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Zhou C, Okuno M, Nakazato I, Tsutsumi N, Arimura SI. Targeted A-to-G base editing in the organellar genomes of Arabidopsis with monomeric programmable deaminases. PLANT PHYSIOLOGY 2024; 194:2278-2287. [PMID: 38128544 PMCID: PMC10980515 DOI: 10.1093/plphys/kiad678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Plastids and mitochondria are 2 intracellular organelles containing DNA-encoding partial but essential components for their roles, photosynthesis, and respiration. Precise base editing in both plastid and mitochondrial genomes would benefit their gene functional analysis and crop breeding. Targeted base editing in organellar genomes relies on a protein-based genome-editing system that uses the TALE-DNA recognition motif with deaminases. This is because the efficient delivery of guide RNA for clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems into organelles is currently impossible. Since TALE-based base editors used in organellar genomes are usually dimeric types, in this study, we used targeted A-to-G base editing in Arabidopsis (Arabidopsis thaliana) plastid and mitochondrial genomes with monomeric TALE-based deaminase for easier assembling of vectors. As a result, inheritable targeted A-to-G base editing of adenosine triphosphatase subunit 6-2 (atp6-2) in plant mitochondrial genomes and of 16S ribosomal RNA (16S rRNA) in plastid genomes of Arabidopsis was successfully induced by monomeric TALE-based adenine deaminase (AD) without off-target mutations. The monomeric TALE-based adenine deaminases also demonstrated a preference for editing the 8th T on the same strand from the recognition end. Phenotypic analysis showed that A-to-G conversion at 1139A of plastid 16S rRNA conferred substantial spectinomycin resistance in Arabidopsis, but not the other 2 potential-resistant mutations at 1131T and 1137T, predicted from the previous bacterial data. Our study demonstrated the feasibility of monomeric TALE-based ADs in plant organelles and their potential contribution to the functional analyses of plant organelles with easier assembling.
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Affiliation(s)
- Chang Zhou
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shin-ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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Mok YG, Hong S, Bae SJ, Cho SI, Kim JS. Targeted A-to-G base editing of chloroplast DNA in plants. NATURE PLANTS 2022; 8:1378-1384. [PMID: 36456803 PMCID: PMC9788985 DOI: 10.1038/s41477-022-01279-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/19/2022] [Indexed: 05/12/2023]
Abstract
Chloroplast DNA (cpDNA) encodes up to 315 (typically, 120-130) genes1, including those for essential components in photosystems I and II and the large subunit of RuBisCo, which catalyses CO2 fixation in plants. Targeted mutagenesis in cpDNA will be broadly useful for studying the functions of these genes in molecular detail and for developing crops and other plants with desired traits. Unfortunately, CRISPR-Cas9 and CRISPR-derived base editors, which enable targeted genetic modifications in nuclear DNA, are not suitable for organellar DNA editing2, owing to the difficulty of delivering guide RNA into organelles. CRISPR-free, protein-only base editors (including DddA-derived cytosine base editors3-8 and zinc finger deaminases9), originally developed for mitochondrial DNA editing in mammalian cells, can be used for C-to-T, rather than A-to-G, editing in cpDNA10-12. Here we show that heritable homoplasmic A-to-G edits can be induced in cpDNA, leading to phenotypic changes, using transcription activator-like effector-linked deaminases13.
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Affiliation(s)
- Young Geun Mok
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- GreenGene Inc., Seoul, Republic of Korea
| | - Sunghyun Hong
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- GreenGene Inc., Seoul, Republic of Korea
| | - Su-Ji Bae
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Sung-Ik Cho
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea.
- GreenGene Inc., Seoul, Republic of Korea.
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Yu M, Zhao Y. Spectinomycin resistance in Lysobacter enzymogenes is due to its rRNA target but also relies on cell-wall recycling and purine biosynthesis. Front Microbiol 2022; 13:988110. [PMID: 36118211 PMCID: PMC9471086 DOI: 10.3389/fmicb.2022.988110] [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: 07/06/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Resistance to spectinomycin emerged after widely used for treatment of gonorrhea. Previous studies revealed that Lysobacter enzymogenes strain C3 (LeC3) exhibited elevated level of intrinsic resistance to spectinomycin. In this study, we screened a Tn5 transposon mutant library of LeC3 to elucidate the underlying molecular mechanisms of spectinomycin resistance. Insertion sites in 15 out of 19 mutants recovered with decreased spectinomycin resistance were located on two ribosomal RNA operons at different loci, indicating the pivotal role of ribosomal RNAs in conferring spectinomycin resistance in L. enzymogenes. The other mutants harbored mutations in the tuf, rpoD, mltB, and purB genes. Among them, the tuf and rpoD genes, respectively, encode a translation elongation factor Tu and an RNA polymerase primary sigma factor. They both contribute to protein biosynthesis, where ribosomal RNAs play essential roles. The mltB gene, whose product is involved in cell-wall recycling, was not only associated with resistance against spectinomycin, but also conferred resistance to osmotic stress and ampicillin. In addition, mutation of the purB gene, for which its product is involved in the biosynthesis of inosine and adenosine monophosphates, led to decreased spectinomycin resistance. Addition of exogenous adenine at lower concentration in medium restored the growth deficiency in the purB mutant and increased bacterial resistance to spectinomycin. These results suggest that while cell-wall recycling and purine biosynthesis might contribute to spectinomycin resistance, target rRNAs play critical role in spectinomycin resistance in L. enzymogenes.
