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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cardoso ACS, Azevedo RS, Brum RJ, Santos LO, Marins LF. Optimization of Recombinant Protein Production in Synechococcus elongatus PCC 7942: Utilizing Native Promoters and Magnetic Fields. Curr Microbiol 2024; 81:143. [PMID: 38627283 DOI: 10.1007/s00284-024-03672-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024]
Abstract
The cyanobacterium Synechococcus elongatus PCC 7942 holds significant potential as a biofactory for recombinant protein (RP) production due to its capacity to harness light energy and utilize CO2. This study aimed to enhance RP production by integration of native promoters and magnetic field application (MF) in S. elongatus PCC 7942. The psbA2 promoter, which responds to stress conditions, was chosen for the integration of the ZsGreen1 gene. Results indicated successful gene integration, affirming prior studies that showed no growth alterations in transgenic strains. Interestingly, exposure to 30 mT (MF30) demonstrated a increase in ZsGreen1 transcription under the psbA2 promoter, revealing the influence of MF on cyanobacterial photosynthetic machinery. This enhancement is likely attributed to stress-induced shifts in gene expression and enzyme activity. MF30 positively impacted photosystem II (PSII) without disrupting the electron transport chain, aligning with the "quantum-mechanical mechanism" theory. Notably, fluorescence levels and gene expression with application of 30 mT were significantly different from control conditions. This study showcases the efficacy of utilizing native promoters and MF for enhancing RP production in S. elongatus PCC 7942. Native promoters eliminate the need for costly exogenous inducers and potential cell stress. Moreover, the study expands the scope of optimizing RP production in photoautotrophic microorganisms, providing valuable insights for biotechnological applications.
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Affiliation(s)
- Arthur C S Cardoso
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande (FURG), Av. Italia Km 8, Rio Grande, RS, CEP 96203-900, Brazil
| | - Raíza S Azevedo
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande (FURG), Av. Italia Km 8, Rio Grande, RS, CEP 96203-900, Brazil
| | - Rayanne J Brum
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande (FURG), Av. Italia Km 8, Rio Grande, RS, CEP 96203-900, Brazil
| | - Lucielen O Santos
- Laboratory of Biotechnology, School of Chemistry and Food, Federal University of Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Luis F Marins
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande (FURG), Av. Italia Km 8, Rio Grande, RS, CEP 96203-900, Brazil.
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Toda N, Inoue-Kashino N, Fujita H, Yoshida R, Nimura-Matsune K, Watanabe S, Kuroda A, Kashino Y, Hirota R. Cell morphology engineering enhances grazing resistance of Synechococcus elongatus PCC 7942 for non-sterile large-scale cultivation. J Biosci Bioeng 2024; 137:245-253. [PMID: 38336581 DOI: 10.1016/j.jbiosc.2024.01.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
In the practical scale of cyanobacterial cultivation, the golden algae Poterioochromonas malhamensis is a well-known predator that causes devastating damage to the culture, referred to as pond crash. The establishment and maintenance of monoculture conditions are ideal for large-scale cultures. However, this is a difficult challenge because microbial contamination is unavoidable in practical-scale culture facilities. In the present study, we unexpectedly observed the pond crash phenomenon during the pilot-scale cultivation of Synechococcus elongatus PCC 7942 using a 100-L photobioreactor. This was due to the contamination with P. malhamensis, which probably originated from residual fouling. Interestingly, we found that S.elongatus PCC 7942 can alter its morphological structure when subjected to continuous grazing pressure from predators, resulting in cells that were more than 100 times longer than those of the wild-type strain. These hyper-elongated S.elongatus PCC 7942 cells had mutations in the genes encoding FtsZ or Ftn2 which are involved in bacterial cell division. Importantly, the elongated phenotype remained stable during cultivation, enabling S.elongatus PCC 7942 to thrive and resist grazing. The cultivation of the elongated S.elongatus PCC 7942 mutant strain in a 100-L pilot-scale photobioreactor under non-sterile conditions resulted in increased cyanobacterial biomass without encountering pond crash. This study demonstrates an efficient strategy for cyanobacterial cell culture in practical-scale bioreactors without the need for extensive decontamination or sterilization of the growth medium and culture facility, which can contribute to economically viable cultivation and bioprocessing of microalgae.
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Affiliation(s)
- Narumi Toda
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Natsuko Inoue-Kashino
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako-gun, Hyogo, 678-1297, Japan
| | - Hazaya Fujita
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako-gun, Hyogo, 678-1297, Japan
| | - Ryosuke Yoshida
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kaori Nimura-Matsune
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, 2445 Mukaishima-cho, Onomichi, Hiroshima 722-0073, Japan
| | - Yasuhiro Kashino
- Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako-gun, Hyogo, 678-1297, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Division of Biological and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, 2445 Mukaishima-cho, Onomichi, Hiroshima 722-0073, Japan.
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Vincent M, Blanc-Garin V, Chenebault C, Cirimele M, Farci S, Garcia-Alles LF, Cassier-Chauvat C, Chauvat F. Impact of Carbon Fixation, Distribution and Storage on the Production of Farnesene and Limonene in Synechocystis PCC 6803 and Synechococcus PCC 7002. Int J Mol Sci 2024; 25:3827. [PMID: 38612633 PMCID: PMC11012175 DOI: 10.3390/ijms25073827] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/04/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Terpenes are high-value chemicals which can be produced by engineered cyanobacteria from sustainable resources, solar energy, water and CO2. We previously reported that the euryhaline unicellular cyanobacteria Synechocystis sp. PCC 6803 (S.6803) and Synechococcus sp. PCC 7002 (S.7002) produce farnesene and limonene, respectively, more efficiently than other terpenes. In the present study, we attempted to enhance farnesene production in S.6803 and limonene production in S.7002. Practically, we tested the influence of key cyanobacterial enzymes acting in carbon fixation (RubisCO, PRK, CcmK3 and CcmK4), utilization (CrtE, CrtR and CruF) and storage (PhaA and PhaB) on terpene production in S.6803, and we compared some of the findings with the data obtained in S.7002. We report that the overproduction of RubisCO from S.7002 and PRK from Cyanothece sp. PCC 7425 increased farnesene production in S.6803, but not limonene production in S.7002. The overexpression of the crtE genes (synthesis of terpene precursors) from S.6803 or S.7002 did not increase farnesene production in S.6803. In contrast, the overexpression of the crtE gene from S.6803, but not S.7002, increased farnesene production in S.7002, emphasizing the physiological difference between these two model cyanobacteria. Furthermore, the deletion of the crtR and cruF genes (carotenoid synthesis) and phaAB genes (carbon storage) did not increase the production of farnesene in S.6803. Finally, as a containment strategy of genetically modified strains of S.6803, we report that the deletion of the ccmK3K4 genes (carboxysome for CO2 fixation) did not affect the production of limonene, but decreased the production of farnesene in S.6803.
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Affiliation(s)
- Marine Vincent
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (M.V.); (V.B.-G.); (C.C.); (M.C.); (S.F.); (C.C.-C.)
| | - Victoire Blanc-Garin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (M.V.); (V.B.-G.); (C.C.); (M.C.); (S.F.); (C.C.-C.)
| | - Célia Chenebault
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (M.V.); (V.B.-G.); (C.C.); (M.C.); (S.F.); (C.C.-C.)
| | - Mattia Cirimele
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (M.V.); (V.B.-G.); (C.C.); (M.C.); (S.F.); (C.C.-C.)
- Université Paris-Saclay, ENS Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sandrine Farci
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (M.V.); (V.B.-G.); (C.C.); (M.C.); (S.F.); (C.C.-C.)
| | - Luis Fernando Garcia-Alles
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, 31077 Toulouse, France;
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (M.V.); (V.B.-G.); (C.C.); (M.C.); (S.F.); (C.C.-C.)
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (M.V.); (V.B.-G.); (C.C.); (M.C.); (S.F.); (C.C.-C.)
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5
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Sengupta A, Bandyopadhyay A, Sarkar D, Hendry JI, Schubert MG, Liu D, Church GM, Maranas CD, Pakrasi HB. Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. mBio 2024; 15:e0353023. [PMID: 38358263 PMCID: PMC10936165 DOI: 10.1128/mbio.03530-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here, we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth, Synechococcus elongatus UTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR-Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55-kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the wild type (WT). This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome-to-phenome relationships.IMPORTANCEGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome-editing tool, and in this study, we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs, which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.
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Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Debolina Sarkar
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - John I. Hendry
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - Max G. Schubert
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Deng Liu
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
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Rautela A, Yadav I, Gangwar A, Chatterjee R, Kumar S. Photosynthetic production of α-farnesene by engineered Synechococcus elongatus UTEX 2973 from carbon dioxide. Bioresour Technol 2024; 396:130432. [PMID: 38346593 DOI: 10.1016/j.biortech.2024.130432] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Cyanobacteria are the prospective biosolar cell factories to produce a range of bioproducts through CO2 sequestration. Farnesene is a sesquiterpene with an array of applications in biofuels, pest management, cosmetics, flavours and fragrances. This is the first time a codon-optimized farnesene synthase (AFS) gene is engineered into the genomic neutral site of Synechococcus elongatus UTEX 2973 for farnesene synthesis through its endogenous methylerythritol phosphate (MEP) pathway, rendering UTEX AFS strain. Similarly, bottleneck gene(s) of the MEP pathway, 1-deoxy-D-xylulose-5-phosphate synthase (dxs) and/or fusion of isopentenyl diphosphate isomerase and farnesyl diphosphate synthase (idispA) were engineered engendering UTEX AFS::dxs, UTEX AFS::idispA and UTEX AFS::dxs::idispA strains. UTEX AFS::dxs::idispA achieves farnesene productivity of 2.57 mg/L/day, the highest among engineered cyanobacterial strains studied so far. It demonstrates farnesene production, which is 31.3-times higher than the UTEX AFS strain. Moreover, the engineered strains show similar productivity over a three-month period, stipulating the genetic stability of the strains.
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Affiliation(s)
- Akhil Rautela
- Biofuel Research Laboratory, School of Biochemical Engineering, IIT(BHU) Varanasi, Varanasi 221005, Uttar Pradesh, India
| | - Indrajeet Yadav
- Biofuel Research Laboratory, School of Biochemical Engineering, IIT(BHU) Varanasi, Varanasi 221005, Uttar Pradesh, India
| | - Agendra Gangwar
- Biofuel Research Laboratory, School of Biochemical Engineering, IIT(BHU) Varanasi, Varanasi 221005, Uttar Pradesh, India
| | - Rishika Chatterjee
- Biofuel Research Laboratory, School of Biochemical Engineering, IIT(BHU) Varanasi, Varanasi 221005, Uttar Pradesh, India
| | - Sanjay Kumar
- Biofuel Research Laboratory, School of Biochemical Engineering, IIT(BHU) Varanasi, Varanasi 221005, Uttar Pradesh, India.
