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Liu X, Cai F, Zhang Y, Luo X, Yuan L, Ma H, Yang M, Ge F. Interactome Analysis of ClpX Reveals Its Regulatory Role in Metabolism and Photosynthesis in Cyanobacteria. J Proteome Res 2024; 23:1174-1187. [PMID: 38427982 DOI: 10.1021/acs.jproteome.3c00610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Protein homeostasis is essential for cyanobacteria to maintain proper cellular function under adverse and fluctuating conditions. The AAA+ superfamily of proteolytic complexes in cyanobacteria plays a critical role in this process, including ClpXP, which comprises a hexameric ATPase ClpX and a tetradecameric peptidase ClpP. Despite the physiological effects of ClpX on growth and photosynthesis, its potential substrates and underlying mechanisms in cyanobacteria remain unknown. In this study, we employed a streptavidin-biotin affinity pull-down assay coupled with label-free proteome quantitation to analyze the interactome of ClpX in the model cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). We identified 503 proteins as potential ClpX-binding targets, many of which had novel interactions. These ClpX-binding targets were found to be involved in various biological processes, with particular enrichment in metabolic processes and photosynthesis. Using protein-protein docking, GST pull-down, and biolayer interferometry assays, we confirmed the direct association of ClpX with the photosynthetic proteins, ferredoxin-NADP+ oxidoreductase (FNR) and phycocyanin subunit (CpcA). Subsequent functional investigations revealed that ClpX participates in the maintenance of FNR homeostasis and functionality in Synechocystis grown under different light conditions. Overall, our study provides a comprehensive understanding of the extensive functions regulated by ClpX in cyanobacteria to maintain protein homeostasis and adapt to environmental challenges.
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Affiliation(s)
- Xin Liu
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China
| | - Fangfang Cai
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yumeng Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Department of Basic Research, Research-And-Development Center, Sinopharm Animal Health Corporation Ltd., Wuhan 430074, China
| | - Xuan Luo
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China
| | - Li Yuan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Haiyan Ma
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Bongirwar R, Shukla P. Metabolic sink engineering in cyanobacteria: Perspectives and applications. BIORESOURCE TECHNOLOGY 2023; 379:128974. [PMID: 36990331 DOI: 10.1016/j.biortech.2023.128974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 05/03/2023]
Abstract
Recent advances in metabolic engineering have made cyanobacteria emerge as promising and attractive microorganisms for sustainable production, by exploiting their natural capability for producing metabolites. The potential of metabolically engineered cyanobacterium would depend on its source-sink balance in the same way as other phototrophs. In cyanobacteria, the amount of light energy harvested (Source) is incompletely utilized by the cell to fix carbon (sink) resulting in wastage of the absorbed energy causing photoinhibition and cellular damage leading to lowered photosynthetic efficiency. Although regulatory pathways like photo-acclimation and photoprotective processes can be helpful unfortunately they limit the cell's metabolic capacity. This review describes approaches for source-sink balance and engineering heterologous metabolic sinks in cyanobacteria for enhanced photosynthetic efficiency. The advances for engineering additional metabolic pathways in cyanobacteria are also described which will provide a better understanding of the cyanobacterial source-sink balance and approaches for efficient cyanobacterial strains for valuable metabolites.
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Affiliation(s)
- Riya Bongirwar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India.
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Jaiswal D, Sahasrabuddhe D, Wangikar PP. Cyanobacteria as cell factories: the roles of host and pathway engineering and translational research. Curr Opin Biotechnol 2021; 73:314-322. [PMID: 34695729 DOI: 10.1016/j.copbio.2021.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/02/2021] [Accepted: 09/20/2021] [Indexed: 11/03/2022]
Abstract
Cyanobacteria, a group of photoautotrophic prokaryotes, are attractive hosts for the sustainable production of chemicals from carbon dioxide and sunlight. However, the rates, yields, and titers have remained well below those needed for commercial deployment. We argue that the following areas will be central to the development of cyanobacterial cell factories: engineered and well-characterized host strains, model-guided pathway design, and advanced synthetic biology tools. Although several foundational studies report improved strain properties, translational research will be needed to develop engineered hosts and deploy them for metabolic engineering. Further, the recent developments in metabolic modeling and synthetic biology of cyanobacteria will enable nimble strategies for strain improvement with the complete cycle of design, build, test, and learn.