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Affiliation(s)
- Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Plant Pathology, WSU-IAREC, Prosser, WA, United States
- *Correspondence: Youfu Zhao,
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Xu S, Liu Y, Zhang J. Transcriptomic mechanisms for the promotion of cyanobacterial growth against eukaryotic microalgae by a ternary antibiotic mixture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:58881-58891. [PMID: 35377122 DOI: 10.1007/s11356-022-20041-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
This study evaluated the responses of a mixed culture of two cyanobacterial species (Microcystis aeruginosa and Synechocystis sp.) and two eukaryotic microalgal species (Raphidocelis subcapitata and Tetradesmus obliquus) to a mixture of three frequently detected antibiotics (tetracycline, ciprofloxacin and sulfamethoxazole) at environmentally relevant exposure doses of 60-300 ng/L. Mixed antibiotics selectively stimulated (p < 0.05) the growth and photosynthetic activity as well as generated transcriptomic responses in cyanobacteria without disrupting co-existing eukaryotic microalgae. Mixed antibiotics stimulated the growth of M. aeruginosa through the regulation of genes related to ribosome, photosynthesis, redox homeostasis, quorum sensing and nutrient metabolism. The proportion of M. aeruginosa among the four phytoplankton species in the mixed-culture system was increased from 33% to 38-44% under antibiotic exposure, which promoted the dominance of M. aeruginosa. Up-regulation of carbon catabolism-related genes contributed to the increased growth of Synechocystis sp. under antibiotic exposure. Since the antibiotic-stimulated growth rate of Synechocystis sp. was still lower than that of M. aeruginosa, the proportion of Synechocystis sp. in the mixed-culture system remained stable. Synechocystis sp. was less adaptive to antibiotic exposure than M. aeruginosa, due to a lower number of up-regulated ribosomal genes and photosynthesis-related genes. Antibiotic exposure reduced the proportions of two eukaryotic microalgal species in the mixed-culture system through a selective promotion of cyanobacterial competitiveness against eukaryotic microalgae, which may facilitate the formation of cyanobacteria bloom.
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Affiliation(s)
- Sijia Xu
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, People's Republic of China
| | - Ying Liu
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Jian Zhang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, People's Republic of China
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Nakazato I, Okuno M, Yamamoto H, Tamura Y, Itoh T, Shikanai T, Takanashi H, Tsutsumi N, Arimura SI. Targeted base editing in the plastid genome of Arabidopsis thaliana. NATURE PLANTS 2021; 7:906-913. [PMID: 34211131 PMCID: PMC8289735 DOI: 10.1038/s41477-021-00954-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/26/2021] [Indexed: 05/17/2023]
Abstract
Bacterial cytidine deaminase fused to the DNA binding domains of transcription activator-like effector nucleases was recently reported to transiently substitute a targeted C to a T in mitochondrial DNA of mammalian cultured cells1. We applied this system to targeted base editing in the Arabidopsis thaliana plastid genome. The targeted Cs were homoplasmically substituted to Ts in some plantlets of the T1 generation and the mutations were inherited by their offspring independently of their nuclear-introduced vectors.
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Affiliation(s)
- Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Miki Okuno
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Hiroshi Yamamoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yoshiko Tamura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hideki Takanashi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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Imchen M, Moopantakath J, Kumavath R, Barh D, Tiwari S, Ghosh P, Azevedo V. Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. Front Genet 2020; 11:563975. [PMID: 33240317 PMCID: PMC7677515 DOI: 10.3389/fgene.2020.563975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Shen J, Liu Z, Yu H, Ye J, Long Y, Zhou P, He B. Systematic stress adaptation of Bacillus subtilis to tetracycline exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 188:109910. [PMID: 31740237 DOI: 10.1016/j.ecoenv.2019.109910] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/24/2019] [Accepted: 11/02/2019] [Indexed: 06/10/2023]
Abstract
To alleviate the harmful effects of antibiotics on the environment and human health, the stress response and molecular network of Bacillus under tetracycline stress were investigated using a proteomics approach. During the exposure process, Bacillus subtilis exhibited a strong adaptation mechanism. Cell membrane and intracellular reactive oxygen species (ROS) level returned to normal after 5 h. A total of 312 upregulated and 65 downregulated proteins were identified, mainly involved in metabolism and the synthesis of ribosomes, DNA, and RNA. After tetracycline exposure, the core metabolism network was accelerated to supply precursors for the synthesis of DNA, RNA, proteins, peptidoglycans, and saturated fatty acids that were involved in ribosome protection, and strengthened the cell wall and cell membrane. The signal transduction pathways involved were analyzed in association with the stress response of B. subtilis at 15 min of exposure to tetracycline. The primary damage to the ribosome by tetracycline activated a series of response proteins. Antitoxin and heat-shock proteins were activated for the global regulation of transcription and metabolism. Trigger factor Tig was upregulated to ensure proper initiation of transcription and aerobic respiration. Temperature-sensor protein VicR from the two-component system was used by the cell to regulate the composition of the cell wall and cell membrane. The over-consumption of metabolites, such as phosphoribosyl diphosphate (PRPP), purine nucleoside triphosphate (GTP), and acetyl-CoA forced the cells to assimilate more sugar for glycolysis. To this end, methyl-accepting chemotaxis proteins (MCPs) and sugar transportation protein PtsG were upregulated, simultaneously. Ultimately, peroxidase was activated to eliminate the redundant ROS, to minimize cell damage. These findings presented a system-level understanding of adaption processes of bacteria to antibiotic stress.
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Affiliation(s)
- Jing Shen
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Ziyi Liu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Henan Yu
- Guangdong Ocean Engineering Technology School, Guangzhou, 510320, China
| | - Jinshao Ye
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Yan Long
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Pulin Zhou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Baoyan He
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China.
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