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Grone J, Poirier C, Abbott K, Wittmers F, Jaeger GS, Mahadevan A, Worden AZ. A single Prochlorococcus ecotype dominates the tropical Bay of Bengal with ultradian growth. Environ Microbiol 2024; 26:e16605. [PMID: 38517690 DOI: 10.1111/1462-2920.16605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/23/2024] [Indexed: 03/24/2024]
Abstract
The Bay of Bengal (BoB) spans >2.2 million km2 in the northeastern Indian Ocean and is bordered by dense populations that depend upon its resources. Over recent decades, a shift from larger phytoplankton to picoplankton has been reported, yet the abundance, activity, and composition of primary producer communities are not well-characterized. We analysed the BoB regions during the summer monsoon. Prochlorococcus ranged up to 3.14 × 105 cells mL-1 in the surface mixed layer, averaging 1.74 ± 0.46 × 105 in the upper 10 m and consistently higher than Synechococcus and eukaryotic phytoplankton. V1-V2 rRNA gene amplicon analyses showed the High Light II (HLII) ecotype formed 98 ± 1% of Prochlorococcus amplicons in surface waters, comprising six oligotypes, with the dominant oligotype accounting for 65 ± 4% of HLII. Diel sampling of a coherent water mass demonstrated evening onset of cell division and rapid Prochlorococcus growth between 1.5 and 3.1 div day-1, based on cell cycle analysis, as confirmed by abundance-based estimates of 2.1 div day-1. Accumulation of Prochlorococcus produced by ultradian growth was restricted by high loss rates. Alongside prior Arabian Sea and tropical Atlantic rates, our results indicate Prochlorococcus growth rates should be reevaluated with greater attention to latitudinal zones and influences on contributions to global primary production.
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Affiliation(s)
- Jonathan Grone
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Kathleen Abbott
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | | | - Amala Mahadevan
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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Jia K, Yang M, Liu X, Zhang Q, Cao G, Ge F, Zhao J. Deciphering the structure, function, and mechanism of lysine acetyltransferase cGNAT2 in cyanobacteria. Plant Physiol 2024; 194:634-661. [PMID: 37770070 DOI: 10.1093/plphys/kiad509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023]
Abstract
Lysine acetylation is a conserved regulatory posttranslational protein modification that is performed by lysine acetyltransferases (KATs). By catalyzing the transfer of acetyl groups to substrate proteins, KATs play critical regulatory roles in all domains of life; however, no KATs have yet been identified in cyanobacteria. Here, we tested all predicted KATs in the cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) and demonstrated that A1596, which we named cyanobacterial Gcn5-related N-acetyltransferase (cGNAT2), can catalyze lysine acetylation in vivo and in vitro. Eight amino acid residues were identified as the key residues in the putative active site of cGNAT2, as indicated by structural simulation and site-directed mutagenesis. The loss of cGNAT2 altered both growth and photosynthetic electron transport in Syn7002. In addition, quantitative analysis of the lysine acetylome identified 548 endogenous substrates of cGNAT2 in Syn7002. We further demonstrated that cGNAT2 can acetylate NAD(P)H dehydrogenase J (NdhJ) in vivo and in vitro, with the inability to acetylate K89 residues, thus decreasing NdhJ activity and affecting both growth and electron transport in Syn7002. In summary, this study identified a KAT in cyanobacteria and revealed that cGNAT2 regulates growth and photosynthesis in Syn7002 through an acetylation-mediated mechanism.
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Affiliation(s)
- Kun Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430070, China
| | - Qi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaoxiang Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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Zhang J, Li S, Sun T, Zong Y, Luo Y, Wei Y, Zhang W, Zhao K. Oscillation of type IV pili regulated by the circadian clock in cyanobacterium Synechococcus elongatus PCC7942. Sci Adv 2024; 10:eadd9485. [PMID: 38266097 PMCID: PMC10807798 DOI: 10.1126/sciadv.add9485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Type IV pili (TFP) are known to be functionally related to cell motilities and natural transformation in many bacteria. However, the molecular and ecological functions of the TFP have rarely been reported for photosynthetic cyanobacteria. Here, by labeling pili in model cyanobacterium Synechococcus elongatus PCC 7942 (Syn7942), we have quantitatively characterized the TFP and its driven twitching motility in situ at the single-cell level. We found an oscillating pattern of TFP in accordance with the light and dark periods during light-dark cycles, which is correlated positively to the oscillating pattern of the natural transformation efficiency. We further showed that the internal circadian clock plays an important role in regulating the oscillating pattern of TFP, which is also supported by evidences at the molecular level by tracking the expression of 16 TFP-related genes. This study adds a detailed picture toward the gap between TFP and its relations to circadian regulations in Syn7942.
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Affiliation(s)
- Jingchao Zhang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
- Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Shubin Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Tao Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, P.R. China
| | - Yiwu Zong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Yan Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Yufei Wei
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Weiwen Zhang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, P.R. China
| | - Kun Zhao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and The Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
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10
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Hasegawa H, Kobayashi I, Bairagi N, Watanabe S, Tanaka K. DnaK2 Mediates a Negative Feedback Regulation of the Heat Shock Responsive Hik2-Rre1 Two-Component System in the Cyanobacterium Synechococcus Elongatus PCC 7942. Plant Cell Physiol 2024; 65:120-127. [PMID: 37856257 DOI: 10.1093/pcp/pcad129] [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] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
The two-component system (TCS) is a conserved signal transduction module in bacteria. The Hik2-Rre1 system is responsible for transcriptional activation upon high-temperature shift as well as plastoquinone-related redox stress in the cyanobacterium Synechococcus elongatus PCC 7942. As heat-induced de novo protein synthesis was previously shown to be required to quench the heat-activated response, we investigated the underlying mechanism in this study. We found that the heat-inducible transcription activation was alleviated by the overexpression of dnaK2, which is an essential homolog of the highly conserved HSP70 chaperone and whose expression is induced under the control of the Hik2-Rre1 TCS. Phosphorylation of Rre1 correlated with transcription of the regulatory target hspA. The redox stress response was found to be similarly repressed by dnaK2 overexpression. Considered together with the previous information, we propose a negative feedback mechanism of the Hik2-Rre1-dependent stress response that maintains the cellular homeostasis mediated by DnaK2.
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Affiliation(s)
- Hazuki Hasegawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Ikki Kobayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Nachiketa Bairagi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
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11
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Arias-Orozco P, Zhou L, Yi Y, Cebrián R, Kuipers OP. Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains. Microbiol Spectr 2024; 12:e0361123. [PMID: 38088546 PMCID: PMC10783134 DOI: 10.1128/spectrum.03611-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Genome mining studies have revealed the remarkable combinatorial diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs) in marine bacteria, including prochlorosins. However, mining strategies also prove valuable in investigating the genomic landscape of associated genes within biosynthetic gene cluster (BGC) specific to targeted RiPPs of interest. Our study contributes to the enrichment of knowledge regarding prochlorosin diversity. It offers insights into potential mechanisms involved in their biosynthesis and modification, such as hyper-modification, which may give rise to active lantibiotics. Additionally, our study uncovers putative novel promiscuous post-translational enzymes, thereby expanding the chemical space explored within the Synechococcus genus. Moreover, this research extends the applications of mining techniques beyond the discovery of new RiPP-like clusters, allowing for a deeper understanding of genomics and diversity. Furthermore, it holds the potential to reveal previously unknown functions within the intriguing RiPP families, particularly in the case of prochlorosins.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs.GRANADA, San Cecilio University Hospital, Granada, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
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12
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Garcia NS, Du M, Guindani M, McIlvin MR, Moran DM, Saito MA, Martiny AC. Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change. ISME J 2024; 18:wrae046. [PMID: 38513256 PMCID: PMC11020310 DOI: 10.1093/ismejo/wrae046] [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] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the "translation-compensation hypothesis" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N:P.
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Affiliation(s)
- Nathan S Garcia
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, United States
| | - Mingyu Du
- Department of Statistics, University of California, Irvine, Irvine, CA 92697, United States
| | - Michele Guindani
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Dawn M Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, United States
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
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13
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Zhang X, Xu J, Dai J, Zhang L, Feng L, Tian X, Yang Q. Taxonomic, Phylogenomic and Bioactivity Profiling of Novel Phycosphere Bacterium from Model Cyanobacterium Synechococcus elongatus PCC 7942. Mar Drugs 2024; 22:36. [PMID: 38248661 PMCID: PMC10817584 DOI: 10.3390/md22010036] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Phycosphere niches host rich microbial consortia that harbor dynamic algae-bacteria interactions with fundamental significance in varied natural ecosystems. Hence, culturing the uncultured microbial majority of the phycosphere microbiota is vital for deep understanding of the intricate mechanisms governing the dynamic interactions, and also to provide novel and rich microbial resources, and to discover new natural bioactive metabolites. Synechococcus elongatus PCC 7942 is a robust model cyanobacterium widely used in environment, synthesis biology, and biotechnology research. To expand the number of novel phycosphere species that were brought into culture and to discover the natural bioactivities, we presented a new yellow-pigmented bacterium named ABI-127-1, which was recovered from the phycosphere of PCC 7942, using an optimized bacterial isolation procedure. Combined polyphasic taxonomic and phylogenomic characterization was performed to confidently identify the new isolate as a potential novel species belonging to the genus Qipengyuania. The observed bioactivity of strain ABI-127-1 with promoting potential towards the growth and CO2 fixation efficiency of the host microalgae was measured. Additionally, the bacterial production of active bioflocculant exopolysaccharides was evaluated after culture optimization. Thus, these findings revealed the potential environmental and biotechnological implications of this new microalgae growth-promoting bacterium isolated from the phycosphere microenvironment.
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Affiliation(s)
- Xiaoling Zhang
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
| | - Jiaquan Xu
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
| | - Jun Dai
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Lei Zhang
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lijuan Feng
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaoqing Tian
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Qiao Yang
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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14
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Santos-Merino M, Sakkos JK, Singh AK, Ducat DC. Coordination of carbon partitioning and photosynthesis by a two-component signaling network in Synechococcus elongatus PCC 7942. Metab Eng 2024; 81:38-52. [PMID: 37925065 DOI: 10.1016/j.ymben.2023.11.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Photosynthetic organisms need to balance the rate of photosynthesis with the utilization of photosynthetic products by downstream reactions. While such "source/sink" pathways are well-interrogated in plants, analogous regulatory systems are unknown or poorly studied in single-celled algal and cyanobacterial species. Towards the identification of energy/sugar sensors in cyanobacteria, we utilized an engineered strain of Synechococcus elongatus PCC 7942 that allows experimental manipulation of carbon status. We conducted a screening of all two-component systems (TCS) and serine/threonine kinases (STKs) encoded in S. elongatus PCC 7942 by analyzing phenotypes consistent with sucrose-induced relaxation of sink inhibition. We narrowed the candidate sensor proteins by analyzing changes observed after sucrose feeding. We show that a clustered TCS network containing RpaA, CikB, ManS and NblS are involved in the regulation of genes related to photosynthesis, pigment synthesis, and Rubisco concentration in response to sucrose. Altogether, these results highlight a regulatory TCS group that may play under-appreciated functions in carbon partitioning and energy balancing in cyanobacteria.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Jonathan K Sakkos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Amit K Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, United States.
