1
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Wang K, Mahbub M, Mastroianni G, Valladares A, Mullineaux CW. mRNA localization and thylakoid protein biogenesis in the filamentous heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. J Bacteriol 2024:e0032824. [PMID: 39329528 DOI: 10.1128/jb.00328-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024] Open
Abstract
Heterocyst-forming cyanobacteria such as Anabaena (Nostoc) sp. PCC 7120 exhibit extensive remodeling of their thylakoid membranes during heterocyst differentiation. Here we investigate the sites of translation of thylakoid membrane proteins in Anabaena vegetative cells and developing heterocysts, using mRNA fluorescent in situ hybridization (FISH) to detect the location of specific mRNA species. We probed mRNAs encoding reaction center core components and the heterocyst-specific terminal oxidases Cox2 and Cox3. As in unicellular cyanobacteria, the mRNAs encoding membrane-integral thylakoid proteins are concentrated in patches at the inner face of the thylakoid membrane system, adjacent to the central cytoplasm. These patches mark the putative sites of translation and membrane insertion of these proteins. Oxidase activity in mature heterocysts is concentrated in the specialized "honeycomb" regions of the thylakoid membranes close to the cell poles. However, cox2 and cox3 mRNAs remain evenly distributed over the inner face of the thylakoids, implying that oxidase proteins migrate extensively after translation to reach their destination in the honeycomb membranes. The RNA-binding protein RbpG is the closest Anabaena homolog of Rbp3 in the unicellular cyanobacterium Synechocystis sp. PCC 6803, which we previously showed to be crucial for the correct location of photosynthetic mRNAs. An rbpG null mutant shows decreased cellular levels of photosynthetic mRNAs and photosynthetic complexes, coupled with perturbations to thylakoid membrane organization and lower efficiency of the Photosystem II repair cycle. This suggests that the chaperoning of photosynthetic mRNAs by RbpG is important for the correct coordination of thylakoid protein translation and assembly.IMPORTANCECyanobacteria have a complex thylakoid membrane system which is the site of the photosynthetic light reactions as well as most of the respiratory activity in the cell. Protein targeting to the thylakoids and the spatial organization of thylakoid protein biogenesis remain poorly understood. Further complexity is found in some filamentous cyanobacteria that produce heterocysts, specialized nitrogen-fixing cells in which the thylakoid membranes undergo extensive remodeling. Here we probe mRNA locations to reveal thylakoid translation sites in a heterocyst-forming cyanobacterium. We identify an RNA-binding protein important for the correct co-ordination of thylakoid protein translation and assembly, and we demonstrate the effectiveness of mRNA fluorescent in situ hybridization (FISH) as a way to probe cell-specific gene expression in multicellular cyanobacteria.
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Affiliation(s)
- Kexin Wang
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Moontaha Mahbub
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Giulia Mastroianni
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Conrad W Mullineaux
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
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2
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Arévalo S, Pérez Rico D, Abarca D, Dijkhuizen LW, Sarasa-Buisan C, Lindblad P, Flores E, Nierzwicki-Bauer S, Schluepmann H. Genome Engineering by RNA-Guided Transposition for Anabaena sp. PCC 7120. ACS Synth Biol 2024; 13:901-912. [PMID: 38445989 PMCID: PMC10949235 DOI: 10.1021/acssynbio.3c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In genome engineering, the integration of incoming DNA has been dependent on enzymes produced by dividing cells, which has been a bottleneck toward increasing DNA insertion frequencies and accuracy. Recently, RNA-guided transposition with CRISPR-associated transposase (CAST) was reported as highly effective and specific in Escherichia coli. Here, we developed Golden Gate vectors to test CAST in filamentous cyanobacteria and to show that it is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide (sg) RNA encoding the leading but not the reverse complement strand of the target were effective with the protospacer-associated motif (PAM) sequence included in the sgRNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic, which could be used to cure the plasmid. In all six cases analyzed, only the transposon cargo defined by the sequence ranging from left and right elements was inserted at the target loci; therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.
