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Koonin EV, Makarova KS. Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back. Genome Biol Evol 2017; 9:2812-2825. [PMID: 28985291 PMCID: PMC5737515 DOI: 10.1093/gbe/evx192] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2017] [Indexed: 12/13/2022] Open
Abstract
The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-CRISPR-associated proteins (Cas) systems of bacterial and archaeal adaptive immunity show multifaceted evolutionary relationships with at least five classes of mobile genetic elements (MGE). First, the adaptation module of CRISPR-Cas that is responsible for the formation of the immune memory apparently evolved from a Casposon, a self-synthesizing transposon that employs the Cas1 protein as the integrase and might have brought additional cas genes to the emerging immunity loci. Second, a large subset of type III CRISPR-Cas systems recruited a reverse transcriptase from a Group II intron, providing for spacer acquisition from RNA. Third, effector nucleases of Class 2 CRISPR-Cas systems that are responsible for the recognition and cleavage of the target DNA were derived from transposon-encoded TnpB nucleases, most likely, on several independent occasions. Fourth, accessory nucleases in some variants of types I and III toxin and type VI effectors RNases appear to be ultimately derived from toxin nucleases of microbial toxin-antitoxin modules. Fifth, the opposite direction of evolution is manifested in the recruitment of CRISPR-Cas systems by a distinct family of Tn7-like transposons that probably exploit the capacity of CRISPR-Cas to recognize unique DNA sites to facilitate transposition as well as by bacteriophages that employ them to cope with host defense. Additionally, individual Cas proteins, such as the Cas4 nuclease, were recruited by bacteriophages and transposons. The two-sided evolutionary connection between CRISPR-Cas and MGE fits the "guns for hire" paradigm whereby homologous enzymatic machineries, in particular nucleases, are shuttled between MGE and defense systems and are used alternately as means of offense or defense.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
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102
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Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O. Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. Mol Cell 2017; 67:633-645.e3. [PMID: 28781234 PMCID: PMC5957536 DOI: 10.1016/j.molcel.2017.06.035] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/07/2017] [Accepted: 06/30/2017] [Indexed: 12/26/2022]
Abstract
The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM. These structures revealed that, depending on the PAM sequences, LbCpf1 undergoes conformational changes to form altered interactions with the PAM-containing DNA duplexes, thereby achieving the relaxed PAM recognition. Collectively, the present structures advance our mechanistic understanding of the PAM-dependent, crRNA-guided DNA cleavage by the Cpf1 family nucleases.
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Affiliation(s)
- Takashi Yamano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Bernd Zetsche
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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103
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Jackson RN, van Erp PB, Sternberg SH, Wiedenheft B. Conformational regulation of CRISPR-associated nucleases. Curr Opin Microbiol 2017. [PMID: 28646675 DOI: 10.1016/j.mib.2017.05.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adaptive immune systems in bacteria and archaea rely on small CRISPR-derived RNAs (crRNAs) to guide specialized nucleases to foreign nucleic acids. The activation of these nucleases is controlled by a series of molecular checkpoints that ensure precise cleavage of nucleic acid targets, while minimizing toxic off-target cleavage events. In this review, we highlight recent advances in understanding regulatory mechanisms responsible for controlling the activation of these nucleases and identify emerging regulatory themes conserved across diverse CRISPR systems.
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Affiliation(s)
- Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States.
| | - Paul Bg van Erp
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, United States.
| | | | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, United States.
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104
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Koonin EV, Makarova KS, Zhang F. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 2017; 37:67-78. [PMID: 28605718 DOI: 10.1016/j.mib.2017.05.008] [Citation(s) in RCA: 838] [Impact Index Per Article: 119.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/15/2017] [Accepted: 05/28/2017] [Indexed: 01/17/2023]
Abstract
The bacterial and archaeal CRISPR-Cas systems of adaptive immunity show remarkable diversity of protein composition, effector complex structure, genome locus architecture and mechanisms of adaptation, pre-CRISPR (cr)RNA processing and interference. The CRISPR-Cas systems belong to two classes, with multi-subunit effector complexes in Class 1 and single-protein effector modules in Class 2. Concerted genomic and experimental efforts on comprehensive characterization of Class 2 CRISPR-Cas systems led to the identification of two new types and several subtypes. The newly characterized type VI systems are the first among the CRISPR-Cas variants to exclusively target RNA. Unexpectedly, in some of the class 2 systems, the effector protein is additionally responsible for the pre-crRNA processing. Comparative analysis of the effector complexes indicates that Class 2 systems evolved from mobile genetic elements on multiple, independent occasions.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Departments of Brain and Cognitive Science and Biological Engineering, Cambridge, MA 02139, USA
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105
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A decade of discovery: CRISPR functions and applications. Nat Microbiol 2017; 2:17092. [PMID: 28581505 DOI: 10.1038/nmicrobiol.2017.92] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/05/2017] [Indexed: 12/26/2022]
Abstract
This year marks the tenth anniversary of the identification of the biological function of CRISPR-Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR-Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond.
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106
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Wu D, Guan X, Zhu Y, Ren K, Huang Z. Structural basis of stringent PAM recognition by CRISPR-C2c1 in complex with sgRNA. Cell Res 2017; 27:705-708. [PMID: 28374750 PMCID: PMC5520857 DOI: 10.1038/cr.2017.46] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Dan Wu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Xiaoyu Guan
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Kuan Ren
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
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107
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Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol 2017. [PMID: 28111461 DOI: 10.1038/nrmicro.2016.184.diversity] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.
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Affiliation(s)
- Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Aaron Smargon
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - David Scott
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Cox
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Neena Pyzocha
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Winston Yan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Omar O Abudayyeh
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Kira S Makarova
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
- McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology Cambridge (MIT), Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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108
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109
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Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol 2017; 15:169-182. [PMID: 28111461 DOI: 10.1038/nrmicro.2016.184] [Citation(s) in RCA: 634] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.
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Affiliation(s)
- Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia.,National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Aaron Smargon
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - David Scott
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Cox
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Neena Pyzocha
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Winston Yan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Omar O Abudayyeh
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Kira S Makarova
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.,McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology Cambridge (MIT), Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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110
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Zhang K, Raboanatahiry N, Zhu B, Li M. Progress in Genome Editing Technology and Its Application in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:177. [PMID: 28261237 PMCID: PMC5306361 DOI: 10.3389/fpls.2017.00177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, protein-dependent DNA cleavage systems (i.e., zinc-finger nucleases, ZFN, and transcription activator-like effector nucleases, TALEN), RNA-dependent DNA cleavage systems (i.e., clustered regularly interspaced short palindromic repeats-CRISPR associated proteins, CRISPR-Cas9, CRISPR-Cpf1, and CRISPR-C2c1), and RNA-dependent RNA cleavage systems (i.e., RNA interference, RNAi, and CRISPR-C2c2). All these techniques can lead to double-stranded (DSB) or single-stranded breaks (SSB), and result in either random mutations via non-homologous end-joining (NHEJ) or targeted mutation via homologous recombination (HR). Thus, site-directed mutagenesis can be induced via targeted gene knock-out, knock-in, or replacement to modify specific characteristics including morphology-modification, resistance-enhancement, and physiological mechanism-improvement along with plant growth and development. In this paper, an non-comprehensive review on the development of different GETs as applied to plants is presented.
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Affiliation(s)
- Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Bin Zhu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
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