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15
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Li J, Wang R, Liu Y, Miao X. Role of ERA protein in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in Synechococcus elongatus PCC 7942. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159431. [PMID: 37977490 DOI: 10.1016/j.bbalip.2023.159431] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Glyceroglycolipids are the primary thylakoid membrane lipids in cyanobacteria. Their diverse bioactivities have led to extensive utilization in the biomedical industry. In this study, we elucidated the role of ERA (E. coli Ras-like protein) in augmenting glyceroglycolipid synthesis and bolstering stress resilience in Synechococcus elongatus PCC 7942 during phosphate starvation. Notably, the ERA overexpression strain (ERA OE) outperformed the wild-type (WT) strain under phosphate-starved conditions, displaying an average 13.9 % increase in biomass over WT during the entire growth period, peaking at 0.185 g L-1 of dry cell weight on day 6. Lipidomic analysis using UHPLC-MS/MS techniques revealed that ERA OE exhibited a higher total glyceroglycolipid content compared to WT under phosphate starvation, representing a 7.95 % increase over WT and constituting a maximum of 5.07 % of dry cell weight on day 6. Transcriptomic analysis identified a significant up-regulation of the gldA gene (encoding glycerol dehydrogenase) involved in glycerolipid metabolism due to overexpression of ERA during phosphate starvation. These findings suggest a potential mechanism by which ERA regulates glyceroglycolipid synthesis through the up-regulation of GldA, thereby enhancing phosphate starvation tolerance in S. elongatus PCC 7942. Furthermore, lipidomic analysis revealed that ERA facilitated the production of glyceroglycolipid molecules containing C16:1 and C18:1 fatty acids. Additionally, ERA redirected lipid flux and promoted glyceroglycolipid accumulation while attenuating triacylglycerol production under phosphate starvation. This study represents the first demonstration of pivotal role of ERA in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in cyanobacteria, offering new insights into the effective utilization of glyceroglycolipids in various applications.
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Affiliation(s)
- Junhao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuhong Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoling Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China.
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16
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Wang T, Zhou Y, Li J, Qin S. Molecular insights into nitrogen constraint for niche partitioning and physiological adaptation of coastal Synechococcus assemblages. Environ Res 2023; 239:117383. [PMID: 37832763 DOI: 10.1016/j.envres.2023.117383] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 10/15/2023]
Abstract
Coastal nitrogen input has substantially increased due to human activity. However, much remains unknown about the nitrogen-driven patterns and the underlying genetic basis of coastal picoplankton. To investigate the response and mechanisms of picoplankton induced by nitrogen variation, we conducted in-situ investigations using high-throughput sequencing in the Bohai Sea and performed laboratory nitrogen simulation experiments accompanied by physiological, genomic, and transcriptomic analyses, with Synechococcus as a representative. The results of in-situ investigation revealed that Synechococcus clades I, III, WPC1, and VI of subcluster 5.1 (S5.1) are prevalent in strait areas characterized by robust water exchange with the North Yellow Sea, while clades II, VIII, and IX of S5.1, as well as subcluster 5.2 (S5.2) and subcluster 5.3 (S5.3) are more abundant in central and bay areas experiencing elevated nitrate and nitrite loads. The laboratory experiments further confirmed that inorganic nitrogen is a crucial determinant of diversity and niche partitioning of Synechococcus lineages. Besides, the raising inorganic nitrogen concentration within the current in-situ range (0.1-10 μmol L-1) enhances photosynthesis and carbon fixation of Synechococcus, however further escalation of inorganic nitrogen (100 μmol L-1) may hinder these processes instead. The phenomenon could be associated with the differential expression of genes in metabolic pathways regulating nitrogen metabolism, photosynthetic system II, and photosynthesis-antenna proteins in response to nitrogen concentration and type variation. These findings expand our understanding of the impact of macronutrient variation resulting from human activities on marine picoplankton and biogeochemical cycles.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuting Zhou
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Jialin Li
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
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17
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Wang R, Song H, Zhang W, Wang N, Zhang S, Shao R, Liu C. Structural insights into the functions of Raf1 and Bsd2 in hexadecameric Rubisco assembly. Mol Plant 2023; 16:1927-1936. [PMID: 37853692 DOI: 10.1016/j.molp.2023.10.011] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
Hexadecameric form I Rubisco, which consisting consists of eight large (RbcL) and eight small (RbcS) subunits, is the most abundant enzyme on earth. Extensive efforts to engineer an improved Rubisco to speed up its catalytic efficiency and ultimately increase agricultural productivity. However, difficulties with correct folding and assembly in foreign hosts or in vitro have hampered the genetic manipulation of hexadecameric Rubisco. In this study, we reconstituted Synechococcus sp. PCC6301 Rubisco in vitro using the chaperonin system and assembly factors from cyanobacteria and Arabidopsis thaliana (At). Rubisco holoenzyme was produced in the presence of cyanobacterial Rubisco accumulation factor 1 (Raf1) alone or both AtRaf1 and bundle-sheath defective-2 (AtBsd2) from Arabidopsis. RbcL released from GroEL is assembly capable in the presence of ATP, and AtBsd2 functions downstream of AtRaf1. Cryo-EM structures of RbcL8-AtRaf18, RbcL8-AtRaf14-AtBsd28, and RbcL8 revealed that the interactions between RbcL and AtRaf1 are looser than those between prokaryotic RbcL and Raf1, with AtRaf1 tilting 7° farther away from RbcL. AtBsd2 stabilizes the flexible regions of RbcL, including the N and C termini, the 60s loop, and loop 6. Using these data, combined with previous findings, we propose the possible biogenesis pathways of prokaryotic and eukaryotic Rubisco.
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Affiliation(s)
- Ran Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Wenjuan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Shijia Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Ruiqi Shao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Cuimin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
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18
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Capovilla G, Castro KG, Collani S, Kearney SM, Kehoe DM, Chisholm SW. Chitin degradation by Synechococcus WH7803. Sci Rep 2023; 13:19944. [PMID: 37968300 PMCID: PMC10651935 DOI: 10.1038/s41598-023-47332-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023] Open
Abstract
Chitin is an abundant, carbon-rich polymer in the marine environment. Chitinase activity has been detected in spent media of Synechococcus WH7803 cultures-yet it was unclear which specific enzymes were involved. Here we delivered a CRISPR tool into the cells via electroporation to generate loss-of-function mutants of putative candidates and identified ChiA as the enzyme required for the activity detected in the wild type.
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Affiliation(s)
- Giovanna Capovilla
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Kurt G Castro
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Silvio Collani
- Department of Fysiologisk Botanik, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, Sweden
| | - Sean M Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Wang B, Zuniga C, Guarnieri MT, Zengler K, Betenbaugh M, Young JD. Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis. Metab Eng 2023; 80:12-24. [PMID: 37678664 DOI: 10.1016/j.ymben.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/28/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
The capability of cyanobacteria to produce sucrose from CO2 and light has a remarkable societal and biotechnological impact since sucrose can serve as a carbon and energy source for a variety of heterotrophic organisms and can be converted into value-added products. However, most metabolic engineering efforts have focused on understanding local pathway alterations that drive sucrose biosynthesis and secretion in cyanobacteria rather than analyzing the global flux re-routing that occurs following induction of sucrose production by salt stress. Here, we investigated global metabolic flux alterations in a sucrose-secreting (cscB-overexpressing) strain relative to its wild-type Synechococcus elongatus 7942 parental strain. We used targeted metabolomics, 13C metabolic flux analysis (MFA), and genome-scale modeling (GSM) as complementary approaches to elucidate differences in cellular resource allocation by quantifying metabolic profiles of three cyanobacterial cultures - wild-type S. elongatus 7942 without salt stress (WT), wild-type with salt stress (WT/NaCl), and the cscB-overexpressing strain with salt stress (cscB/NaCl) - all under photoautotrophic conditions. We quantified the substantial rewiring of metabolic fluxes in WT/NaCl and cscB/NaCl cultures relative to WT and identified a metabolic bottleneck limiting carbon fixation and sucrose biosynthesis. This bottleneck was subsequently mitigated through heterologous overexpression of glyceraldehyde-3-phosphate dehydrogenase in an engineered sucrose-secreting strain. Our study also demonstrates that combining 13C-MFA and GSM is a useful strategy to both extend the coverage of MFA beyond central metabolism and to improve the accuracy of flux predictions provided by GSM.
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Affiliation(s)
- Bo Wang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Center for Microbiome Innovation, University of California, San Diego, CA, 92093, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA.
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20
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Taton A, Gilderman TS, Ernst DC, Omaga CA, Cohen LA, Rey-Bedon C, Golden JW, Golden SS. Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids. mBio 2023; 14:e0184323. [PMID: 37791787 PMCID: PMC10653904 DOI: 10.1128/mbio.01843-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.
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Affiliation(s)
- Arnaud Taton
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Tami S. Gilderman
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Dustin C. Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Carla A. Omaga
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Lucas A. Cohen
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Camilo Rey-Bedon
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - James W. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Susan S. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
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21
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Sun J, Zhang Z, Zhang S, Dan Y, Sun H, Wu Y, Luan G, Lu X. Engineering Cyanobacterial Cell Factories for Photosynthetic Production of Fructose. ACS Synth Biol 2023; 12:3008-3019. [PMID: 37728873 DOI: 10.1021/acssynbio.3c00338] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Fructose is an important monosaccharide product widely applied in the food, medicine, and chemical industries. Currently, fructose is mainly manufactured with plant biomass-sourced polysaccharides through multiple steps of digestion, conversion, separation, and purification. The development of cyanobacterial metabolic engineering provides an attractive alternative route for the one-step direct production of fructose utilizing carbon dioxide and solar energy. In this work, we developed a paradigm for engineering cyanobacterial chassis cells into efficient cell factories for the photosynthetic production of fructose. In a representative cyanobacterial strain, Synechococcus elongatus PCC 7942, knockout of fructokinase effectively activated the synthesis and secretion of fructose in hypersaline conditions, independent of any heterologous transporters. The native sucrose synthesis pathway was identified as playing a primary role in fructose synthesis. Through combinatory optimizations on the levels of metabolism, physiology, and cultivation, the fructose yield of the Synechococcus cell factories was stepwise improved to 3.9 g/L. Such a paradigm was also adopted to engineer another Synechococcus strain, the marine species Synechococcus sp. PCC 7002, and facilitated an even higher fructose yield of over 6 g/L. Finally, the fructose synthesized and secreted by the cyanobacterial photosynthetic cell factories was successfully extracted and prepared from the culture broth in the form of products with 86% purity through multistep separation-purification operations. This work demonstrated a paradigm for systematically engineering cyanobacteria for photosynthetic production of desired metabolites, and it also confirmed the feasibility and potential of cyanobacterial photosynthetic biomanufacturing as a simple and efficient route for fructose production.
