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Zhang J, Sun T, Zhang W, Chen L. Identification of acidic stress-responsive genes and acid tolerance engineering in Synechococcus elongatus PCC 7942. Appl Microbiol Biotechnol 2024; 108:115. [PMID: 38204133 PMCID: PMC10781874 DOI: 10.1007/s00253-023-12984-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Cyanobacteria are excellent autotrophic photosynthetic chassis employed in synthetic biology, and previous studies have suggested that they have alkaline tolerance but low acid tolerance, significantly limiting their productivity as photosynthetic chassis and necessitating investigations into the acid stress resistance mechanism. In this study, differentially expressed genes were obtained by RNA sequencing-based comparative transcriptomic analysis under long-term acidic stress conditions and acidic shock treatment, in the model cyanobacterium Synechococcus elongatus PCC 7942. A pathway enrichment analysis revealed the upregulated and downregulated pathways during long-term acidic and shock stress treatment. The subsequent single gene knockout and phenotype analysis showed that under acidic stress conditions, the strains with chlL, chlN, pex, synpcc7942_2038, synpcc7942_1890, or synpcc7942_2547 knocked out grew worse than the wild type, suggesting their involvement in acid tolerance. This finding was further confirmed by introducing the corresponding genes back into the knockout mutant individually. Moreover, individual overexpression of the chlL and chlN genes in the wild type successfully improved the tolerance of S. elongatus PCC 7942 to acidic stress. This work successfully identified six genes involved in acidic stress responses, and overexpressing chIL or chIN individually successfully improved acid tolerance in S. elongatus PCC 7942, providing valuable information to better understand the acid resistance mechanism in S. elongatus PCC 7942 and novel insights into the robustness and tolerance engineering of cyanobacterial chassis. KEY POINTS: • DEGs were identified by RNA-seq based transcriptomics analysis in response to acidic stress in S. elongatus PCC 7942. • Six genes were identified to be involved in acid tolerance in S. elongatus PCC 7942. • Overexpression of chIL or chIN individually successfully improved the acid tolerance of S. elongatus PCC 7942.
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Affiliation(s)
- Jie Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China.
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2
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Daakour S, Nelson DR, Fu W, Jaiswal A, Dohai B, Alzahmi AS, Koussa J, Huang X, Shen Y, Twizere JC, Salehi-Ashtiani K. Adaptive Evolution Signatures in Prochlorococcus: Open Reading Frame (ORF)eome Resources and Insights from Comparative Genomics. Microorganisms 2024; 12:1720. [PMID: 39203562 PMCID: PMC11357015 DOI: 10.3390/microorganisms12081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology.
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Affiliation(s)
- Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - David R. Nelson
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Weiqi Fu
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Ashish Jaiswal
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Bushra Dohai
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Helmholtz Center Munich, Institute of Network Biology (INET), German Research Center for Environmental Health, 85764 Munich, Germany
| | - Amnah Salem Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Joseph Koussa
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Biology, New York University, New York, NY 10012, USA
- Department of Chemical and Biological Sciences, Montgomery College, Germantown, MD 20850, USA
| | - Xiaoluo Huang
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Beijing 100045, China
| | - Yue Shen
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
| | - Jean-Claude Twizere
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
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Grettenberger CL, Abou‐Shanab R, Hamilton TL. Limiting factors in the operation of photosystems I and II in cyanobacteria. Microb Biotechnol 2024; 17:e14519. [PMID: 39101352 PMCID: PMC11298993 DOI: 10.1111/1751-7915.14519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/16/2024] [Indexed: 08/06/2024] Open
Abstract
Cyanobacteria are important targets for biotechnological applications due to their ability to grow in a wide variety of environments, rapid growth rates, and tractable genetic systems. They and their bioproducts can be used as bioplastics, biofertilizers, and in carbon capture and produce important secondary metabolites that can be used as pharmaceuticals. However, the photosynthetic process in cyanobacteria can be limited by a wide variety of environmental factors such as light intensity and wavelength, exposure to UV light, nutrient limitation, temperature, and salinity. Carefully considering these limitations, modifying the environment, and/or selecting cyanobacterial species will allow cyanobacteria to be used in biotechnological applications.