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Affiliation(s)
- Sergio Arévalo
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Daniel Pérez Rico
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dolores Abarca
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Laura W. Dijkhuizen
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cristina Sarasa-Buisan
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Peter Lindblad
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
| | - Enrique Flores
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Sandra Nierzwicki-Bauer
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Henriette Schluepmann
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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3
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Castillo M, Guevara G, Baldanta S, Rodríguez PS, Agudo L, Nogales J, Carrasco AD, Arribas-Aguilar F, Pérez-Pérez J, García JL, Galán B, Navarro Llorens JM. Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems. Microbiol Res 2024; 279:127572. [PMID: 38101163 DOI: 10.1016/j.micres.2023.127572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The filamentous cyanobacterium Limnospira platensis, formerly known as Arthrospira platensis or spirulina, is one of the most commercially important species of microalgae. Due to its high nutritional value, pharmacological and industrial applications it is extensively cultivated on a large commercial scale. Despite its widespread use, its precise manipulation is still under development due to the lack of effective genetic protocols. Genetic transformation of Limnospira has been attempted but the methods reported have not been generally reproducible in other laboratories. Knowledge of the transformation defense mechanisms is essential for understanding its physiology and for broadening their applications. With the aim to understand more about the genetic defenses of L. platensis, in this work we have identified the restriction-modification and CRISPR-Cas systems and we have cloned and characterized thirteen methylases. In parallel, we have also characterized the methylome and orphan methyltransferases using genome-wide analysis of DNA methylation patterns and RNA-seq. The identification and characterization of these enzymes will be a valuable resource to know how this strain avoids being genetically manipulated and for further genomics studies.
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Affiliation(s)
- María Castillo
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Govinda Guevara
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Sara Baldanta
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Patricia Suárez Rodríguez
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Lucía Agudo
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Asunción Díaz Carrasco
- DNA Sequencing facility, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Fernando Arribas-Aguilar
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Julián Pérez-Pérez
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - José Luis García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Beatriz Galán
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
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4
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Liu SJ, Lin GM, Yuan YQ, Chen W, Zhang JY, Zhang CC. A conserved protein inhibitor brings under check the activity of RNase E in cyanobacteria. Nucleic Acids Res 2024; 52:404-419. [PMID: 38000383 PMCID: PMC10783494 DOI: 10.1093/nar/gkad1094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The bacterial ribonuclease RNase E plays a key role in RNA metabolism. Yet, with a large substrate spectrum and poor substrate specificity, its activity must be well controlled under different conditions. Only a few regulators of RNase E are known, limiting our understanding on posttranscriptional regulatory mechanisms in bacteria. Here we show that, RebA, a protein universally present in cyanobacteria, interacts with RNase E in the cyanobacterium Anabaena PCC 7120. Distinct from those known regulators of RNase E, RebA interacts with the catalytic region of RNase E, and suppresses the cleavage activities of RNase E for all tested substrates. Consistent with the inhibitory function of RebA on RNase E, depletion of RNase E and overproduction of RebA caused formation of elongated cells, whereas the absence of RebA and overproduction of RNase E resulted in a shorter-cell phenotype. We further showed that the morphological changes caused by altered levels of RNase E or RebA are dependent on their physical interaction. The action of RebA represents a new mechanism, potentially conserved in cyanobacteria, for RNase E regulation. Our findings provide insights into the regulation and the function of RNase E, and demonstrate the importance of balanced RNA metabolism in bacteria.
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Affiliation(s)
- Su-Juan Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gui-Ming Lin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
| | - Yu-Qi Yuan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ju-Yuan Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
| | - Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China
- Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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5
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Graf J, Schöpperle M, Pernil R, Schleiff E. Two TonB-dependent outer membrane transporters involved in heme uptake in Anabaena sp. PCC 7120. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:16-28. [PMID: 38234586 PMCID: PMC10792254 DOI: 10.15698/mic2024.01.812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 01/19/2024]
Abstract
Low availability of micronutrients such as iron has enforced the evolution of uptake systems in all kingdoms of life. In Gram-negative bacteria, outer membrane, periplasmatic and plasma membrane localized proteins facilitate the uptake of iron-loaded chelators, which are energized by TonB proteins. The specificity of different uptake systems likely depends either on the endogenously produced siderophore or on the bioavailability of iron-chelator complexes in the environment. Hence, an uptake system for schizokinen produced by the model cyanobacterium Anabaena sp. PCC 7120 exists, while bioinformatics analysis suggests the existence of additional systems, likely for uptake of xenosiderophores. Consistently, proteins encoded by alr2153 (hutA1) and alr3242 (hutA2) are assigned as outer membrane heme transporters. Indeed, Anabaena sp. PCC 7120 can utilize external heme as an iron source. The addition of heme resulted in an induction of genes involved in heme degradation and chlorophyll a synthesis and in an increase of the chlorophyll a content. Moreover, iron starvation induced the expression of hutA1, while the addition of heme led to its repression. Remarkably, the addition of a high concentration of heme but not iron starvation resulted in hutA2 induction. Plasmid insertion mutants of both genes exhibited a reduced capacity to recover from iron starvation by heme addition, which indicates a dependence of heme uptake on functional HutA1 and HutA2 proteins. The structural model generated by bioinformatics methods is further in agreement with a role in heme uptake. Thus, we provide evidence that Anabaena sp. PCC 7120 uses a heme uptake system in parallel to other iron acquisition systems.