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Affiliation(s)
- Jiahui Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhichao Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Shanshan Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yu Dan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Huili Sun
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yannan Wu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
| | - Guodong Luan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning 116023, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning 116023, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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22
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McKnight BM, Kang S, Le TH, Fang M, Carbonel G, Rodriguez E, Govindarajan S, Albocher-Kedem N, Tran AL, Duncan NR, Amster-Choder O, Golden SS, Cohen SE. Roles for the Synechococcus elongatus RNA-Binding Protein Rbp2 in Regulating the Circadian Clock. J Biol Rhythms 2023; 38:447-460. [PMID: 37515350 PMCID: PMC10528358 DOI: 10.1177/07487304231188761] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The cyanobacterial circadian oscillator, consisting of KaiA, KaiB, and KaiC proteins, drives global rhythms of gene expression and compaction of the chromosome and regulates the timing of cell division and natural transformation. While the KaiABC posttranslational oscillator can be reconstituted in vitro, the Kai-based oscillator is subject to several layers of regulation in vivo. Specifically, the oscillator proteins undergo changes in their subcellular localization patterns, where KaiA and KaiC are diffuse throughout the cell during the day and localized as a focus at or near the pole of the cell at night. Here, we report that the CI domain of KaiC, when in a hexameric state, is sufficient to target KaiC to the pole. Moreover, increased ATPase activity of KaiC correlates with enhanced polar localization. We identified proteins associated with KaiC in either a localized or diffuse state. We found that loss of Rbp2, found to be associated with localized KaiC, results in decreased incidence of KaiC localization and long-period circadian phenotypes. Rbp2 is an RNA-binding protein, and it appears that RNA-binding activity of Rbp2 is required to execute clock functions. These findings uncover previously unrecognized roles for Rbp2 in regulating the circadian clock and suggest that the proper localization of KaiC is required for a fully functional clock in vivo.
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Affiliation(s)
- Briana M. McKnight
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Shannon Kang
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Tam H. Le
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Genelyn Carbonel
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Esbeydi Rodriguez
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Sutharsan Govindarajan
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
- Department of Biological Sciences, SRM University AP, Amaravati, India
| | - Nitsan Albocher-Kedem
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Amanda L. Tran
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Nicholas R. Duncan
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Susan S. Golden
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Susan E. Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
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23
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Zedler JAZ, Michel M, Pohnert G, Russo DA. Cell surface composition, released polysaccharides, and ionic strength mediate fast sedimentation in the cyanobacterium Synechococcus elongatus PCC 7942. Environ Microbiol 2023; 25:1955-1966. [PMID: 37259888 DOI: 10.1111/1462-2920.16426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes of high ecological and biotechnological relevance that have been cultivated in laboratories around the world for more than 70 years. Prolonged laboratory culturing has led to multiple microevolutionary events and the appearance of a large number of 'domesticated' substrains among model cyanobacteria. Despite its widespread occurrence, strain domestication is still largely ignored. In this work we describe Synechococcus elongatus PCC 7942-KU, a novel domesticated substrain of the model cyanobacterium S. elongatus PCC 7942, which presents a fast-sedimenting phenotype. Under higher ionic strengths the sedimentation rate increased leading to complete sedimentation in just 12 h. Through whole genome sequencing and gene deletion, we demonstrated that the Group 3 alternative sigma factor F plays a key role in cell sedimentation. Further analysis showed that significant changes in cell surface structures and a three-fold increase in released polysaccharides lead to the appearance of a fast-sedimenting phenotype. This work sheds light on the determinants of the planktonic to benthic transitions and provides genetic targets to generate fast-sedimenting strains that could unlock cost-effective cyanobacterial harvesting at scale.
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Affiliation(s)
- Julie A Z Zedler
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Synthetic Biology of Photosynthetic Organisms, Jena, Germany
| | - Marlene Michel
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Jena, Germany
| | - Georg Pohnert
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Jena, Germany
| | - David A Russo
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Jena, Germany
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24
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Ngoennet S, Sirisattha S, Kusolkumbot P, Hibino T, Kageyama H, Waditee-Sirisattha R. Active role of the protein translation machinery in protecting against stress tolerance in Synechococcus elongatus PCC7942. Arch Biochem Biophys 2023; 746:109734. [PMID: 37648010 DOI: 10.1016/j.abb.2023.109734] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 07/11/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
In vivo protein synthesis is crucial for all domains of life. It is accomplished through translational machinery, and a key step is the translocation of tRNA-mRNA by elongation factor G (EF-G). Genome-based analysis revealed two EF-G encoding genes (S0885 and S2082) in the freshwater cyanobacterium model Synechococcus elongatus PCC7942. S0885 is the essential EF-G gene for photosynthesis. We generated a strain of S. elongatus PCC7942 that overexpressed S0885 (OX-S0885) to identify EF-G functionality. RT-PCR and Western blot analyses revealed increased transcriptional and translational levels in OX-S0885 at 10.5-13.5 and 2.0-3.0 fold, respectively. Overexpression of S0885 led to an increase in specific growth rate. Additionally, polysome-to-monosome ratio (P/M) and RNA-to-protein ratio (R/P) were elevated in OX-S0885 compared with the empty vector. Interestingly, R/P in OX-S0885 was retained at more than 70% under oxidative stress while R/P in the empty vector was severely depleted, suggesting the maintenance of translation. Thus, S0885 appeared to be the important target of oxidative stress because it was protected by the stress response system to maintain its function. These results suggest that cyanobacterial EF-G has a primary function in translation and an unrelated activity during stress conditions. These findings support the substantial role of EF-G in the formation and maintenance of cellular protein formation, and in the protection of the global translational mechanism under oxidative stress condition.
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Affiliation(s)
- Siripat Ngoennet
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand; Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Sophon Sirisattha
- Thailand Institute of Scientific and Technological Research (TISTR), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Pokchut Kusolkumbot
- Thailand Institute of Scientific and Technological Research (TISTR), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Takashi Hibino
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Aichi, 468-8502, Japan; Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Hakuto Kageyama
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Aichi, 468-8502, Japan; Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Aichi, 468-8502, Japan.
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25
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Berube PM, O'Keefe TJ, Rasmussen A, LeMaster T, Chisholm SW. Production and cross-feeding of nitrite within Prochlorococcus populations. mBio 2023; 14:e0123623. [PMID: 37404012 PMCID: PMC10470740 DOI: 10.1128/mbio.01236-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Prochlorococcus is an abundant photosynthetic bacterium in the open ocean, where nitrogen (N) often limits phytoplankton growth. In the low-light-adapted LLI clade of Prochlorococcus, nearly all cells can assimilate nitrite (NO2-), with a subset capable of assimilating nitrate (NO3-). LLI cells are maximally abundant near the primary NO2- maximum layer, an oceanographic feature that may, in part, be due to incomplete assimilatory NO3- reduction and subsequent NO2- release by phytoplankton. We hypothesized that some Prochlorococcus exhibit incomplete assimilatory NO3- reduction and examined NO2- accumulation in cultures of three Prochlorococcus strains (MIT0915, MIT0917, and SB) and two Synechococcus strains (WH8102 and WH7803). Only MIT0917 and SB accumulated external NO2- during growth on NO3-. Approximately 20-30% of the NO3- transported into the cell by MIT0917 was released as NO2-, with the rest assimilated into biomass. We further observed that co-cultures using NO3- as the sole N source could be established for MIT0917 and Prochlorococcus strain MIT1214 that can assimilate NO2- but not NO3-. In these co-cultures, the NO2- released by MIT0917 is efficiently consumed by its partner strain, MIT1214. Our findings highlight the potential for emergent metabolic partnerships that are mediated by the production and consumption of N cycle intermediates within Prochlorococcus populations. IMPORTANCE Earth's biogeochemical cycles are substantially driven by microorganisms and their interactions. Given that N often limits marine photosynthesis, we investigated the potential for N cross-feeding within populations of Prochlorococcus, the numerically dominant photosynthetic cell in the subtropical open ocean. In laboratory cultures, some Prochlorococcus cells release extracellular NO2- during growth on NO3-. In the wild, Prochlorococcus populations are composed of multiple functional types, including those that cannot use NO3- but can still assimilate NO2-. We show that metabolic dependencies arise when Prochlorococcus strains with complementary NO2- production and consumption phenotypes are grown together on NO3-. These findings demonstrate the potential for emergent metabolic partnerships, possibly modulating ocean nutrient gradients, that are mediated by cross-feeding of N cycle intermediates.
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Affiliation(s)
- Paul M. Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Tyler J. O'Keefe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anna Rasmussen
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Trent LeMaster
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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26
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Sengupta A, Bandyopadhyay A, Schubert MG, Church GM, Pakrasi HB. Antenna Modification in a Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973 Leads to Improved Efficiency and Carbon-Neutral Productivity. Microbiol Spectr 2023; 11:e0050023. [PMID: 37318337 PMCID: PMC10433846 DOI: 10.1128/spectrum.00500-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023] Open
Abstract
Our planet is sustained by sunlight, the primary energy source made accessible to all life forms by photoautotrophs. Photoautotrophs are equipped with light-harvesting complexes (LHCs) that enable efficient capture of solar energy, particularly when light is limiting. However, under high light, LHCs can harvest photons in excess of the utilization capacity of cells, causing photodamage. This damaging effect is most evident when there is a disparity between the amount of light harvested and carbon available. Cells strive to circumvent this problem by dynamically adjusting the antenna structure in response to the changing light signals, a process known to be energetically expensive. Much emphasis has been laid on elucidating the relationship between antenna size and photosynthetic efficiency and identifying strategies to synthetically modify antennae for optimal light capture. Our study is an effort in this direction and investigates the possibility of modifying phycobilisomes, the LHCs present in cyanobacteria, the simplest of photoautotrophs. We systematically truncate the phycobilisomes of Synechococcus elongatus UTEX 2973, a widely studied, fast-growing model cyanobacterium and demonstrate that partial truncation of its antenna can lead to a growth advantage of up to 36% compared to the wild type and an increase in sucrose titer of up to 22%. In contrast, targeted deletion of the linker protein which connects the first phycocyanin rod to the core proved detrimental, indicating that the core alone is not enough, and it is essential to maintain a minimal rod-core structure for efficient light harvest and strain fitness. IMPORTANCE Light energy is essential for the existence of life on this planet, and only photosynthetic organisms, equipped with light-harvesting antenna protein complexes, can capture this energy, making it readily accessible to all other life forms. However, these light-harvesting antennae are not designed to function optimally under extreme high light, a condition which can cause photodamage and significantly reduce photosynthetic productivity. In this study, we attempt to assess the optimal antenna structure for a fast-growing, high-light tolerant photosynthetic microbe with the goal of improving its productivity. Our findings provide concrete evidence that although the antenna complex is essential, antenna modification is a viable strategy to maximize strain performance under controlled growth conditions. This understanding can also be translated into identifying avenues to improve light harvesting efficiency in higher photoautotrophs.