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Affiliation(s)
- Christen L. Grettenberger
- Department of Earth and Planetary SciencesUniversity of California DavisDavisCaliforniaUSA
- Department of Environmental ToxicologyUniversity of California DavisDavisCaliforniaUSA
| | - Reda Abou‐Shanab
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Trinity L. Hamilton
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
- The Biotechnology Institute, University of MinnesotaSt. PaulMinnesotaUSA
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4
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Krynická V, Komenda J. The Role of FtsH Complexes in the Response to Abiotic Stress in Cyanobacteria. PLANT & CELL PHYSIOLOGY 2024; 65:1103-1114. [PMID: 38619128 PMCID: PMC11287208 DOI: 10.1093/pcp/pcae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/24/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
FtsH proteases (FtsHs) belong to intramembrane ATP-dependent metalloproteases which are widely distributed in eubacteria, mitochondria and chloroplasts. The best-studied roles of FtsH in Escherichia coli include quality control of membrane proteins, regulation of response to heat shock, superoxide stress and viral infection, and control of lipopolysaccharide biosynthesis. While heterotrophic bacteria mostly contain a single indispensable FtsH complex, photosynthetic cyanobacteria usually contain three FtsH complexes: two heterocomplexes and one homocomplex. The essential cytoplasmic FtsH1/3 most probably fulfills a role similar to other bacterial FtsHs, whereas the thylakoid FtsH2/3 heterocomplex and FtsH4 homocomplex appear to maintain the photosynthetic apparatus of cyanobacteria and optimize its functionality. Moreover, recent studies suggest the involvement of all FtsH proteases in a complex response to nutrient stresses. In this review, we aim to comprehensively evaluate the functions of the cyanobacterial FtsHs specifically under stress conditions with emphasis on nutrient deficiency and high irradiance. We also point to various unresolved issues concerning FtsH functions, which deserve further attention.
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Affiliation(s)
- Vendula Krynická
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický Mlýn, Novohradská 237, Třeboň 37901, The Czech Republic
| | - Josef Komenda
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický Mlýn, Novohradská 237, Třeboň 37901, The Czech Republic
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Santin A, Collura F, Singh G, Morlino MS, Bizzotto E, Bellan A, Gupte AP, Favaro L, Campanaro S, Treu L, Morosinotto T. Deciphering the genetic landscape of enhanced poly-3-hydroxybutyrate production in Synechocystis sp. B12. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:101. [PMID: 39014484 PMCID: PMC11253406 DOI: 10.1186/s13068-024-02548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Microbial biopolymers such as poly-3-hydroxybutyrate (PHB) are emerging as promising alternatives for sustainable production of biodegradable bioplastics. Their promise is heightened by the potential utilisation of photosynthetic organisms, thus exploiting sunlight and carbon dioxide as source of energy and carbon, respectively. The cyanobacterium Synechocystis sp. B12 is an attractive candidate for its superior ability to accumulate high amounts of PHB as well as for its high-light tolerance, which makes it extremely suitable for large-scale cultivation. Beyond its practical applications, B12 serves as an intriguing model for unravelling the molecular mechanisms behind PHB accumulation. RESULTS Through a multifaceted approach, integrating physiological, genomic and transcriptomic analyses, this work identified genes involved in the upregulation of chlorophyll biosynthesis and phycobilisome degradation as the possible candidates providing Synechocystis sp. B12 an advantage in growth under high-light conditions. Gene expression differences in pentose phosphate pathway and acetyl-CoA metabolism were instead recognised as mainly responsible for the increased Synechocystis sp. B12 PHB production during nitrogen starvation. In both response to strong illumination and PHB accumulation, Synechocystis sp. B12 showed a metabolic modulation similar but more pronounced than the reference strain, yielding in better performances. CONCLUSIONS Our findings shed light on the molecular mechanisms of PHB biosynthesis, providing valuable insights for optimising the use of Synechocystis in economically viable and sustainable PHB production. In addition, this work supplies crucial knowledge about the metabolic processes involved in production and accumulation of these molecules, which can be seminal for the application to other microorganisms as well.
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Grants
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- Ministero dell’Istruzione, dell’Università e della Ricerca
- Università degli Studi di Padova
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Affiliation(s)
- Anna Santin
- Department of Biology, University of Padova, 35131, Padua, Italy.