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Affiliation(s)
- Julia Graf
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Martin Schöpperle
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Current address: Lonza Cologne GmbH, Köln, Germany:
| | - Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Max von Laue Str. 11, 60438 Frankfurt, Germany
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6
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Zedler JAZ, Schirmacher AM, Russo DA, Hodgson L, Gundersen E, Matthes A, Frank S, Verkade P, Jensen PE. Self-Assembly of Nanofilaments in Cyanobacteria for Protein Co-localization. ACS NANO 2023; 17:25279-25290. [PMID: 38065569 PMCID: PMC10754207 DOI: 10.1021/acsnano.3c08600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/27/2023]
Abstract
Cyanobacteria offer great potential as alternative biotechnological hosts due to their photoautotrophic capacities. However, in comparison to established heterotrophic hosts, several key aspects, such as product titers, are still lagging behind. Nanobiotechnology is an emerging field with great potential to improve existing hosts, but so far, it has barely been explored in microbial photosynthetic systems. Here, we report the establishment of large proteinaceous nanofilaments in the unicellular model cyanobacterium Synechocystis sp. PCC 6803 and the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. Transmission electron microscopy and electron tomography demonstrated that expression of pduA*, encoding a modified bacterial microcompartment shell protein, led to the generation of bundles of longitudinally aligned nanofilaments in S. elongatus UTEX 2973 and shorter filamentous structures in Synechocystis sp. PCC 6803. Comparative proteomics showed that PduA* was at least 50 times more abundant than the second most abundant protein in the cell and that nanofilament assembly had only a minor impact on cellular metabolism. Finally, as a proof-of-concept for co-localization with the filaments, we targeted a fluorescent reporter protein, mCitrine, to PduA* by fusion with an encapsulation peptide that natively interacts with PduA. The establishment of nanofilaments in cyanobacterial cells is an important step toward cellular organization of heterologous pathways and the establishment of cyanobacteria as next-generation hosts.
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Affiliation(s)
- Julie A. Z. Zedler
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alexandra M. Schirmacher
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - David A. Russo
- Bioorganic
Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Lorna Hodgson
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Emil Gundersen
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Annemarie Matthes
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Stefanie Frank
- Department
of Biochemical Engineering, University College
London, London, WC1E 6BT, United
Kingdom
| | - Paul Verkade
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Poul Erik Jensen
- Department
of Food Science, University of Copenhagen, 1958 Frederiksberg, Denmark
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7
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Valladares A, Picossi S, Corrales-Guerrero L, Herrero A. The role of SepF in cell division and diazotrophic growth in the multicellular cyanobacterium Anabaena sp. strain PCC 7120. Microbiol Res 2023; 277:127489. [PMID: 37716126 DOI: 10.1016/j.micres.2023.127489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/23/2023] [Accepted: 09/09/2023] [Indexed: 09/18/2023]
Abstract
The cyanobacterium Anabaena forms filaments of cells that grow by intercalary cell division producing adjoined daughter cells connected by septal junction protein complexes that provide filament cohesion and intercellular communication, representing a genuine case of bacterial multicellularity. In spite of their diderm character, cyanobacterial genomes encode homologs of SepF, a protein normally found in Gram-positive bacteria. In Anabaena, SepF is an essential protein that localized to the cell division ring and the intercellular septa. Overexpression of sepF had detrimental effects on growth, provoking conspicuous alterations in cell morphology that resemble the phenotype of mutants impaired in cell division, and altered the localization of the division-ring. SepF interacted with FtsZ and with the essential FtsZ tether ZipN. Whereas SepF from unicellular bacteria generally induces the bundling of FtsZ filaments, Anabaena SepF inhibited FtsZ bundling, reducing the thickness of the toroidal aggregates formed by FtsZ alone and eventually preventing FtsZ polymerization. Thus, in Anabaena SepF appears to have an essential role in cell division by limiting the polymerization of FtsZ to allow the correct formation and localization of the Z-ring. Expression of sepF is downregulated during heterocyst differentiation, likely contributing to the inhibition of Z-ring formation in heterocysts. Finally, the localization of SepF in intercellular septa and its interaction with the septal-junction related proteins SepJ and SepI suggest a role of SepF in the formation or stability of the septal complexes that mediate cell-cell adhesion and communication, processes that are key for the multicellular behavior of Anabaena.
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Affiliation(s)
- A Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - S Picossi
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - L Corrales-Guerrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - A Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain.