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Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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27
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Datta D, Weiss EL, Wangpraseurt D, Hild E, Chen S, Golden JW, Golden SS, Pokorski JK. Phenotypically complex living materials containing engineered cyanobacteria. Nat Commun 2023; 14:4742. [PMID: 37550278 PMCID: PMC10406891 DOI: 10.1038/s41467-023-40265-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
The field of engineered living materials lies at the intersection of materials science and synthetic biology with the aim of developing materials that can sense and respond to the environment. In this study, we use 3D printing to fabricate a cyanobacterial biocomposite material capable of producing multiple functional outputs in response to an external chemical stimulus and demonstrate the advantages of utilizing additive manufacturing techniques in controlling the shape of the fabricated photosynthetic material. As an initial proof-of-concept, a synthetic riboswitch is used to regulate the expression of a yellow fluorescent protein reporter in Synechococcus elongatus PCC 7942 within a hydrogel matrix. Subsequently, a strain of S. elongatus is engineered to produce an oxidative laccase enzyme; when printed within a hydrogel matrix the responsive biomaterial can decolorize a common textile dye pollutant, indigo carmine, potentially serving as a tool in environmental bioremediation. Finally, cells are engineered for inducible cell death to eliminate their presence once their activity is no longer required, which is an important function for biocontainment and minimizing environmental impact. By integrating genetically engineered stimuli-responsive cyanobacteria in volumetric 3D-printed designs, we demonstrate programmable photosynthetic biocomposite materials capable of producing functional outputs including, but not limited to, bioremediation.
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Affiliation(s)
- Debika Datta
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
| | - Elliot L Weiss
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Daniel Wangpraseurt
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Erica Hild
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
| | - Shaochen Chen
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA
| | - James W Golden
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Susan S Golden
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
| | - Jonathan K Pokorski
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, USA.
- Center for Nano-ImmunoEngineering and Institute for Materials Discovery and Design, University of California San Diego, La Jolla, CA, USA.
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Madhu S, Sengupta A, Sarnaik AP, Sahasrabuddhe D, Wangikar PP. Global Transcriptome-Guided Identification of Neutral Sites for Engineering Synechococcus elongatus PCC 11801. ACS Synth Biol 2023; 12:1677-1685. [PMID: 37252895 DOI: 10.1021/acssynbio.3c00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Engineered cyanobacteria are attractive hosts for the phototrophic conversion of CO2 to chemicals. Synechococcus elongatus PCC11801, a novel, fast-growing, and stress-tolerant cyanobacterium, has the potential to be a platform cell factory, and hence, it necessitates the development of a synthetic biology toolbox. Considering the widely followed cyanobacterial engineering strategy of chromosomal integration of heterologous DNA, it is of interest to discover and validate new chromosomal neutral sites (NSs) in this strain. To that end, global transcriptome analysis was performed using RNA Seq under the conditions of high temperature (HT), carbon (HC), and salt (HS) and ambient growth conditions. We found upregulation of 445, 138, and 87 genes and downregulation of 333, 125, and 132 genes, under HC, HT, and HS, respectively. Following nonhierarchical clustering, gene enrichment, and bioinformatics analysis, 27 putative NSs were predicted. Six of them were experimentally tested, and five showed confirmed neutrality, based on unaltered cell growth. Thus, global transcriptomic analysis was effectively exploited for NS annotation and would be advantageous for multiplexed genome editing.
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Affiliation(s)
- Swati Madhu
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Aditya P Sarnaik
- 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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Zhang S, Sun J, Feng D, Sun H, Cui J, Zeng X, Wu Y, Luan G, Lu X. Unlocking the potentials of cyanobacterial photosynthesis for directly converting carbon dioxide into glucose. Nat Commun 2023; 14:3425. [PMID: 37296173 PMCID: PMC10256809 DOI: 10.1038/s41467-023-39222-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Glucose is the most abundant monosaccharide, serving as an essential energy source for cells in all domains of life and as an important feedstock for the biorefinery industry. The plant-biomass-sugar route dominates the current glucose supply, while the direct conversion of carbon dioxide into glucose through photosynthesis is not well studied. Here, we show that the potential of Synechococcus elongatus PCC 7942 for photosynthetic glucose production can be unlocked by preventing native glucokinase activity. Knocking out two glucokinase genes causes intracellular accumulation of glucose and promotes the formation of a spontaneous mutation in the genome, which eventually leads to glucose secretion. Without heterologous catalysis or transportation genes, glucokinase deficiency and spontaneous genomic mutation lead to a glucose secretion of 1.5 g/L, which is further increased to 5 g/L through metabolic and cultivation engineering. These findings underline the cyanobacterial metabolism plasticities and demonstrate their applications for supporting the direct photosynthetic production of glucose.
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Affiliation(s)
- Shanshan Zhang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiahui Sun
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dandan Feng
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Huili Sun
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jinyu Cui
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Xuexia Zeng
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Yannan Wu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Guodong Luan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning, 116023, China.
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning, 116023, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China.
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Zheng Y, Xue C, Chen H, Jia A, Zhao L, Zhang J, Zhang L, Wang Q. Reconstitution and expression of mcy gene cluster in the model cyanobacterium Synechococcus 7942 reveals a role of MC-LR in cell division. New Phytol 2023; 238:1101-1114. [PMID: 36683448 DOI: 10.1111/nph.18766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Cyanobacterial blooms pose a serious threat to public health due to the presence of cyanotoxins. Microcystin-LR (MC-LR) produced by Microcystis aeruginosa is the most common cyanotoxins. Due to the limitation of isolation, purification, and genetic manipulation techniques, it is difficult to study and verify in situ the biosynthetic pathways and molecular mechanisms of MC-LR. We reassembled the biosynthetic gene cluster (mcy cluster) of MC-LR in vitro by synthetic biology, designed and constructed the strong bidirectional promoter biPpsbA2 , transformed it into Synechococcus 7942, and successfully expressed MC-LR at a level of 0.006-0.018 fg cell-1 d-1 . We found the expression of MC-LR led to abnormal cell division and cellular filamentation, further using various methods proved that by irreversibly competing its GTP-binding site, MC-LR inhibits assembly of the cell division protein FtsZ. The study represents the first reconstitution and expression of the mcy cluster and the autotrophic production of MC-LR in model cyanobacterium, which lays the foundation for resolving the microcystins biosynthesis pathway. The discovered role of MC-LR in cell division reveals a mechanism of how blooming cyanobacteria gain a competitive edge over their nonblooming counterparts.
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Affiliation(s)
- Yanli Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chunling Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Anqi Jia
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lixin Zhang
- 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, Kaifeng, 475004, 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, Kaifeng, 475004, China
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31
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Luo L, Ma X, Guo R, Jiang T, Wang T, Shao H, He H, Wang H, Liang Y, McMinn A, Guo C, Wang M. Characterization and genomic analysis of a novel Synechococcus phage S-H9-2 belonging to Bristolvirus genus isolated from the Yellow Sea. Virus Res 2023; 328:199072. [PMID: 36781075 DOI: 10.1016/j.virusres.2023.199072] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Cyanophages are known to influence the population dynamics and community structure of cyanobacteria and thus play an important role in biogeochemical cycles in aquatic ecosystems. In this study, a novel Synechococcus phage S-H9-2 infecting Synechococcus sp. WH 8102 was isolated from the coastal water of the Yellow Sea. Synechococcus phage S-H9-2 contains a 187,320 bp genome of double-stranded DNA with a G + C content of 40.3%, 202 potential open reading frames (ORFs), and 15 tRNAs. Phylogenetic analysis and nucleotide-based intergenomic similarity suggest that Synechococcus phage S-H9-2 belongs to the Bristolvirus genus under the family Kyanoviridae. Homologs of the S-H9-2 open reading frame can be found in a variety of marine environments, as shown by the results of mapping the genome sequence of S-H9-2 to the Global Ocean Viromes 2.0 dataset. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as phylogenetic relationships based on complete genome sequences, reflect the mechanism of phage-host interaction and host-specific strategies for adaptation to environmental conditions. This study enriches the current genomic database of cyanophage and contributed to our understanding of the virus-host interactions and their adaption to the environment.
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Affiliation(s)
- Lin Luo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiaohong Ma
- Department of Pediatrics, Qingdao Municipal Hospital, Qingdao266011, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Tiancong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, SA
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China.
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; UMT-OUC Joint Centre for Marine Studies, Qingdao 266003, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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32
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Fang M, Chavan AG, LiWang A, Golden SS. Synchronization of the circadian clock to the environment tracked in real time. Proc Natl Acad Sci U S A 2023; 120:e2221453120. [PMID: 36940340 PMCID: PMC10068778 DOI: 10.1073/pnas.2221453120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/08/2023] [Indexed: 03/22/2023] Open
Abstract
The circadian system of the cyanobacterium Synechococcus elongatus PCC 7942 relies on a three-protein nanomachine (KaiA, KaiB, and KaiC) that undergoes an oscillatory phosphorylation cycle with a period of ~24 h. This core oscillator can be reconstituted in vitro and is used to study the molecular mechanisms of circadian timekeeping and entrainment. Previous studies showed that two key metabolic changes that occur in cells during the transition into darkness, changes in the ATP/ADP ratio and redox status of the quinone pool, are cues that entrain the circadian clock. By changing the ATP/ADP ratio or adding oxidized quinone, one can shift the phase of the phosphorylation cycle of the core oscillator in vitro. However, the in vitro oscillator cannot explain gene expression patterns because the simple mixture lacks the output components that connect the clock to genes. Recently, a high-throughput in vitro system termed the in vitro clock (IVC) that contains both the core oscillator and the output components was developed. Here, we used IVC reactions and performed massively parallel experiments to study entrainment, the synchronization of the clock with the environment, in the presence of output components. Our results indicate that the IVC better explains the in vivo clock-resetting phenotypes of wild-type and mutant strains and that the output components are deeply engaged with the core oscillator, affecting the way input signals entrain the core pacemaker. These findings blur the line between input and output pathways and support our previous demonstration that key output components are fundamental parts of the clock.
