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Ye C, Hong H, Gao J, Li M, Gou Y, Gao D, Dong C, Huang L, Xu Z, Lian J. Characterization and engineering of peroxisome targeting sequences for compartmentalization engineering in Pichia pastoris. Biotechnol Bioeng 2024. [PMID: 38568751 DOI: 10.1002/bit.28706] [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: 12/27/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Peroxisomal compartmentalization has emerged as a highly promising strategy for reconstituting intricate metabolic pathways. In recent years, significant progress has been made in the peroxisomes through harnessing precursor pools, circumventing metabolic crosstalk, and minimizing the cytotoxicity of exogenous pathways. However, it is important to note that in methylotrophic yeasts (e.g. Pichia pastoris), the abundance and protein composition of peroxisomes are highly variable, particularly when peroxisome proliferation is induced by specific carbon sources. The intricate subcellular localization of native proteins, the variability of peroxisomal metabolic pathways, and the lack of systematic characterization of peroxisome targeting signals have limited the applications of peroxisomal compartmentalization in P. pastoris. Accordingly, this study established a high-throughput screening method based on β-carotene biosynthetic pathway to evaluate the targeting efficiency of PTS1s (Peroxisome Targeting Signal Type 1) in P. pastoris. First, 25 putative endogenous PTS1s were characterized and 3 PTS1s with high targeting efficiency were identified. Then, directed evolution of PTS1s was performed by constructing two PTS1 mutant libraries, and a total of 51 PTS1s (29 classical and 22 noncanonical PTS1s) with presumably higher peroxisomal targeting efficiency were identified, part of which were further characterized via confocal microscope. Finally, the newly identified PTS1s were employed for peroxisomal compartmentalization of the geraniol biosynthetic pathway, resulting in more than 30% increase in the titer of monoterpene compared with when the pathway was localized to the cytosol. The present study expands the synthetic biology toolkit and lays a solid foundation for peroxisomal compartmentalization in P. pastoris.
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Affiliation(s)
- Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Haosen Hong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
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Deng Q, Li H, Feng Y, Xu R, Li W, Zhu R, Akhter D, Shen X, Hu J, Jiang H, Pan R. Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large-scale in silico and in vivo analyses. Plant J 2022; 111:567-582. [PMID: 35603488 PMCID: PMC9542071 DOI: 10.1111/tpj.15840] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/01/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes are universal eukaryotic organelles essential to plants and animals. Most peroxisomal matrix proteins carry peroxisome targeting signal type 1 (PTS1), a C-terminal tripeptide. Studies from various kingdoms have revealed influences from sequence upstream of the tripeptide on peroxisome targeting, supporting the view that positive charges in the upstream region are the major enhancing elements. However, a systematic approach to better define the upstream elements influencing PTS1 targeting capability is needed. Here, we used protein sequences from 177 plant genomes to perform large-scale and in-depth analysis of the PTS1 domain, which includes the PTS1 tripeptide and upstream sequence elements. We identified and verified 12 low-frequency PTS1 tripeptides and revealed upstream enhancing and inhibiting sequence patterns for peroxisome targeting, which were subsequently validated in vivo. Follow-up analysis revealed that nonpolar and acidic residues have relatively strong enhancing and inhibiting effects, respectively, on peroxisome targeting. However, in contrast to the previous understanding, positive charges alone do not show the anticipated enhancing effect and that both the position and property of the residues within these patterns are important for peroxisome targeting. We further demonstrated that the three residues immediately upstream of the tripeptide are the core influencers, with a 'basic-nonpolar-basic' pattern serving as a strong and universal enhancing pattern for peroxisome targeting. These findings have significantly advanced our knowledge of the PTS1 domain in plants and likely other eukaryotic species as well. The principles and strategies employed in the present study may also be applied to deciphering auxiliary targeting signals for other organelles.
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Affiliation(s)
- Qianwen Deng
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
| | - He Li
- Center for Data ScienceZhejiang UniversityHangzhou310058China
| | - Yanlei Feng
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
| | - Ruonan Xu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Weiran Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Rui Zhu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Delara Akhter
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- Department of Genetics and Plant BreedingSylhet Agricultural UniversitySylhet3100Bangladesh
| | - Xingxing Shen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology DepartmentMichigan State UniversityEast LansingMichigan48824USA
| | - Hangjin Jiang
- Center for Data ScienceZhejiang UniversityHangzhou310058China
| | - Ronghui Pan
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
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