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8
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Wu S, Zheng H, Wang Y, Wang L, Chen W. Cyanobacterial bioreporter of nitrate bioavailability in aquatic ecosystems. WATER RESEARCH 2023; 247:120749. [PMID: 37918203 DOI: 10.1016/j.watres.2023.120749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The water eutrophication, resulting from the discharge of industrial and agricultural wastewater, leads to ecological degradation. However, to date, how to assess and manage the risks of water pollution, especially nitrogen pollution, remains a particularly noteworthy issue. Nitrate, the most important nitrogen compound, has become a bottleneck restricting total nitrogen management. The development of bioreporters monitoring nitrate pollution contributes to the estimation of water quality, especially the availability of nutrients. In this study, we obtained 9 bioreporters from 40 cyanobacterial derivatives which were constructed based on different hosts, copy numbers, and sensing elements and evaluated the performance of bioreporters. The results showed that single-celled Synechocystis was more sensitive to nitrate than filamentous Anabaena, that the reporter gene luxABCDE responded faster than sfgfp in most bioreporters, and that relatively medium-copy plasmid improved the performance of sensing elements. Nine bioreporters performed well in bioavailable nitrate detection, of which AD-AS-X and AR-NI-X, activated by nitrate repletion, had the shortest response time (2 h) and the widest response range (20-800 μM), respectively. Moreover, SR-GLN-SG, activated by nitrate deficiency, exhibited the best linear response (R2 = 0.998). After parameter optimization, exponential growth phase bioreporters, culture temperature of 30 °C, sample volume of 200 μL were determined as optimal monitoring conditions. We found that common water contaminants (copper, cadmium, and phosphorus) had no impact on the performance of bioreporters, indicating the stability of bioreporters. Six out of 9 bioreporters, especially the SR-NB-X, were highly effective in detecting the bioavailable nitrate in wastewater sample. This study provides valuable references for developing more cyanobacterial bioreporters and their practical application in nitrate detection.
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Affiliation(s)
- Shanyu Wu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hongyan Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuwei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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9
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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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10
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Velázquez-Suárez C, Springstein BL, Nieves-Morión M, Helbig AO, Kieninger AK, Maldener I, Nürnberg DJ, Stucken K, Luque I, Dagan T, Herrero A. SepT, a novel protein specific to multicellular cyanobacteria, influences peptidoglycan growth and septal nanopore formation in Anabaena sp. PCC 7120. mBio 2023; 14:e0098323. [PMID: 37650636 PMCID: PMC10653889 DOI: 10.1128/mbio.00983-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Multicellular organization is a requirement for the development of complex organisms, and filamentous cyanobacteria such as Anabaena represent a paradigmatic case of bacterial multicellularity. The Anabaena filament can include hundreds of communicated cells that exchange nutrients and regulators and, depending on environmental conditions, can include different cell types specialized in distinct biological functions. Hence, the specific features of the Anabaena filament and how they are propagated during cell division represent outstanding biological issues. Here, we studied SepT, a novel coiled-coil-rich protein of Anabaena that is located in the intercellular septa and influences the formation of the septal specialized structures that allow communication between neighboring cells along the filament, a fundamental trait for the performance of Anabaena as a multicellular organism.
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Affiliation(s)
| | | | - Mercedes Nieves-Morión
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Andreas O. Helbig
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Ann-Katrin Kieninger
- Department of Microbiology/Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Iris Maldener
- Department of Microbiology/Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics and Dahlem Centre of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Karina Stucken
- Department of Food Engineering, Universidad de La Serena, La Serena, Chile
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
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11
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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12
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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] [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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13
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Chen Y, Ge P, Sun T, Feng J, Li G, Zhang J, Zhou J, Jiang J. Coexpression of Tail Fiber and Tail Protein Genes of the Cyanophage PP Using a Synthetic Genomics Approach Enhances the Salt Tolerance of Synechocystis PCC 6803. Microbiol Spectr 2023; 11:e0500922. [PMID: 37125914 PMCID: PMC10269589 DOI: 10.1128/spectrum.05009-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
Cyanophages are viruses that specifically infect cyanobacteria and are capable of regulating the population densities and seasonal distributions of cyanobacteria. However, few studies have investigated the interactions between cyanophages and heterologous hosts, owing to the inability of cyanophages to infect heterologous cyanobacterial hosts. Here, a truncated artificial cyanophage genome, Syn-P4-8, was designed and assembled that contained 18 genes for viral coat assembly proteins but not genes related to host infection or DNA replication. Syn-P4-8 was transferred into the heterologous host Synechocystis sp. PCC 6803 by conjugation. The growth of strain CS-02 carrying Syn-P4-8 was significantly better than that of the control strain when grown in medium containing 5% NaCl. Only two cyanophage genes, encoding the tail protein (open reading frame 25 [ORF25]) and the tail fiber protein (ORF26), were transcribed in Synechocystis PCC 6803 grown in BG11 medium supplemented with 5% NaCl. However, expression of either ORF25 or ORF26 alone could not recover this phenotype. In addition, transcriptomic analysis revealed the presence of 334 differentially expressed genes in CS-02 compared to the control strain, corresponding to 151 downregulated and 183 upregulated genes that may affect cyanobacterial salt tolerances. In this study, synthetic biology methods were used to strengthen our understanding of the interactions between cyanophage genes and heterologous hosts. IMPORTANCE We synthesized and assembled a truncated cyanophage genome called Syn-P4-8, containing 18 genes for viral coat assembly proteins, and transferred it into a nonhost strain, Synechocystis sp. PCC 6803, to investigate interactions between Syn-P4-8 and Synechocystis PCC 6803. We found that coexpression of tail fiber and tail protein genes enhanced the salt tolerance of Synechocystis PCC 6803.