| | - Flavio Collura
- Department of Biology, University of Padova, 35131, Padua, Italy
| | - Garima Singh
- Department of Biology, University of Padova, 35131, Padua, Italy
| | | | - Edoardo Bizzotto
- Department of Biology, University of Padova, 35131, Padua, Italy
| | | | - Ameya Pankaj Gupte
- Waste to Bioproducts Lab, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova - Agripolis, 35020, Legnaro, PD, Italy
| | - Lorenzo Favaro
- Waste to Bioproducts Lab, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova - Agripolis, 35020, Legnaro, PD, Italy
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | | | - Laura Treu
- Department of Biology, University of Padova, 35131, Padua, Italy
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Akhtar P, Jana S, Lambrev PH, Tan HS. Inhomogeneous energy transfer dynamics from iron-stress-induced protein A to photosystem I. FRONTIERS IN PLANT SCIENCE 2024; 15:1393886. [PMID: 38817933 PMCID: PMC11137255 DOI: 10.3389/fpls.2024.1393886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
Cyanobacteria respond to iron limitation by producing the pigment-protein complex IsiA, forming rings associated with photosystem I (PSI). Initially considered a chlorophyll-storage protein, IsiA is known to act as an auxiliary light-harvesting antenna of PSI, increasing its absorption cross-section and reducing the need for iron-rich PSI core complexes. Spectroscopic studies have demonstrated efficient energy transfer from IsiA to PSI. Here we investigate the room-temperature excitation dynamics in isolated PSI-IsiA, PSI, IsiA monomer complexes and IsiA aggregates using two-dimensional electronic spectroscopy. Cross analyses of the data from these three samples allow us to resolve components of energy transfer between IsiA and PSI with lifetimes of 2-3 ps and around 20 ps. Structure-based Förster theory calculations predict a single major timescale of IsiA-PSI equilibration, that depends on multiple energy transfer routes between different IsiA subunits in the ring. Despite the experimentally observed lifetime heterogeneity, which is attributed to structural heterogeneity of the supercomplexes, IsiA is found to be a unique, highly efficient, membrane antenna complex in cyanobacteria.
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Affiliation(s)
- Parveen Akhtar
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Sanjib Jana
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore
| | - Petar H. Lambrev
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Howe-Siang Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore
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Usai G, Cordara A, Mazzocchi E, Re A, Fino D, Pirri CF, Menin B. Coupling dairy wastewaters for nutritional balancing and water recycling: sustainable heterologous 2-phenylethanol production by engineered cyanobacteria. Front Bioeng Biotechnol 2024; 12:1359032. [PMID: 38497052 PMCID: PMC10940361 DOI: 10.3389/fbioe.2024.1359032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Microalgae biotechnology is hampered by the high production costs and the massive usage of water during large-volume cultivations. These drawbacks can be softened by the production of high-value compounds and by adopting metabolic engineering strategies to improve their performances and productivity. Today, the most sustainable approach is the exploitation of industrial wastewaters for microalgae cultivation, which couples valuable biomass production with water resource recovery. Among the food processing sectors, the dairy industry generates the largest volume of wastewaters through the manufacturing process. These effluents are typically rich in dissolved organic matter and nutrients, which make it a challenging and expensive waste stream for companies to manage. Nevertheless, these rich wastewaters represent an appealing resource for microalgal biotechnology. In this study, we propose a sustainable approach for high-value compound production from dairy wastewaters through cyanobacteria. This strategy is based on a metabolically engineered strain of the model cyanobacterium Synechococcus elongatus PCC 7942 (already published elsewhere) for 2-phenylethanol (2-PE). 2-PE is a high-value aromatic compound that is widely employed as a fragrance in the food and cosmetics industry thanks to its pleasant floral scent. First, we qualitatively assessed the impact of four dairy effluents on cyanobacterial growth to identify the most promising substrates. Both tank-washing water and the liquid effluent of exhausted sludge resulted as suitable nutrient sources. Thus, we created an ideal buffer system by combining the two wastewaters while simultaneously providing balanced nutrition and completely avoiding the need for fresh water. The combination of 75% liquid effluent of exhausted sludge and 25% tank-washing water with a fine-tuning ammonium supplementation yielded 180 mg L-1 of 2-PE and a biomass concentration of 0.6 gDW L-1 within 10 days. The mixture of 90% exhausted sludge and 10% washing water produced the highest yield of 2-PE (205 mg L-1) and biomass accumulation (0.7 gDW L-1), although in 16 days. Through these treatments, the phosphates were completely consumed, and nitrogen was removed in a range of 74%-77%. Overall, our approach significantly valorized water recycling and the exploitation of valuable wastewaters to circularly produce marketable compounds via microalgae biotechnology, laying a promising groundwork for subsequent implementation and scale-up.