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Affiliation(s)
- Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA92093
| | - Archana G. Chavan
- School of Natural Sciences, University of California, Merced, CA95343
| | - Andy LiWang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA92093
- School of Natural Sciences, University of California, Merced, CA95343
- Department of Chemistry & Biochemistry, University of California, Merced, CA95343
| | - Susan S. Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA92093
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA92093
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Chenebault C, Blanc-Garin V, Vincent M, Diaz-Santos E, Goudet A, Cassier-Chauvat C, Chauvat F. Exploring the Potential of the Model Cyanobacteria Synechococcus PCC 7002 and PCC 7942 for the Photoproduction of High-Value Terpenes: A Comparison with Synechocystis PCC 6803. Biomolecules 2023; 13:biom13030504. [PMID: 36979439 PMCID: PMC10046388 DOI: 10.3390/biom13030504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
We have performed the first comparative analysis of the potential of two physiologically-diverse model cyanobacteria, Synechococcus PCC 7002 (S.7002) and Synechococcus elongatus PCC 7942 (S.7942), for the photosynthetic production of four chemically-different high-value terpenes: two monoterpenes limonene and pinene, and two sesquiterpenes bisabolene and farnesene. We showed, for the first time, that S.7002 and S.7942 can produce farnesene and bisabolene, respectively. Both cyanobacteria produced farnesene (S.7942 produced more efficiently than S.7002) more efficiently than the other tested terpenes (especially pinene, the weakest produced terpene). S.7002 produced limonene more efficiently than bisabolene, whereas S.7942 produced bisabolene more efficiently than limonene. These findings suggest that S.7942 is better suited to produce sesquiterpenes than monoterpenes. Interestingly, higher levels of terpenes were produced by S.7942 and S.7002 expressing a terpene-synthase gene from both an RSF1010-derived replicating plasmid and a neutral chromosomal site, as compared to either the plasmid alone or the chromosome alone. These results suggest that in both cyanobacteria, the production of terpenes is more limited by the activity of terpene synthases than the abundance of terpene precursors. Finally, higher levels of terpenes were produced by S.7002 growing on urea (a frequent pollutant) as compared to nitrate or ammonium, the standard nitrogen sources for cyanobacteria.
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Affiliation(s)
- Célia Chenebault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Victoire Blanc-Garin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marine Vincent
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Encarnación Diaz-Santos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Amélie Goudet
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, SCBM, 91191 Gif-sur-Yvette, France
| | - Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Franck Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
- Correspondence:
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Yang J, Chi XP, Li M, He WH, Jia R, He PM. Oral administration of Synechococcus sp. PCC7942 trans-vp19 and trans-vp (19+28) genes improve the immune and antioxidant capacity in Procambarus clarkii under white spot syndrome virus stress. Fish Shellfish Immunol 2023; 132:108471. [PMID: 36509413 DOI: 10.1016/j.fsi.2022.108471] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
This study aimed to evaluate antioxidant capacity and protection from white spot syndrome virus (WSSV) challenge of Procambarus clarkii fed trans-vp19 and trans-vp (19 + 28) genes of Synechococcus sp. PCC7942 (Syn7942). P. clarkii were fed transgenic cyanobacteria continuously for 7 days, and then infected with WSSV after 12 h starvation. The daily mortality in each group was measured for 10 days and hepatopancreas and muscle of P. clarkii were examined for enzymes phenoloxidase (PO) activity, catalase (CAT) activity, glutathione peroxidase (GSH-px) activity, and malondialdehyde (MDA) concentration after immunization and viral challenge at different times. Compared with the WSSV-infected crayfish in positive control group (challenge and no vaccination) and wild type group (challenge, feeding wild-type Syn7942), vp19 group (challenge, feeding Syn7942 trans-vp19 gene) and vp (19 + 28) group [challenge, feeding Syn7942 trans-vp (19 + 28) genes] significantly improved the survival rate from 0% to 60% and 56.7%, respectively. Consistently, significantly greater PO, CAT, and GSH-px activity and significantly lower MDA concentration in the vp19 and vp (19 + 28) groups compared to the control group. These results demonstrate that the trans-vp19 and trans-vp (19 + 28) gene of Syn7942 significantly facilitated the immune and antioxidant capacity of crayfish. Therefore, the trans-vp19 and trans-vp (19 + 28) genes of Syn7942 could provide protection for crayfish as an anti-WSSV oral medication.
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Affiliation(s)
- Jia Yang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiao-Ping Chi
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
| | - Man Li
- Department of Pharmacy, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, 201700, China
| | - Wen-Hui He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of River and Lake Biochain Construction and Resource Utilization, Shanghai, 201702, China
| | - Rui Jia
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.
| | - Pei-Min He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.
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Zhong KX, Wirth JF, Chan AM, Suttle CA. Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis. ISME J 2023; 17:105-116. [PMID: 36209336 PMCID: PMC9751121 DOI: 10.1038/s41396-022-01327-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022]
Abstract
Microbes are by far the dominant biomass in the world's oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic, spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here, we show that extracellular ribosomal RNA (rRNAext) is produced by viral lysis, and that specific lysed populations can be identified by sequencing rRNAext recovered from seawater samples. In ten seawater samples collected at five depths between the surface and 265 m during and following a phytoplankton bloom, lysis was detected in about 15% of 16,946 prokaryotic taxa, identified from amplicon sequence variants (ASVs), with lysis occurring in up to 34% of taxa within a water sample. The ratio of rRNAext to cellular rRNA (rRNAcell) was used as an index of taxon-specific lysis, and revealed that higher relative lysis was most commonly associated with copiotrophic bacteria that were in relatively low abundance, such as those in the genera Escherichia and Shigella spp., as well as members of the Bacteriodetes; whereas, relatively low lysis was more common in taxa that are often relatively abundant, such as members of the Pelagibacterales (i.e., SAR11 clade), cyanobacteria in the genus Synechococcus, and members of the phylum Thaumarchaeota (synonym, Nitrososphaerota) that comprised about 13-15% of the 16 S rRNA gene sequences below 30 m. These results provide an explanation for the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. The ability to estimate taxon-specific cell lysis will help explore the distribution and abundance of microbial populations in nature.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Jennifer F Wirth
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Amy M Chan
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada.
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36
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Wang SY, Li X, Wang SG, Xia PF. Base editing for reprogramming cyanobacterium Synechococcus elongatus. Metab Eng 2023; 75:91-99. [PMID: 36403709 DOI: 10.1016/j.ymben.2022.11.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022]
Abstract
Cyanobacteria can directly convert carbon dioxide (CO2) at the atmospheric level to biofuels, value-added chemicals and food products, making them ideal candidates to alleviate global climate change. Despite decades-long pioneering successes, the development of genome-editing tools, especially the CRISPR-Cas-based approaches, seems to lag behind other microbial chassis, slowing down the innovations of cyanobacteria. Here, we adapted and tailored base editing for cyanobacteria based on the CRISPR-Cas system and deamination. We achieved precise and efficient genome editing at a single-nucleotide resolution and demonstrated multiplex base editing in the model cyanobacterium Synechococcus elongatus. By using the base-editing tool, we successfully manipulated the glycogen metabolic pathway via the introduction of premature STOP codons in the relevant genes, building engineered strains with elevated potentials to produce chemicals and food from CO2. We present here the first report of base editing in the phylum of cyanobacteria, and a paradigm for applying CRISPR-Cas systems in bacteria. We believe that our work will accelerate the metabolic engineering and synthetic biology of cyanobacteria and drive more innovations to alleviate global climate change.
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Affiliation(s)
- Shu-Yan Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Xin Li
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China; Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao, 266237, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China.
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Casazza AP, Lombardi A, Menin B, Santabarbara S. Temperature-induced zeaxanthin overproduction in Synechococcus elongatus PCC 7942. Photochem Photobiol Sci 2022; 22:783-794. [PMID: 36536270 DOI: 10.1007/s43630-022-00352-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
Abstract
The exogenous crtZ gene from Brevundimonas sp. SD212, coding for a 3,3' β-car hydroxylase, was expressed in Synechococcus elongatus PCC 7942 under the control of a temperature-inducible promoter in an attempt to engineer the carotenoid metabolic pathway, to increase the content of zeaxanthin and its further hydroxylated derivatives caloxanthin and nostoxanthin. These molecules are of particular interest due to their renowned antioxidant properties. Cultivation of the engineered strain S7942Z-Ti at 35 °C, a temperature which is well tolerated by the wild-type strain and at which the inducible expression system is activated, led to a significant redistribution of the relative carotenoid content. β-Carotene decreased to about 10% of the pool that is an excess of a threefold decrease with respect to the control, and concomitantly, zeaxanthin became the dominant carotenoid accounting for about half of the pool. As a consequence, zeaxanthin and its derivatives caloxanthin and nostoxanthin collectively accounted for about 90% of the accumulated carotenoids. Yet, upon induction of CrtZ expression at 35 °C the S7942Z-Ti strain displayed a substantial growth impairment accompanied, initially, by a relative loss of carotenoids and successively by the appearance of chlorophyll degradation products which can be interpreted as markers of cellular stress. These observations suggest a limit to the exploitation of Synechococcus elongatus PCC 7942 for biotechnological purposes aimed at increasing the production of hydroxylated carotenoids.
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Affiliation(s)
- Anna Paola Casazza
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Via Bassini 15a, 20133, Milan, Italy.
| | - Alessandro Lombardi
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Via Bassini 15a, 20133, Milan, Italy
| | - Barbara Menin
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Via Bassini 15a, 20133, Milan, Italy
| | - Stefano Santabarbara
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Via Bassini 15a, 20133, Milan, Italy.
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Lai MJ, Tsai JC, Lan EI. CRISPRi-enhanced direct photosynthetic conversion of carbon dioxide to succinic acid by metabolically engineered cyanobacteria. Bioresource Technology 2022; 366:128131. [PMID: 36252759 DOI: 10.1016/j.biortech.2022.128131] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering photoautotrophic microorganisms to directly convert carbon dioxide into platform chemicals is an attractive approach for chemical sustainability and carbon mitigation. Here, an engineered cyanobacterium Synechococcus elongatus PCC 7942 was developed to produce succinic acid directly from ambient carbon dioxide. Inhibition of succinate dehydrogenase and glycogen synthase by CRIPSR interference increased carbon flux towards succinic acid. Dual inhibition of these two genes led to an 82 % increase in titer. The resulting strain produced 4.8 g/L of succinic acid in a 28-days cultivation. However, cells after the 28-days cultivation became non-viable and cannot continue production. This issue was addressed by re-inoculation with fresh cells into the production medium. This strategy enabled continuous succinic acid accumulation, reaching a final titer of 8.9 g/L. This study provides a sustainable route to succinic acid directly from carbon dioxide and a potential method to overcome the low titer limitation of cyanobacterial-based bioproduction for practical applications.
