs produced by endophytic bacteria investigated in the current study can manage crown gall disease and increase our knowledge on the role of VOCs in microbial interactions.
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Affiliation(s)
- Faegheh Etminani
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Behrouz Harighi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Ali Akbar Mozafari
- Department of Horticultural Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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Jin K, Tian N, da Silva Ferreira JF, Sandhu D, Xiao L, Gu M, Luo Y, Zhang X, Liu G, Liu Z, Huang J, Liu S. Comparative Transcriptome Analysis of Agrobacterium tumefaciens Reveals the Molecular Basis for the Recalcitrant Genetic Transformation of Camellia sinensis L. Biomolecules 2022; 12:688. [PMID: 35625616 PMCID: PMC9138961 DOI: 10.3390/biom12050688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
Tea (Camellia sinensis L.), an important economic crop, is recalcitrant to Agrobacterium-mediated transformation (AMT), which has seriously hindered the progress of molecular research on this species. The mechanisms leading to low efficiency of AMT in tea plants, related to the morphology, growth, and gene expression of Agrobacterium tumefaciens during tea-leaf explant infection, were compared to AMT of Nicotiana benthamiana leaves in the present work. Scanning electron microscopy (SEM) images showed that tea leaves induced significant morphological aberrations on bacterial cells and affected pathogen-plant attachment, the initial step of a successful AMT. RNA sequencing and transcriptomic analysis on Agrobacterium at 0, 3 and 4 days after leaf post-inoculation resulted in 762, 1923 and 1656 differentially expressed genes (DEGs) between the tea group and the tobacco group, respectively. The expressions of genes involved in bacterial fundamental metabolic processes, ATP-binding cassette (ABC) transporters, two-component systems (TCSs), secretion systems, and quorum sensing (QS) systems were severely affected in response to the tea-leaf phylloplane. Collectively, these results suggest that compounds in tea leaves, especially gamma-aminobutyrate (GABA) and catechins, interfered with plant-pathogen attachment, essential minerals (iron and potassium) acquisition, and quorum quenching (QQ) induction, which may have been major contributing factors to hinder AMT efficiency of the tea plant.
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Affiliation(s)
- Ke Jin
- Department of Tea Science, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (K.J.); (N.T.); (L.X.); (M.G.)
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
| | - Na Tian
- Department of Tea Science, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (K.J.); (N.T.); (L.X.); (M.G.)
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
| | - Jorge Freire da Silva Ferreira
- United States Salinity Laboratory, United States Department of Agriculture, Agricultural Research Service, Riverside, CA 92507, USA; (J.F.d.S.F.); (D.S.)
| | - Devinder Sandhu
- United States Salinity Laboratory, United States Department of Agriculture, Agricultural Research Service, Riverside, CA 92507, USA; (J.F.d.S.F.); (D.S.)
| | - Lizheng Xiao
- Department of Tea Science, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (K.J.); (N.T.); (L.X.); (M.G.)
| | - Meiyi Gu
- Department of Tea Science, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (K.J.); (N.T.); (L.X.); (M.G.)
| | - Yiping Luo
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
| | - Xiangqin Zhang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
| | - Guizhi Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
| | - Zhonghua Liu
- Department of Tea Science, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (K.J.); (N.T.); (L.X.); (M.G.)
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
| | - Jianan Huang
- Department of Tea Science, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (K.J.); (N.T.); (L.X.); (M.G.)
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
| | - Shuoqian Liu
- Department of Tea Science, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (K.J.); (N.T.); (L.X.); (M.G.)
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha 410128, China; (Y.L.); (X.Z.); (G.L.)
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Li M, Huo YX, Guo S. CRISPR-Mediated Base Editing: From Precise Point Mutation to Genome-Wide Engineering in Nonmodel Microbes. BIOLOGY 2022; 11:571. [PMID: 35453770 PMCID: PMC9024924 DOI: 10.3390/biology11040571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 12/23/2022]
Abstract
Nonmodel microbes with unique and diverse metabolisms have become rising stars in synthetic biology; however, the lack of efficient gene engineering techniques still hinders their development. Recently, the use of base editors has emerged as a versatile method for gene engineering in a wide range of organisms including nonmodel microbes. This method is a fusion of impaired CRISPR/Cas9 nuclease and base deaminase, enabling the precise point mutation at the target without inducing homologous recombination. This review updates the latest advancement of base editors in microbes, including the conclusion of all microbes that have been researched by base editors, the introduction of newly developed base editors, and their applications. We provide a list that comprehensively concludes specific applications of BEs in nonmodel microbes, which play important roles in industrial, agricultural, and clinical fields. We also present some microbes in which BEs have not been fully established, in the hope that they are explored further and so that other microbial species can achieve arbitrary base conversions. The current obstacles facing BEs and solutions are put forward. Lastly, the highly efficient BEs and other developed versions for genome-wide reprogramming of cells are discussed, showing great potential for future engineering of nonmodel microbes.
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Affiliation(s)
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China;
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China;
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Qian Y, Kong W, Lu T. Precise and reliable control of gene expression in Agrobacterium tumefaciens. Biotechnol Bioeng 2021; 118:3962-3972. [PMID: 34180537 DOI: 10.1002/bit.27872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 11/07/2022]
Abstract
Agrobacterium tumefaciens is a soil-borne bacterium that is known for its DNA delivery ability and widely exploited for plant transformation. Despite continued interest in improving the utility of the organism, the lack of well-characterized engineering tools limits the realization of its full potential. Here, we present a synthetic biology toolkit that enables precise and effective control of gene expression in A. tumefaciens. We constructed and characterized six inducible expression systems. Then, we optimized the one regulated by cumic acid through amplifier introduction and promoter engineering and evaluated its 15 cognate promoters. To establish fine-tunability, we constructed a series of spacers and a promoter library to systematically modulate both translational and transcriptional rates. We finally demonstrated the application of the tools by co-expressing genes with altered expression levels using a single signal. This study provides precise expression tools for A. tumefaciens, facilitating rational engineering of the bacterium for advanced plant biotechnological applications.
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Affiliation(s)
- Yuanchao Qian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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