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Affiliation(s)
- Giulia Usai
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Alessandro Cordara
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Environment, Land and Infrastructure Engineering—DIATI, Politecnico di Torino, Turin, Italy
| | - Elena Mazzocchi
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Angela Re
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Debora Fino
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA-CNR, Milan, Italy
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Akhtar P, Balog-Vig F, Kuntam S, Tóth SZ, Lambrev PH. Function of iron-stress-induced protein A in cyanobacterial cells with monomeric and trimeric photosystem I. PLANT PHYSIOLOGY 2024; 194:1397-1410. [PMID: 37850879 DOI: 10.1093/plphys/kiad562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/12/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023]
Abstract
The acclimation of cyanobacteria to iron deficiency is crucial for their survival in natural environments. In response to iron deficiency, many cyanobacterial species induce the production of a pigment-protein complex called iron-stress-induced protein A (IsiA). IsiA proteins associate with photosystem I (PSI) and can function as light-harvesting antennas or dissipate excess energy. They may also serve as chlorophyll storage during iron limitation. In this study, we examined the functional role of IsiA in cells of Synechocystis sp. PCC 6803 grown under iron limitation conditions by measuring the cellular IsiA content and its capability to transfer energy to PSI. We specifically tested the effect of the oligomeric state of PSI by comparing wild-type (WT) Synechocystis sp. PCC 6803 with mutants lacking specific subunits of PSI, namely PsaL/PsaI (PSI subunits XI/VIII) and PsaF/PsaJ (PSI subunits III/IX). Time-resolved fluorescence spectroscopy revealed that IsiA formed functional PSI3-IsiA18 supercomplexes, wherein IsiA effectively transfers energy to PSI on a timescale of 10 ps at room temperature-measured in isolated complexes and in vivo-confirming the primary role of IsiA as an accessory light-harvesting antenna to PSI. However, a notable fraction (40%) remained unconnected to PSI, supporting the notion of a dual functional role of IsiA. Cells with monomeric PSI under iron deficiency contained, on average, only 3 to 4 IsiA complexes bound to PSI. These results show that IsiA can transfer energy to trimeric and monomeric PSI but to varying degrees and that the acclimatory production of IsiA under iron stress is controlled by its ability to perform its light-harvesting function.
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Affiliation(s)
- Parveen Akhtar
- HUN-REN Biological Research Centre, Szeged, Institute of Plant Biology, Temesvári krt. 62, Szeged 6726, Hungary
| | - Fanny Balog-Vig
- HUN-REN Biological Research Centre, Szeged, Institute of Plant Biology, Temesvári krt. 62, Szeged 6726, Hungary
| | - Soujanya Kuntam
- HUN-REN Biological Research Centre, Szeged, Institute of Plant Biology, Temesvári krt. 62, Szeged 6726, Hungary
| | - Szilvia Z Tóth
- HUN-REN Biological Research Centre, Szeged, Institute of Plant Biology, Temesvári krt. 62, Szeged 6726, Hungary
| | - Petar H Lambrev
- HUN-REN Biological Research Centre, Szeged, Institute of Plant Biology, Temesvári krt. 62, Szeged 6726, Hungary
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Koník P, Skotnicová P, Gupta S, Tichý M, Sharma S, Komenda J, Sobotka R, Krynická V. The cyanobacterial FtsH4 protease controls accumulation of protein factors involved in the biogenesis of photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149017. [PMID: 37827327 DOI: 10.1016/j.bbabio.2023.149017] [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: 05/30/2023] [Revised: 09/18/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Membrane-bound FtsH proteases are universally present in prokaryotes and in mitochondria and chloroplasts of eukaryotic cells. These metalloproteases are often critical for viability and play both protease and chaperone roles to maintain cellular homeostasis. In contrast to most bacteria bearing a single ftsH gene, cyanobacteria typically possess four FtsH proteases (FtsH1-4) forming heteromeric (FtsH1/3 and FtsH2/3) and homomeric (FtsH4) complexes. The functions and substrate repertoire of each complex are however poorly understood. To identify substrates of the FtsH4 protease complex we established a trapping assay in the cyanobacterium Synechocystis PCC 6803 utilizing a proteolytically inactivated trapFtsH4-His. Around 40 proteins were specifically enriched in trapFtsH4 pulldown when compared with the active FtsH4. As the list of putative FtsH4 substrates contained Ycf4 and Ycf37 assembly factors of Photosystem I (PSI), its core PsaB subunit and the IsiA chlorophyll-binding protein that associates with PSI during iron stress, we focused on these PSI-related proteins. Therefore, we analysed their degradation by FtsH4 in vivo in Synechocystis mutants and in vitro using purified substrates. The data confirmed that FtsH4 degrades Ycf4, Ycf37, IsiA, and also the individual PsaA and PsaB subunits in the unassembled state but not when assembled within the PSI complexes. A possible role of FtsH4 in the PSI life-cycle is discussed.