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Affiliation(s)
- Martin J Lai
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City 300, Taiwan
| | - Jemmy C Tsai
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City 300, Taiwan
| | - Ethan I Lan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 1001 Daxue Road, Hsinchu City 300, Taiwan.
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Cabello-Yeves PJ, Scanlan DJ, Callieri C, Picazo A, Schallenberg L, Huber P, Roda-Garcia JJ, Bartosiewicz M, Belykh OI, Tikhonova IV, Torcello-Requena A, De Prado PM, Millard AD, Camacho A, Rodriguez-Valera F, Puxty RJ. α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats. ISME J 2022; 16:2421-2432. [PMID: 35851323 PMCID: PMC9477826 DOI: 10.1038/s41396-022-01282-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/25/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet's carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain.
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | | | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET., Av. Intendente Marino Km 8,200, 7130, Chascomús, Buenos Aires, Argentina
- Instituto Nacional de Limnología (INALI), CONICET-UNL., Ciudad Universitaria-Paraje el Pozo s/n, 3000, Santa Fé, Argentina
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Olga I Belykh
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | - Irina V Tikhonova
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | | | | | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980 Paterna, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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Giordano M, Goodman CA, Huang F, Raven JA, Ruan Z. A mechanistic study of the influence of nitrogen and energy availability on the NH4+ sensitivity of nitrogen assimilation in Synechococcus. J Exp Bot 2022; 73:5596-5611. [PMID: 35595516 PMCID: PMC9467657 DOI: 10.1093/jxb/erac219] [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] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/19/2022] [Indexed: 05/23/2023]
Abstract
In most algae, NO3- assimilation is tightly controlled and is often inhibited by the presence of NH4+. In the marine, non-colonial, non-diazotrophic cyanobacterium Synechococcus UTEX 2380, NO3- assimilation is sensitive to NH4+ only when N does not limit growth. We sequenced the genome of Synechococcus UTEX 2380, studied the genetic organization of the nitrate assimilation related (NAR) genes, and investigated expression and kinetics of the main NAR enzymes, under N or light limitation. We found that Synechococcus UTEX 2380 is a β-cyanobacterium with a full complement of N uptake and assimilation genes and NAR regulatory elements. The nitrate reductase of our strain showed biphasic kinetics, previously observed only in freshwater or soil diazotrophic Synechococcus strains. Nitrite reductase and glutamine synthetase showed little response to our growth treatments, and their activity was usually much higher than that of nitrate reductase. NH4+ insensitivity of NAR genes may be associated with the stimulation of the binding of the regulator NtcA to NAR gene promoters by the high 2-oxoglutarate concentrations produced under N limitation. NH4+ sensitivity in energy-limited cells fits with the fact that, under these conditions, the use of NH4+ rather than NO3- decreases N-assimilation cost, whereas it would exacerbate N shortage under N limitation.
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Affiliation(s)
- Mario Giordano
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona 60131, Italy
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA
- Institute of Microbiology ASCR, Algatech, Trebon, Czech Republic
- National Research Council, Institute of Marine Science, Venezia, Italy
| | - Charles A Goodman
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA
| | - Fengying Huang
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5 DA, UK
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo NSW 2007, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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Konarzewska Z, Śliwińska-Wilczewska S, Felpeto AB, Latała A. Effects of light intensity, temperature, and salinity in allelopathic interactions between coexisting Synechococcus sp. phenotypes. Mar Environ Res 2022; 179:105671. [PMID: 35675719 DOI: 10.1016/j.marenvres.2022.105671] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Organisms from the Synechococcus genus constitute one of the major contributors to oceanic primary production, broadly distributed in waters with wide range of environmental conditions. This work investigated the influence of abiotic factors (temperature, irradiance, and salinity) on the strength of allelopathic interactions between different phenotypes of picoplanktonic cyanobacteria of the genus Synechococcus sp. (Type 1, Type 2, and Type 3a) employing mixed cultures and cell-free filtrate assays. The response variables studied were population growth and content of photosynthetic pigments: chlorophyll a (Chl a), carotenoids (Car), phycocyanin (PC), phycoerythrin (PE), and allophycocyanin (APC). Temperature was shown to be the most significant abiotic factor impacting the allelopathy of Synechococcus sp. phenotypes, with the Type 2 most significantly impacted. Irradiance also had a significant effect, having the largest effect on allelopathy of Type 3a phenotype. Changes in salinity had the greatest effect on allelopathy of Type 1. Our study has shown the significant influence of temperature, irradiance, and salinity on the strength of allelopathic compounds secreted by Synechococcus sp. phenotypes, with temperature the most significantly affecting allelopathic properties. Moreover, we discovered that the allelopathic response to changing environmental factors is highly phenotype-specific. This differential response of allelopathy could help different phenotypes of Synechococcus sp. to coexist in the water column.
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Affiliation(s)
- Zofia Konarzewska
- Division of Marine Ecosystems Functioning, Institute of Oceanography, University of Gdańsk, Av. Piłsudskiego 46, 81-378, Gdynia, Poland.
| | - Sylwia Śliwińska-Wilczewska
- Division of Marine Ecosystems Functioning, Institute of Oceanography, University of Gdańsk, Av. Piłsudskiego 46, 81-378, Gdynia, Poland; Mount Allison University, 62 York St, Sackville, NBE4L 1E2, Canada
| | - Aldo Barreiro Felpeto
- Interdisciplinary Center of Marine and Environmental Research-CIMAR/CIIMAR, University of Porto, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Adam Latała
- Division of Marine Ecosystems Functioning, Institute of Oceanography, University of Gdańsk, Av. Piłsudskiego 46, 81-378, Gdynia, Poland
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Mills LA, Moreno-Cabezuelo JÁ, Włodarczyk A, Victoria AJ, Mejías R, Nenninger A, Moxon S, Bombelli P, Selão TT, McCormick AJ, Lea-Smith DJ. Development of a Biotechnology Platform for the Fast-Growing Cyanobacterium Synechococcus sp. PCC 11901. Biomolecules 2022; 12:biom12070872. [PMID: 35883428 PMCID: PMC9313322 DOI: 10.3390/biom12070872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
Synechococcus sp. PCC 11901 reportedly demonstrates the highest, most sustained growth of any known cyanobacterium under optimized conditions. Due to its recent discovery, our knowledge of its biology, including the factors underlying sustained, fast growth, is limited. Furthermore, tools specific for genetic manipulation of PCC 11901 are not established. Here, we demonstrate that PCC 11901 shows faster growth than other model cyanobacteria, including the fast-growing species Synechococcuselongatus UTEX 2973, under optimal growth conditions for UTEX 2973. Comparative genomics between PCC 11901 and Synechocystis sp. PCC 6803 reveal conservation of most metabolic pathways but PCC 11901 has a simplified electron transport chain and reduced light harvesting complex. This may underlie its superior light use, reduced photoinhibition, and higher photosynthetic and respiratory rates. To aid biotechnology applications, we developed a vitamin B12 auxotrophic mutant but were unable to generate unmarked knockouts using two negative selectable markers, suggesting that recombinase- or CRISPR-based approaches may be required for repeated genetic manipulation. Overall, this study establishes PCC 11901 as one of the most promising species currently available for cyanobacterial biotechnology and provides a useful set of bioinformatics tools and strains for advancing this field, in addition to insights into the factors underlying its fast growth phenotype.
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Affiliation(s)
- Lauren A. Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - José Ángel Moreno-Cabezuelo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Artur Włodarczyk
- Bondi Bio Pty Ltd., c/o Climate Change Cluster, University of Technology Sydney, 745 Harris Street, Ultimo, NSW 2007, Australia;
| | - Angelo J. Victoria
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Rebeca Mejías
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Anja Nenninger
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK;
| | - Tiago T. Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
- Correspondence:
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43
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Singh AK, Santos-Merino M, Sakkos JK, Walker BJ, Ducat DC. Rubisco regulation in response to altered carbon status in the cyanobacterium Synechococcus elongatus PCC 7942. Plant Physiol 2022; 189:874-888. [PMID: 35201348 PMCID: PMC9157067 DOI: 10.1093/plphys/kiac065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/22/2021] [Indexed: 05/19/2023]
Abstract
Photosynthetic organisms possess a variety of mechanisms to achieve balance between absorbed light (source) and the capacity to metabolically utilize or dissipate this energy (sink). While regulatory processes that detect changes in metabolic status/balance are relatively well studied in plants, analogous pathways remain poorly characterized in photosynthetic microbes. Here, we explored systemic changes that result from alterations in carbon availability in the model cyanobacterium Synechococcus elongatus PCC 7942 by taking advantage of an engineered strain where influx/efflux of a central carbon metabolite, sucrose, can be regulated experimentally. We observed that induction of a high-flux sucrose export pathway leads to depletion of internal carbon storage pools (glycogen) and concurrent increases in estimates of photosynthetic activity. Further, a proteome-wide analysis and fluorescence reporter-based analysis revealed that upregulated factors following the activation of the metabolic sink are concentrated on ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) and auxiliary modules involved in Rubisco maturation. Carboxysome number and Rubisco activity also increased following engagement of sucrose secretion. Conversely, reversing the flux of sucrose by feeding exogenous sucrose through the heterologous transporter resulted in increased glycogen pools, decreased Rubisco abundance, and carboxysome reorganization. Our data suggest that Rubisco activity and organization are key variables connected to regulatory pathways involved in metabolic balancing in cyanobacteria.