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Affiliation(s)
- Yu Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China
| | - Pingbo Ge
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China
| | - Tao Sun
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Jia Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China
| | - Guorui Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China
| | - Jiabao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China
| | - Jianting Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology, Tianjin University, Tianjin, China
| | - Jianlan Jiang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology, Tianjin University, Tianjin, China
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14
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Wang ZQ, Yang Y, Zhang JY, Zeng X, Zhang CC. Global translational control by the transcriptional repressor TrcR in the filamentous cyanobacterium Anabaena sp. PCC 7120. Commun Biol 2023; 6:643. [PMID: 37322092 PMCID: PMC10272220 DOI: 10.1038/s42003-023-05012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Transcriptional and translational regulations are important mechanisms for cell adaptation to environmental conditions. In addition to house-keeping tRNAs, the genome of the filamentous cyanobacterium Anabaena sp. strain PCC 7120 (Anabaena) has a long tRNA operon (trn operon) consisting of 26 genes present on a megaplasmid. The trn operon is repressed under standard culture conditions, but is activated under translational stress in the presence of antibiotics targeting translation. Using the toxic amino acid analog β-N-methylamino-L-alanine (BMAA) as a tool, we isolated and characterized several BMAA-resistance mutants from Anabaena, and identified one gene of unknown function, all0854, named as trcR, encoding a transcription factor belonging to the ribbon-helix-helix (RHH) family. We provide evidence that TrcR represses the expression of the trn operon and is thus the missing link between the trn operon and translational stress response. TrcR represses the expression of several other genes involved in translational control, and is required for maintaining translational fidelity. TrcR, as well as its binding sites, are highly conserved in cyanobacteria, and its functions represent an important mechanism for the coupling of the transcriptional and translational regulations in cyanobacteria.
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Affiliation(s)
- Zi-Qian Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- Institute AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei, People's Republic of China.
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15
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Ortiz Charneco G, Kelleher P, Buivydas A, Dashko S, de Waal PP, van Peij NNME, Roberts RJ, Mahony J, van Sinderen D. Delineation of a lactococcal conjugation system reveals a restriction-modification evasion system. Microb Biotechnol 2023; 16:1250-1263. [PMID: 36942662 DOI: 10.1111/1751-7915.14221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 03/23/2023] Open
Abstract
Plasmid pUC11B is a 49.3-kb plasmid harboured by the fermented meat isolate Lactococcus lactis subsp. lactis UC11. Among other features, pUC11B encodes a pMRC01-like conjugation system and tetracycline-resistance. In this study, we demonstrate that this plasmid can be conjugated at high frequencies to recipient strains. Mutational analysis of the 22 genes encompassing the presumed pUC11B conjugation cluster revealed the presence of several genes with essential conjugation functions, as well as a gene, trsR, encoding a putative transcriptional repressor of this conjugation cluster. Furthermore, plasmid pUC11B encodes an anti-restriction protein, TrsAR, which facilitates higher conjugation frequencies when pUC11B is transferred into recipient strains containing Type II or Type III RM systems. These findings demonstrate how RM mechanisms can be circumvented when they act as a biological barrier for conjugation events.