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Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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Ciebiada M, Kubiak K, Daroch M. Modifying the Cyanobacterial Metabolism as a Key to Efficient Biopolymer Production in Photosynthetic Microorganisms. Int J Mol Sci 2020; 21:E7204. [PMID: 33003478 PMCID: PMC7582838 DOI: 10.3390/ijms21197204] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 12/22/2022] Open
Abstract
Cyanobacteria are photoautotrophic bacteria commonly found in the natural environment. Due to the ecological benefits associated with the assimilation of carbon dioxide from the atmosphere and utilization of light energy, they are attractive hosts in a growing number of biotechnological processes. Biopolymer production is arguably one of the most critical areas where the transition from fossil-derived chemistry to renewable chemistry is needed. Cyanobacteria can produce several polymeric compounds with high applicability such as glycogen, polyhydroxyalkanoates, or extracellular polymeric substances. These important biopolymers are synthesized using precursors derived from central carbon metabolism, including the tricarboxylic acid cycle. Due to their unique metabolic properties, i.e., light harvesting and carbon fixation, the molecular and genetic aspects of polymer biosynthesis and their relationship with central carbon metabolism are somehow different from those found in heterotrophic microorganisms. A greater understanding of the processes involved in cyanobacterial metabolism is still required to produce these molecules more efficiently. This review presents the current state of the art in the engineering of cyanobacterial metabolism for the efficient production of these biopolymers.
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Affiliation(s)
- Maciej Ciebiada
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Rd., Shenzhen 518055, China;
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 4/40 Stefanowskiego Str, 90-924 Lodz, Poland
| | - Katarzyna Kubiak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 4/40 Stefanowskiego Str, 90-924 Lodz, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Rd., Shenzhen 518055, China;
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Konert G, Steinbach G, Canonico M, Kaňa R. Protein arrangement factor: a new photosynthetic parameter characterizing the organization of thylakoid membrane proteins. PHYSIOLOGIA PLANTARUM 2019; 166:264-277. [PMID: 30817002 DOI: 10.1111/ppl.12952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 05/18/2023]
Abstract
A proper spatial distribution of photosynthetic pigment-protein complexes - PPCs (photosystems, light-harvesting antennas) is crucial for photosynthesis. In plants, photosystems I and II (PSI and PSII) are heterogeneously distributed between granal and stromal thylakoids. Here we have described similar heterogeneity in the PSI, PSII and phycobilisomes (PBSs) distribution in cyanobacteria thylakoids into microdomains by applying a new image processing method suitable for the Synechocystis sp. PCC6803 strain with yellow fluorescent protein-tagged PSI. The new image processing method is able to analyze the fluorescence ratios of PPCs on a single-cell level, pixel per pixel. Each cell pixel is plotted in CIE1931 color space by forming a pixel-color distribution of the cell. The most common position in CIE1931 is then defined as protein arrangement (PA) factor with xy coordinates. The PA-factor represents the most abundant fluorescence ratio of PSI/PSII/PBS, the 'mode color' of studied cell. We proved that a shift of the PA-factor from the center of the cell-pixel distribution (the 'median' cell color) is an indicator of the presence of special subcellular microdomain(s) with a unique PSI/PSII/PBS fluorescence ratio in comparison to other parts of the cell. Furthermore, during a 6-h high-light (HL) treatment, 'median' and 'mode' color (PA-factor) of the cell changed similarly on the population level, indicating that such microdomains with unique PSI/PSII/PBS fluorescence were not formed during HL (i.e. fluorescence changed equally in the whole cell). However, the PA-factor was very sensitive in characterizing the fluorescence ratios of PSI/PSII/PBS in cyanobacterial cells during HL by depicting a 4-phase acclimation to HL, and their physiological interpretation has been discussed.
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Affiliation(s)
- Grzegorz Konert
- Institute of Microbiology, CAS, Centrum Algatech, Třeboň, Czech Republic
| | - Gabor Steinbach
- Institute of Microbiology, CAS, Centrum Algatech, Třeboň, Czech Republic
| | - Myriam Canonico
- Institute of Microbiology, CAS, Centrum Algatech, Třeboň, Czech Republic
| | - Radek Kaňa
- Institute of Microbiology, CAS, Centrum Algatech, Třeboň, Czech Republic
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Abstract
As the transcriptional and post-transcriptional regulators of gene expression, small RNAs (sRNAs) play important roles in every domain of life in organisms. It has been discovered gradually that bacteria possess multiple means of gene regulation using RNAs. They have been continuously used as model organisms for photosynthesis, metabolism, biotechnology, evolution, and nitrogen fixation for many decades. Cyanobacteria, one of the most ancient life forms, constitute all kinds of photoautotrophic bacteria and exist in almost any environment on this planet. It is believed that a complex RNA-based regulatory mechanism functions in cyanobacteria to help them adapt to changes and stresses in diverse environments. Although lagging far behind other model microorganisms, such as yeast and Escherichia coli, more and more non-coding regulatory sRNAs have been recognized in cyanobacteria during the past decades. In this article, by focusing on cyanobacterial sRNAs, the approaches for detection and targeting of sRNAs will be summarized, four major mechanisms and regulatory functions will be generalized, eight types of cis-encoded sRNA and four types of trans-encoded sRNAs will be reviewed in detail, and their possible physiological functions will be further discussed.
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Affiliation(s)
- Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Qiang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, China.,University of the Chinese Academy of Sciences, Beijing, China
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