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Affiliation(s)
- Peter Koník
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Petra Skotnicová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic
| | - Sadanand Gupta
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Martin Tichý
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic
| | - Surbhi Sharma
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Josef Komenda
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Vendula Krynická
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic.
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10
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Nagao R, Kato K, Hamaguchi T, Ueno Y, Tsuboshita N, Shimizu S, Furutani M, Ehira S, Nakajima Y, Kawakami K, Suzuki T, Dohmae N, Akimoto S, Yonekura K, Shen JR. Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120. Nat Commun 2023; 14:920. [PMID: 36805598 PMCID: PMC9938196 DOI: 10.1038/s41467-023-36504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.
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Affiliation(s)
- Ryo Nagao
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan. .,Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
| | - Koji Kato
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.,Structural Biology Division, Japan Synchrotron Radiation Research Institute (JASRI), Hyogo, 679-5198, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
| | - Yoshifumi Ueno
- Graduate School of Science, Kobe University, Hyogo, 657-8501, Japan.,Institute of Arts and Science, Tokyo University of Science, Tokyo, 162-8601, Japan
| | - Naoki Tsuboshita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shota Shimizu
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Miyu Furutani
- Graduate School of Science, Kobe University, Hyogo, 657-8501, Japan
| | - Shigeki Ehira
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan
| | - Seiji Akimoto
- Graduate School of Science, Kobe University, Hyogo, 657-8501, Japan.
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan. .,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan. .,Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, Hyogo, 679-5148, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
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11
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Zhao LS, Li CY, Chen XL, Wang Q, Zhang YZ, Liu LN. Native architecture and acclimation of photosynthetic membranes in a fast-growing cyanobacterium. PLANT PHYSIOLOGY 2022; 190:1883-1895. [PMID: 35947692 PMCID: PMC9614513 DOI: 10.1093/plphys/kiac372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Efficient solar energy conversion is ensured by the organization, physical association, and physiological coordination of various protein complexes in photosynthetic membranes. Here, we visualize the native architecture and interactions of photosynthetic complexes within the thylakoid membranes from a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) using high-resolution atomic force microscopy. In the Syn2973 thylakoid membranes, both photosystem I (PSI)-enriched domains and crystalline photosystem II (PSII) dimer arrays were observed, providing favorable membrane environments for photosynthetic electron transport. The high light (HL)-adapted thylakoid membranes accommodated a large amount of PSI complexes, without the incorporation of iron-stress-induced protein A (IsiA) assemblies and formation of IsiA-PSI supercomplexes. In the iron deficiency (Fe-)-treated thylakoid membranes, in contrast, IsiA proteins densely associated with PSI, forming the IsiA-PSI supercomplexes with varying assembly structures. Moreover, type-I NADH dehydrogenase-like complexes (NDH-1) were upregulated under the HL and Fe- conditions and established close association with PSI complexes to facilitate cyclic electron transport. Our study provides insight into the structural heterogeneity and plasticity of the photosynthetic apparatus in the context of their native membranes in Syn2973 under environmental stress. Advanced understanding of the photosynthetic membrane organization and adaptation will provide a framework for uncovering the molecular mechanisms of efficient light harvesting and energy conversion.
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Affiliation(s)
| | - Chun-Yang Li
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, 475004 Kaifeng, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, and Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lu-Ning Liu
- Author of correspondence: (L.-N.L.), (L.-S.Z.)
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12
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Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa. Nat Commun 2022; 13:1679. [PMID: 35354806 PMCID: PMC8967866 DOI: 10.1038/s41467-022-29303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/24/2022] [Indexed: 11/08/2022] Open
Abstract
Photosystem I (PSI) is one of the two photosystems functioning in light-energy harvesting, transfer, and electron transfer in photosynthesis. However, the oligomerization state of PSI is variable among photosynthetic organisms. We present a 3.8-Å resolution cryo-electron microscopic structure of tetrameric PSI isolated from the glaucophyte alga Cyanophora paradoxa, which reveals differences with PSI from other organisms in subunit composition and organization. The PSI tetramer is organized in a dimer of dimers with a C2 symmetry. Unlike cyanobacterial PSI tetramers, two of the four monomers are rotated around 90°, resulting in a completely different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and excitation-energy transfer in the Cyanophora PSI tetramer, suggesting that the Cyanophora PSI could represent a turning point in the evolution of PSI from prokaryotes to eukaryotes.
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