1
|
Zhang XR, Zhao L, Suo F, Gao Y, Wu Q, Qi X, Du LL. An improved auxin-inducible degron system for fission yeast. G3 (BETHESDA, MD.) 2022; 12:6440046. [PMID: 34849776 PMCID: PMC8727963 DOI: 10.1093/g3journal/jkab393] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/25/2021] [Indexed: 01/09/2023]
Abstract
Conditional degron technologies, which allow a protein of interest to be degraded in an inducible manner, are important tools for biological research, and are especially useful for creating conditional loss-of-function mutants of essential genes. The auxin-inducible degron (AID) technology, which utilizes plant auxin signaling components to control protein degradation in nonplant species, is a widely used small-molecular-controlled degradation method in yeasts and animals. However, the currently available AID systems still have room for further optimization. Here, we have improved the AID system for the fission yeast Schizosaccharomyces pombe by optimizing all three components: the AID degron, the small-molecule inducer, and the inducer-responsive F-box protein. We chose a 36-amino-acid sequence of the Arabidopsis IAA17 protein as the degron and employed three tandem copies of it to enhance efficiency. To minimize undesirable side effects of the inducer, we adopted a bulky analog of auxin, 5-adamantyl-IAA, and paired it with the F-box protein OsTIR1 that harbors a mutation (F74A) at the auxin-binding pocket. 5-adamantyl-IAA, when utilized with OsTIR1-F74A, is effective at concentrations thousands of times lower than auxin used in combination with wild-type OsTIR1. We tested our improved AID system on 10 essential genes and achieved inducible lethality for all of them, including ones that could not be effectively inactivated using a previously published AID system. Our improved AID system should facilitate the construction of conditional loss-of-function mutants in fission yeast.
Collapse
Affiliation(s)
- Xiao-Ran Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lei Zhao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yadong Gao
- National Institute of Biological Sciences, Beijing 102206, China.,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Qingcui Wu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| |
Collapse
|
2
|
Zhang JY, Niu TC, Lin GM, Zhang CC. A CRISPR-Based Method for Constructing Conditional Mutations of Essential Genes in Cyanobacteria. Methods Mol Biol 2022; 2377:143-157. [PMID: 34709615 DOI: 10.1007/978-1-0716-1720-5_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cyanobacteria, a group of diverse bacteria capable of oxygenic photosynthesis, are excellent models for investigating many important cellular processes, such as photosynthesis, nitrogen fixation, and prokaryotic cell differentiation. They also have great potential to become the next-generation cell factories for sustainable biosynthesis of valuable products. However, genetic manipulation in cyanobacteria is not as convenient as in other model bacteria. Particularly, handling essential genes in cyanobacteria has been difficult due to the lack of appropriate tools, limiting our understanding of many important cellular functions encoded by them. We recently develop a CRISPR-based method for constructing the conditional mutants of cyanobacterial essential genes by engineering the ribosome binding site to a theophylline-responsive riboswitch. Here, we provide the details of this method. The principle of this method could be used to construct conditional mutants in a wide range of bacterial species.
Collapse
Affiliation(s)
- Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China.
| | - Tian-Cai Niu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Gui-Ming Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| |
Collapse
|
3
|
Taj A, Jia L, Sha S, Wang C, Ullah H, Haris M, Ma X, Ma Y. Functional analysis and enzyme characterization of Mannose-1-phosphate guanylyl transferase (ManB) from Mycobacterium tuberculosis. Res Microbiol 2021; 173:103884. [PMID: 34644596 DOI: 10.1016/j.resmic.2021.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Mycobacterium tuberculosis cell wall consist variety of mannose containing glycoconjugates including lipomannan (LM) and lipoarabinomannan (LAM). These lipoglycans are involved in cell wall integrity and play role in virulence of M. tuberculosis by modulating host immune response. GDP-mannose, required for the synthesis of lipoglycans, is catalyzed by enzyme Mannose-1-phosphate guanylyl transferase (ManB). The enzyme with similar function has been studied in variety of species of prokaryotes and eukaryotes. However, biological role of ManB and its enzymatic activity remains uncharacterized in M. tuberculosis. In present study, we elucidated the role of enzyme by constructing manB knockdown strain of M. tuberculosis H37Ra. The manB knockdown decreased the cell growth and also effected the morphology of M. tuberculosis by altering the permeability of cell membrane. These findings provide the understanding on ManB function and suggesting that ManB could be the potential target for novel anti-tuberculosis drug. Furthermore, we also characterized ManB enzyme by establishing 96 well plate colorimetric assay and determined the kinetic properties including initial velocity, optimum temperature, optimum pH and other kinetic parameters. Our established assay will be helpful for further high throughput screening of potential inhibitors against ManB.
Collapse
Affiliation(s)
- Ayaz Taj
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Liqiu Jia
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Chao Wang
- College of Pharmacy, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Hayan Ullah
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Muhammad Haris
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Xiaochi Ma
- College of Pharmacy, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China; Department of Microbiology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| |
Collapse
|