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Affiliation(s)
- Amit K Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Jonathan K Sakkos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Berkley J Walker
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Wang T, Li J, Jing H, Qin S. Picocyanobacterial Synechococcus in marine ecosystem: Insights from genetic diversity, global distribution, and potential function. Mar Environ Res 2022; 177:105622. [PMID: 35429822 DOI: 10.1016/j.marenvres.2022.105622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Marine Synechococcus, a main group of picocyanobacteria, has been ubiquitously observed across the global oceans. Synechococcus exhibits high phylogenetical and phenotypical diversity, and horizontal gene transfer makes its genetic evolution much more intricate. With the development of measurement technologies and analysis methods, the genomic information and niche partition of each Synechococcus lineage tend to be precisely described, but the global analysis is still lacking. Therefore, it is necessary to summarize existing studies and integrate published data to gain a comprehensive understanding of Synechococcus on genetic variation, niche division, and potential functions. In this review, the maximum likelihood trees are constructed based on existing sequence data, including both phylogenetic and pigmentary gene markers. The global distribution characteristics of abundance, lineages, and pigment types are concluded through pooled analysis of more than 700 samples obtained from approximately 50 scientific research cruises. The potential functions of Synechococcus are explored in element cycles and biological interactions. Future work on Synechococcus is suggested to focus on not only elucidating the nature of Synechococcus biodiversity but also demonstrating its interactions with the ecosystem by combining bioinformatics and macroscopic isotope-labeled environmental parameters.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jialin Li
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Conservation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264000, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
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45
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Takatani N, Uenosono M, Hara Y, Yamakawa H, Fujita Y, Omata T. Chlorophyll and Pheophytin Dephytylating Enzymes Required for Efficient Repair of PSII in Synechococcus elongatus PCC 7942. Plant Cell Physiol 2022; 63:410-420. [PMID: 35024866 DOI: 10.1093/pcp/pcac006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The Chlorophyll Dephytylase1 (CLD1) and pheophytinase (PPH) proteins of Arabidopsis thaliana are homologous proteins characterized respectively as a dephytylase for chlorophylls (Chls) and pheophytin a (Phein a) and a Phein a-specific dephytylase. Three genes encoding CLD1/PPH homologs (dphA1, dphA2 and dphA3) were found in the genome of the cyanobacterium Synechococcus elongatus PCC 7942 and shown to be conserved in most cyanobacteria. His6-tagged DphA1, DphA2 and DphA3 proteins were expressed in Escherichia coli, purified to near homogeneity, and shown to exhibit significant levels of dephytylase activity for Chl a and Phein a. Each DphA protein showed similar dephytylase activities for Chl a and Phein a, but the three proteins were distinct in their kinetic properties, with DphA3 showing the highest and lowest Vmax and Km values, respectively, among the three. Transcription of dphA1 and dphA3 was enhanced under high-light conditions, whereas that of dphA2 was not affected by the light conditions. None of the dphA single mutants of S. elongatus showed profound growth defects under low (50 µmol photons m-2 s-1) or high (400 µmol photons m-2 s-1) light conditions. The triple dphA mutant did not show obvious growth defects under these conditions, either, but under illumination of 1,000 µmol photons m-2 s-1, the mutant showed more profound growth retardation compared with wild type (WT). The repair of photodamaged photosystem II (PSII) was much slower in the triple mutant than in WT. These results revealed that dephytylation of Chl a or Phein a or of both is required for efficient repair of photodamaged PSII.
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Affiliation(s)
- Nobuyuki Takatani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Makoto Uenosono
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Yuriko Hara
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Hisanori Yamakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Tatsuo Omata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
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Bairagi N, Watanabe S, Nimura-Matsune K, Tanaka K, Tsurumaki T, Nakanishi S, Tanaka K. Conserved Two-component Hik2-Rre1 Signaling Is Activated Under Temperature Upshift and Plastoquinone-reducing Conditions in the Cyanobacterium Synechococcus elongatus PCC 7942. Plant Cell Physiol 2022; 63:176-188. [PMID: 34750635 DOI: 10.1093/pcp/pcab158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/25/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
The highly conserved Hik2-Rre1 two-component system is a multi-stress responsive signal-transducing module that controls the expression of hsp and other genes in cyanobacteria. Previously, we found in Synechococcus elongatus PCC 7942 that the heat-inducible phosphorylation of Rre1 was alleviated in a hik34 mutant, suggesting that Hik34 positively regulates signaling. In this study, we examined the growth of the hik34 deletion mutant in detail, and newly identified suppressor mutations located in rre1 or sasA gene negating the phenotype. Subsequent analyses indicated that heat-inducible Rre1 phosphorylation is dependent on Hik2 and that Hik34 modulates this Hik2-dependent response. In the following part of this study, we focused on the mechanism to control the Hik2 activity. Other recent studies reported that Hik2 activity is regulated by the redox status of plastoquinone (PQ) through the 3Fe-4S cluster attached to the cyclic GMP, adenylyl cyclase, FhlA (GAF) domain. Consistent with this, Rre1 phosphorylation occurred after the addition of 2,5-dibromo-6-isopropyl-3-methyl-1,4-benzoquinone but not after the addition of 3-(3,4-dichlorophenyl)-1,1-dimethylurea to the culture medium, which corresponded to PQ-reducing or -oxidizing conditions, respectively, suggesting that the Hik2-to-Rre1 phosphotransfer was activated under PQ-reducing conditions. However, there was no correlation between the measured PQ redox status and Rre1 phosphorylation during the temperature upshift. Therefore, changes in the PQ redox status are not the direct reason for the heat-inducible Rre1 phosphorylation, while some redox regulation is likely involved as oxidation events dependent on 2,6-dichloro-1,4-benzoquinone prevented heat-inducible Rre1 phosphorylation. On the basis of these results, we propose a model for the control of Hik2-dependent Rre1 phosphorylation.
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Affiliation(s)
- Nachiketa Bairagi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503 Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Kaori Nimura-Matsune
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531 Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Tatsuhiro Tsurumaki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503 Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531 Japan
- Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503 Japan
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Chen J, Li Y, Jing H, Zhang X, Xu Z, Xu J, Liu H. Genomic and transcriptomic evidence for the diverse adaptations of Synechococcus subclusters 5.2 and 5.3 to mesoscale eddies. New Phytol 2022; 233:1828-1842. [PMID: 34870848 DOI: 10.1111/nph.17903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in the deep euphotic layer. Further analysis indicated that syn-bin1 had a strong ability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. By contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and HCO3- transporters in the deep euphotic layer, which might contribute to its predominance in low-light environments. Overall, this study expands our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.
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Affiliation(s)
- Jiawei Chen
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Yingdong Li
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Sanya, 572000, China
| | - Xiaodong Zhang
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518000, China
| | - Jie Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Sanya, 572000, China
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Jaiswal D, Nenwani M, Mishra V, Wangikar PP. Probing the metabolism of γ-glutamyl peptides in cyanobacteria via metabolite profiling and 13 C labeling. Plant J 2022; 109:708-726. [PMID: 34727398 DOI: 10.1111/tpj.15564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacteria are attractive model organisms for the study of photosynthesis and diurnal metabolism and as hosts for photoautotrophic production of chemicals. Exposure to bright light or environmental pollutants and a diurnal lifestyle of these prokaryotes may result in significant oxidative stress. Glutathione is a widely studied γ-glutamyl peptide that plays a key role in managing oxidative stress and detoxification of xenobiotics in cyanobacteria. The functional role and biosynthesis pathways of this tripeptide have been studied in detail in various phyla, including cyanobacteria. However, other γ-glutamyl peptides remain largely unexplored. We use an integrated approach to identify a number of γ-glutamyl peptides based on signature mass fragments and mass shifts in them in 13 C and 15 N enriched metabolite extracts. The newly identified compounds include γ-glutamyl dipeptides and derivatives of glutathione. Carbon backbones of the former turn over much faster than that of glutathione, suggesting that they follow a distinct biosynthesis pathway. Further, transients of isotopic 13 C enrichment show positional labeling in these peptides, which allows us to delineate the alternative biosynthesis pathways. Importantly, the amino acid of γ-glutamyl dipeptides shows much faster turnover compared to the glutamate moiety. The significant accumulation of γ-glutamyl dipeptides under slow-growth conditions combined with the results from dynamic 13 C labeling suggests that these compounds may act as reservoirs of amino acids in cyanobacteria.
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Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Minal Nenwani
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Vivek Mishra
- 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
- DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
- Wadhwani Research Centre for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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Wendt KE, Walker P, Sengupta A, Ungerer J, Pakrasi HB. Engineering Natural Competence into the Fast-Growing Cyanobacterium Synechococcus elongatus Strain UTEX 2973. Appl Environ Microbiol 2022; 88:e0188221. [PMID: 34705549 PMCID: PMC8752150 DOI: 10.1128/aem.01882-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/25/2021] [Indexed: 11/20/2022] Open
Abstract
Natural transformation is the process by which bacteria actively take up and integrate extracellular DNA into their genomes. In cyanobacteria, natural transformation has only been experimentally demonstrated in a few species. Although cyanobacteria are important model systems for studying photosynthesis and circadian cycling, natural transformation in cyanobacteria has not been characterized to the degree that the process has been studied in other Gram-negative bacteria. Two cyanobacterial species that are 99.8% genetically identical provide a unique opportunity to better understand the nuances of natural transformation in cyanobacteria: Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973 (hereafter called Synechococcus 7942 and Synechococcus 2973, respectively). Synechococcus 7942 is a naturally transformable model system, while Synechococcus 2973 is a recently discovered species that is not naturally competent. Taking only 1.5 h to replicate, Synechococcus 2973 is the fastest-growing cyanobacterial species known and thus is a strong candidate for serving as a model organism. However, its inability to undergo natural transformation has prevented it from becoming a widely used model system. By substituting polymorphic alleles from Synechococcus 7942 for native Synechococcus 2973 alleles, natural transformation was introduced into Synechococcus 2973. Two genetic loci were found to be involved in differential natural competence between the two organisms: transformation pilus component pilN and circadian transcriptional master regulator rpaA. By using targeted genome editing and enrichment outgrowth, a strain that was both naturally transformable and fast-growing was created. This new Synechococcus 2973-T strain will serve as a valuable resource to the cyanobacterial research community. IMPORTANCE Certain bacterial species have the ability to take up naked extracellular DNA and integrate it into their genomes. This process is known as natural transformation and is widely considered to play a major role in bacterial evolution. Because of the ease of introducing new genes into naturally transformable organisms, this capacity is also highly valued in the laboratory. Cyanobacteria are photosynthetic and can therefore serve as model systems for some important aspects of plant physiology. Here, we describe the creation of a modified cyanobacterial strain (Synechococcus 2973-T) that is capable of undergoing natural transformation and has a replication time on par with that of the fastest-growing cyanobacterium discovered to date. This new cyanobacterium has the potential to serve as a new model organism for the cyanobacterial research community and will allow experiments to be completed in a fraction of the time it has taken to complete previous assays.
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Affiliation(s)
- Kristen E. Wendt
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Patricia Walker
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Justin Ungerer
- Department of Biology, Washington University, St. Louis, Missouri, USA
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Vijayakumar S, Angione C. Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002. STAR Protoc 2021; 2:100837. [PMID: 34632416 PMCID: PMC8488602 DOI: 10.1016/j.xpro.2021.100837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Combining a computational framework for flux balance analysis with machine learning improves the accuracy of predicting metabolic activity across conditions, while enabling mechanistic interpretation. This protocol presents a guide to condition-specific metabolic modeling that integrates regularized flux balance analysis with machine learning approaches to extract key features from transcriptomic and fluxomic data. We demonstrate the protocol as applied to Synechococcus sp. PCC 7002; we also outline how it can be adapted to any species or community with available multi-omic data. For complete details on the use and execution of this protocol, please refer to Vijayakumar et al. (2020).
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Affiliation(s)
- Supreeta Vijayakumar
- School of Computing, Engineering & Digital Technologies, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
| | - Claudio Angione
- School of Computing, Engineering & Digital Technologies, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
- Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK
- Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK
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