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Lu H, Xue M, Nie X, Luo H, Tan Z, Yang X, Shi H, Li X, Wang T. Glycoside hydrolases in the biodegradation of lignocellulosic biomass. 3 Biotech 2023; 13:402. [PMID: 37982085 PMCID: PMC10654287 DOI: 10.1007/s13205-023-03819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/15/2023] [Indexed: 11/21/2023] Open
Abstract
Lignocellulose is a plentiful and intricate biomass substance made up of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are polysaccharides characterized by different compositions and degrees of polymerization. As renewable resources, their applications are eco-friendly and can help reduce reliance on petrochemical resources. This review aims to illustrate cellulose, hemicellulose, and their structures and hydrolytic enzymes. To obtain desirable enzyme sources for the high hydrolysis of lignocellulose, highly stable, efficient and thermophilic enzyme sources, and new technologies, such as rational design and machine learning, have been introduced in detail. Generally, the efficient biodegradation of abundant natural biomass into fermentable sugars or other intermediates has great potential in practical applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03819-1.
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Affiliation(s)
- Honglin Lu
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Maoyuan Xue
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xinling Nie
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Hongzheng Luo
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Zhongbiao Tan
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xiao Yang
- Department of Poultry Science, The University of Georgia, Athens, GA 30602 USA
| | - Hao Shi
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Tao Wang
- Department of Microbiology, The University of Georgia, Athens, GA 30602 USA
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Yu F, Li X, Wang F, Liu Y, Zhai C, Li W, Ma L, Chen W. TLTC, a T5 exonuclease-mediated low-temperature DNA cloning method. Front Bioeng Biotechnol 2023; 11:1167534. [PMID: 37635997 PMCID: PMC10457141 DOI: 10.3389/fbioe.2023.1167534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/11/2023] [Indexed: 08/29/2023] Open
Abstract
Molecular cloning is used in a wide variety of biological and medical research. Here, we developed a rapid and efficient DNA-assembling method for routine laboratory work. We discovered that the cleavage speed of T5 exonuclease is approximately 3 nt/min at 0°C and hence developed a T5 exonuclease-mediated low-temperature sequence- and ligation-independent cloning method (TLTC). Two homologous regions of 15 bp-25 bp compatible with the ends of the vector backbones were introduced into the inserts through PCR. Approximately 120 fmol of inserts and linear vectors was mixed at a molar ratio of approximately 3:1 and treated with 0.5 U of T5 exonuclease at 0°C for 5 min. Then, the mixture was transformed into Escherichia coli to generate recombinant plasmids. Single segment and multi-segments can be assembled efficiently using TLTC. For single segment, the overall cloning efficiency is above 95%. Moreover, extra nucleotides in the vectors can be removed during TLTC. In conclusion, an extremely simple and fast DNA cloning/assembling method was established in the present study. This method facilitates routine DNA cloning and synthesis of DNA fragments.
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Affiliation(s)
- Fang Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xia Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Yang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Wenqiang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
- School of Pharmacy, Qingdao University, Qingdao, China
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Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
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Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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Zhang G, Wang J, Li Y, Shang G. CRISPR/Cas9-assisted ssDNA recombineering for site-directed mutagenesis and saturation mutagenesis of plasmid-encoded genes. Biotechnol Lett 2023; 45:629-637. [PMID: 36930400 DOI: 10.1007/s10529-023-03363-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 03/18/2023]
Abstract
Site-directed and saturation mutagenesis are critical DNA methodologies for studying protein structure and function. For plasmid-based gene mutation, PCR and overlap-extension PCR involve tedious cloning steps. When the plasmid size is large, PCR yield may be too low for cloning; and for saturation mutagenesis of a single codon, one experiment may not enough to generate all twenty coding variants. Oligo-mediated recombineering sidesteps the complicated cloning process by homologous recombination between a mutagenic oligo and its target site. However, the low recombineering efficiency and inability to select for the recombinant makes it necessary to screen a large number of clones. Herein, we describe two plasmid-based mutagenic strategies: CRISPR/Cas9-assisted ssDNA recombineering for site-directed mutagenesis (CRM) and saturation mutagenesis (CRSM). CRM and CRSM involve co-electroporation of target plasmid, sgRNA expression plasmid and mutagenic oligonucleotide into Escherichia coli cells with induced expression of λ-Red recombinase and Cas9, followed by plasmid extraction and characterization. We established CRM and CRSM via ampicillin resistance gene repair and mutagenesis of N-acetyl‑D‑neuraminic acid aldolase. The mutational efficiency was between 80 and 100% and all twenty amino acid coding variants were obtained at a target site via a single CRSM strategy. CRM and CRSM have the potential to be general plasmid-based gene mutagenesis tools.
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Affiliation(s)
- Guoyi Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China
| | - Junyu Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China
| | - Yiwen Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China
| | - Guangdong Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No.1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu Province, People's Republic of China.
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Dong M, Wang F, Lv B, Mei M, Ma L, Hu Y, Zhai C. CT5, a subtle in vitro DNA assembling method based on the combination of FnCas12a and T5 exonuclease. Biotechnol Lett 2021; 43:899-907. [PMID: 33389273 DOI: 10.1007/s10529-020-03064-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/12/2020] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To develop a new DNA assembly method based on FnCas12a and T5 exonuclease. RESULTS We developed a method named as FnCas12a and T5 exonuclease (CT5) cloning system. FnCas12a performs site-directed cleavage to the target DNA fragments, and T5 exonuclease generates 20-30 nt single-stranded region at each end of the DNA fragments for homologous recombination-mediated DNA assembly. CT5 was applied to multi-fragment assembly and DNA cloning of large vectors (> 10 kb). The efficiencies were approximately 91.4% and 97%, respectively. In addition, CT5 cloning is also utilized for the "walking" of DNA elements, which enables subtle modification of the relative distances of DNA elements in plasmids. CONCLUSIONS The CT5 method was a precise and exquisite DNA operating system and provided an ideal platform for the study of gene functions, genetic engineering and synthetic biology.
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