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Affiliation(s)
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Sofia Dashko
- DSM Food and Beverage, Center for Food Innovation, Delft, The Netherlands
| | - Paul P de Waal
- DSM Food and Beverage, Center for Food Innovation, Delft, The Netherlands
| | | | | | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork, Ireland
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16
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Control of Cell Size by c-di-GMP Requires a Two-Component Signaling System in the Cyanobacterium Anabaena sp. Strain PCC 7120. Microbiol Spectr 2023; 11:e0422822. [PMID: 36625639 PMCID: PMC9927289 DOI: 10.1128/spectrum.04228-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Each bacterial species possesses a specific cell size and morphology, which constitute important and recognizable physical traits. How bacteria maintain their particular cell size and morphology remains an essential question in microbiology. Cyanobacteria are oxygen-evolving photosynthetic prokaryotes. Although monophyletic, these organisms are highly diverse in their cell morphology and cell size. How these physical traits of cyanobacteria are controlled is poorly understood. Here, we report the identification of a two-component signaling system, composed of a histidine kinase CdgK and a response regulator CdgS, involved in cell size regulation in the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Inactivation of cdgK or cdgS led to reduction of cell length and width with little effect on cell growth capacity. CdgS has a GGDEF domain responsible for the synthesis of the second messenger c-di-GMP. Based on genetic and biochemical studies, we proposed a signaling pathway initiated by CdgK, leading to the phosphorylation of CdgS, and thereby an enhanced enzymatic activity for c-di-GMP synthesis of the latter. The GGDEF domain of CdgS was essential in cell size control, and the reduction of cell size observed in various mutants could be rescued by the expression of a c-di-GMP synthetase from E. coli. These results provided evidence that a minimal threshold of c-di-GMP level was required for maintaining cell size in Anabaena. IMPORTANCE Cyanobacteria are considered the first organisms to produce oxygen on Earth, and their activities shaped the evolution of our ecosystems. Cell size is an important trait fixed early in evolution, with the diversification of micro- and macrocyanobacterial species during the Great Oxidation Event. However, the genetic basis underlying cell size control in cyanobacteria was not understood. Our studies demonstrated that the CdgK-CdgS signaling pathway participates in the control of cell size, and their absence did not affect cell growth. CdgK has multiple domains susceptible to signal input, which are necessary for cell size regulation. This observation suggests that cell size in Anabaena could respond to environmental signals. These studies paved the way for genetic dissection of cell size regulation in cyanobacteria.
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17
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Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:455. [PMID: 36838420 PMCID: PMC9964548 DOI: 10.3390/microorganisms11020455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Department of Biology, University of Padua, 35100 Padua, Italy
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Natha, QLD 4111, Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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18
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Sakamaki Y, Maeda K, Nimura-Matsune K, Chibazakura T, Watanabe S. Characterization of a cyanobacterial rep protein with broad-host range and its utilization for expression vectors. Front Microbiol 2023; 14:1111979. [PMID: 37032853 PMCID: PMC10079941 DOI: 10.3389/fmicb.2023.1111979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Owing to their photosynthetic capabilities, cyanobacteria are regarded as ecologically friendly hosts for production of biomaterials. However, compared to other bacteria, tools for genetic engineering, especially expression vector systems, are limited. In this study, we characterized a Rep protein, exhibiting replication activity in multiple cyanobacteria and established an expression vector using this protein. Our comprehensive screening using a genomic library of Synechocystis sp. PCC 6803 revealed that a certain region encoding a Rep-related protein (here named Cyanobacterial Rep protein A2: CyRepA2) exhibits high autonomous replication activity in a heterologous host cyanobacterium, Synechococcus elongatus PCC 7942. A reporter assay using GFP showed that the expression vector pYS carrying CyRepA2 can be maintained in not only S. 6803 and S. 7942, but also Synechococcus sp. PCC 7002 and Anabaena sp. PCC 7120. In S. 7942, GFP expression in the pYS-based system was tightly regulated by IPTG, achieving 10-fold higher levels than in the chromosome-based system. Furthermore, pYS could be used together with the conventional vector pEX, which was constructed from an endogenous plasmid in S. 7942. The combination of pYS with other vectors is useful for genetic engineering, such as modifying metabolic pathways, and is expected to improve the performance of cyanobacteria as bioproduction chassis.
