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Takeshita D. Protein expression and purification, molecular interaction, and X-ray crystallographic analysis of baculovirus protein PK2. Protein Expr Purif 2023; 202:106188. [PMID: 36229000 DOI: 10.1016/j.pep.2022.106188] [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: 07/04/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
Abstract
Phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α) by eIF2α kinases is a common mechanism to regulate the initiation of translation under stress conditions. The PK2 protein from baculovirus Autographica californica multiple nucleopolyhedrovirus (AcMNPV) binds and inhibits eIF2α kinases to ensure efficient virus propagation. The C-terminal region of PK2 shares a homology with the C-lobe of eIF2α kinases, but the N-terminal region of PK2 is unique to the orthologous proteins. In order to understand the detailed structure and function of PK2, both the full-length PK2 and its N-terminal truncated protein (PK2Δ22) were expressed as a His-tag fusion protein in Escherichia coli and purified by three steps of chromatography. Notably, the cysteine mutant, PK2 C181S/C211S, promotes the solubility and stability of the PK2 protein. The results of the size-exclusion chromatography showed that the full-length PK2 exists in both multimeric and monomeric forms, and the molecular interaction of PK2 and the eIF2α kinase domain. The purified proteins were used further to screen various conditions to obtain these crystals. Crystals of the full-length PK2 and PK2Δ22 were obtained by a sitting-drop vapour-diffusion method using lithium sulfate and PEG3350 as the precipitant, respectively. The crystal of PK2 belonged to space group P41212, and diffracted X-rays to 2.7 Å resolution. The asymmetric unit contained four molecules of the protein, and the solvent content was 67.4%. Whereas, the crystal of the PK2Δ22 belonged to space group P212121, diffracted X-rays to 2.8 Å resolution. The asymmetric unit contained three molecules of the protein, and the solvent content was 48.1%. The crystallographic study of the PK2 protein will provide mechanistic insights into the inhibition of eIF2α kinase by the PK2 protein, and also pave the way for the improvement of the baculovirus-based protein expression system.
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Affiliation(s)
- Daijiro Takeshita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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Advances in Komagataella phaffii Engineering for the Production of Renewable Chemicals and Proteins. FERMENTATION 2022. [DOI: 10.3390/fermentation8110575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast Komagataella phaffii has been extensively used in the production of heterologous proteins. More recently, it has been explored as a host organism to produce various chemicals through new metabolic engineering and synthetic biology tools. This review first summarizes Komagataella taxonomy and diversity and then highlights the recent approaches in cell engineering to produce renewable chemicals and proteins. Finally, strategies to optimize and develop new fermentative processes using K. phaffii as a cell factory are presented and discussed. The yeast K. phaffii shows an outstanding performance for renewable chemicals and protein production due to its ability to metabolize different carbon sources and the availability of engineering tools. Indeed, it has been employed in producing alcohols, carboxylic acids, proteins, and other compounds using different carbon sources, including glycerol, glucose, xylose, methanol, and even CO2.
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Kojima K, Sunagawa N, Mikkelsen NE, Hansson H, Karkehabadi S, Samejima M, Sandgren M, Igarashi K. Comparison of Glycoside Hydrolase family 3 β-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems. J Biol Chem 2022; 298:101670. [PMID: 35120929 PMCID: PMC8913315 DOI: 10.1016/j.jbc.2022.101670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Xylan is the most common hemicellulose in plant cell walls, though the structure of xylan polymers differs between plant species. Here, to gain a better understanding of fungal xylan degradation systems, which can enhance enzymatic saccharification of plant cell walls in industrial processes, we conducted a comparative study of two glycoside hydrolase family 3 (GH3) β-xylosidases (Bxls), one from the basidiomycete Phanerochaete chrysosporium (PcBxl3), and the other from the ascomycete Trichoderma reesei (TrXyl3A). A comparison of the crystal structures of the two enzymes, both with saccharide bound at the catalytic center, provided insight into the basis of substrate binding at each subsite. PcBxl3 has a substrate-binding pocket at subsite -1, while TrXyl3A has an extra loop that contains additional binding subsites. Furthermore, kinetic experiments revealed that PcBxl3 degraded xylooligosaccharides faster than TrXyl3A, while the KM values of TrXyl3A were lower than those of PcBxl3. The relationship between substrate specificity and degree of polymerization of substrates suggested that PcBxl3 preferentially degrades xylobiose (X2), while TrXyl3A degrades longer xylooligosaccharides. Moreover, docking simulation supported the existence of extended positive subsites of TrXyl3A in the extra loop located at the N-terminus of the protein. Finally, phylogenetic analysis suggests that wood-decaying basidiomycetes use Bxls such as PcBxl3 that act efficiently on xylan structures from woody plants, whereas molds use instead Bxls that efficiently degrade xylan from grass. Our results provide added insights into fungal efficient xylan degradation systems.
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Affiliation(s)
- Keisuke Kojima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano 380-8533, Japan
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; VTT Technical Research Centre of Finland, PO Box 1000, Tietotie 2, Espoo FI-02044 VTT, Finland.
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Demura T. Preface to the special issue "Approaches for strategies of mechanical optimization in plants". PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:393-395. [PMID: 33850425 PMCID: PMC8034703 DOI: 10.5511/plantbiotechnology.20.0001p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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