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Affiliation(s)
- Yutaka Sakamaki
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Kaisei Maeda
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | | | - Taku Chibazakura
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
- *Correspondence: Satoru Watanabe,
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19
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Baldanta S, Arnal R, Blanco-Rivero A, Guevara G, Navarro Llorens JM. First characterization of cultivable extremophile Chroococcidiopsis isolates from a solar panel. Front Microbiol 2023; 14:982422. [PMID: 36876112 PMCID: PMC9982165 DOI: 10.3389/fmicb.2023.982422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Introduction Microorganisms colonize a wide range of natural and artificial environments. Even though most of them are unculturable in laboratory conditions, some ecosystems are ideal niches for bioprospecting extremophiles with unique properties. Up today, there are few reports concerning microbial communities found on solar panels, a widespread, artificial, extreme habitat. Microorganisms found in this habitat belong to drought-, heat- and radiation-adapted genera, including fungi, bacteria, and cyanobacteria. Methods Here we isolated and identified several cyanobacteria from a solar panel. Then, some strains isolated were characterizated for their resistance to desiccation, UV-C exposition, and their growth on a range of temperature, pH, NaCl concentration or diverse carbon and nitrogen sources. Finally, gene transfer to these isolates was evaluated using several SEVA plasmids with different replicons to assess their potential in biotechnological applications. Results and discussion This study presents the first identification and characterization of cultivable extremophile cyanobacteria from a solar panel in Valencia, Spain. The isolates are members of the genera Chroococcidiopsis, Leptolyngbya, Myxacorys, and Oculatella all genera with species commonly isolated from deserts and arid regions. Four of the isolates were selected, all of them Chroococcidiopsis, and characterized. Our results showed that all Chroococcidiopsis isolates chosen were resistant up to a year of desiccation, viable after exposition to high doses of UV-C, and capable of being transformed. Our findings revealed that a solar panel is a useful ecological niche in searching for extremophilic cyanobacteria to further study the desiccation and UV-tolerance mechanisms. We conclude that these cyanobacteria can be modified and exploited as candidates for biotechnological purposes, including astrobiology applications.
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Affiliation(s)
- Sara Baldanta
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raquel Arnal
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Amaya Blanco-Rivero
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Govinda Guevara
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Juana María Navarro Llorens
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
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20
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Zhang T, Xu B, Feng J, Ge P, Li G, Zhang J, Zhou J, Jiang J. Synthesis and assembly of full-length cyanophage A-4L genome. Synth Syst Biotechnol 2022; 8:121-128. [PMID: 36605707 PMCID: PMC9803696 DOI: 10.1016/j.synbio.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Artificial cyanophages are considered to be an effective biological method to control harmful cyanobacterial bloom. However, no synthetic cyanophage genome has been constructed and where its obstacles are unclear. Here, we survey a stretch of 16 kb length sequence of cyanophage A-4L that is unclonable in Escherichia coli. We test 12 predicted promoters of cyanophage A-4L which were verified all active in E. coli. Next, we screen for eight ORFs that hindered the assembly of intermediate DNA fragments in E. coli and describe that seven ORFs in the 16 kb sequence could not be separately cloned in E. coli. All of unclonable ORFs in high-copy-number plasmid were successfully cloned using low-copy-number vector, suggesting that these ORFs were copy-number-dependent. We propose a clone strategy abandoned the promotor and the start codon that could be applied for unclonable ORFs. Last, we de novo synthesized and assembled the full-length genome of cyanophage A-4L. This work deepens the understanding of synthetic cyanophages studies.
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Affiliation(s)
- Ting Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Bonan Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Jia Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Pingbo Ge
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Guorui Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Jiabao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Jianting Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China,Corresponding author. School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Jianlan Jiang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China,Corresponding author. School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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21
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Baldanta S, Guevara G, Navarro-Llorens JM. SEVA-Cpf1, a CRISPR-Cas12a vector for genome editing in cyanobacteria. Microb Cell Fact 2022; 21:103. [PMID: 35643551 PMCID: PMC9148489 DOI: 10.1186/s12934-022-01830-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/13/2022] [Indexed: 12/01/2022] Open
Abstract
Background Cyanobacteria are photosynthetic autotrophs that have tremendous potential for fundamental research and industrial applications due to their high metabolic plasticity and ability to grow using CO2 and sunlight. CRISPR technology using Cas9 and Cpf1 has been applied to different cyanobacteria for genome manipulations and metabolic engineering. Despite significant advances with genome editing in several cyanobacteria strains, the lack of proper genetic toolboxes is still a limiting factor compared to other model laboratory species. Among the limitations, it is essential to have versatile plasmids that could ease the benchwork when using CRISPR technology. Results In the present study, several CRISPR-Cpf1 vectors were developed for genetic manipulations in cyanobacteria using SEVA plasmids. SEVA collection is based on modular vectors that enable the exchangeability of diverse elements (e.g. origins of replication and antibiotic selection markers) and the combination with many cargo sequences for varied end-applications. Firstly, using SEVA vectors containing the broad host range RSF1010 origin we demonstrated that these vectors are replicative not only in model cyanobacteria but also in a new cyanobacterium specie, Chroococcidiopsis sp., which is different from those previously published. Then, we constructed SEVA vectors by harbouring CRISPR elements and showed that they can be easily assimilated not only by conjugation, but also by natural transformation. Finally, we used our SEVA-Cpf1 tools to delete the nblA gene in Synechocystis sp. PCC 6803, demonstrating that our plasmids can be applied for CRISPR-based genome editing technology. Conclusions The results of this study provide new CRISPR-based vectors based on the SEVA (Standard European Vector Architecture) collection that can improve editing processes using the Cpf1 nuclease in cyanobacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01830-4.
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22
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Opel F, Siebert NA, Klatt S, Tüllinghoff A, Hantke JG, Toepel J, Bühler B, Nürnberg DJ, Klähn S. Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria. ACS Synth Biol 2022; 11:1758-1771. [PMID: 35405070 DOI: 10.1021/acssynbio.1c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria have raised great interest in biotechnology due to their potential for a sustainable, photosynthesis-driven production of fuels and value-added chemicals. This has led to a concomitant development of molecular tools to engineer the metabolism of those organisms. In this regard, however, even cyanobacterial model strains lag behind compared to their heterotrophic counterparts. For instance, replicative shuttle vectors that allow gene transfer independent of recombination into host DNA are still scarce. Here, we introduce the pSOMA shuttle vector series comprising 10 synthetic plasmids for comprehensive genetic engineering of Synechocystis sp. PCC 6803. The series is based on the small endogenous plasmids pCA2.4 and pCB2.4, each combined with a replicon from Escherichia coli, different selection markers as well as features facilitating molecular cloning and the insulated introduction of gene expression cassettes. We made use of genes encoding green fluorescent protein (GFP) and a Baeyer-Villiger monooxygenase (BVMO) to demonstrate functional gene expression from the pSOMA plasmids in vivo. Moreover, we demonstrate the expression of distinct heterologous genes from individual plasmids maintained in the same strain and thereby confirmed compatibility between the two pSOMA subseries as well as with derivatives of the broad-host-range plasmid RSF1010. We also show that gene transfer into the filamentous model strain Anabaena sp. PCC 7120 is generally possible, which is encouraging to further explore the range of cyanobacterial host species that could be engineered via pSOMA plasmids. Altogether, the pSOMA shuttle vector series displays an attractive alternative to existing plasmid series and thus meets the current demand for the introduction of complex genetic setups and to perform extensive metabolic engineering of cyanobacteria.
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Affiliation(s)
- Franz Opel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Nina A. Siebert
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Sabine Klatt
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Adrian Tüllinghoff
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Janis G. Hantke
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Toepel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stephan Klähn
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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23
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Whitman BT, Murray CRA, Whitford DS, Paul SS, Fahlman RP, Glover MJN, Owttrim GW. Degron-mediated proteolysis of CrhR-like DEAD-box RNA helicases in cyanobacteria. J Biol Chem 2022; 298:101925. [PMID: 35413287 PMCID: PMC9117542 DOI: 10.1016/j.jbc.2022.101925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 11/18/2022] Open
Abstract
Conditional proteolytic degradation is an irreversible and highly regulated process that fulfills crucial regulatory functions in all organisms. As proteolytic targets tend to be critical metabolic or regulatory proteins, substrates are targeted for degradation only under appropriate conditions through the recognition of an amino acid sequence referred to as a “degron”. DEAD-box RNA helicases mediate all aspects of RNA metabolism, contributing to cellular fitness. However, the mechanism by which abiotic-stress modulation of protein stability regulates bacterial helicase abundance has not been extensively characterized. Here, we provide in vivo evidence that proteolytic degradation of the cyanobacterial DEAD-box RNA helicase CrhR is conditional, being initiated by a temperature upshift from 20 to 30 °C in the model cyanobacterium, Synechocystis sp. PCC 6803. We show degradation requires a unique, highly conserved, inherently bipartite degron located in the C-terminal extension found only in CrhR-related RNA helicases in the phylum Cyanobacteria. However, although necessary, the degron is not sufficient for proteolysis, as disruption of RNA helicase activity and/or translation inhibits degradation. These results suggest a positive feedback mechanism involving a role for CrhR in expression of a crucial factor required for degradation. Furthermore, AlphaFold structural prediction indicated the C-terminal extension is a homodimerization domain with homology to other bacterial RNA helicases, and mass photometry data confirmed that CrhR exists as a dimer in solution at 22 °C. These structural data suggest a model wherein the CrhR degron is occluded at the dimerization interface but could be exposed if dimerization was disrupted by nonpermissive conditions.
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Affiliation(s)
- Brendan T Whitman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Cameron R A Murray
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Denise S Whitford
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Simanta S Paul
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Richard P Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mark J N Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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24
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Divya TV, Acharya C. AzuR From the SmtB/ArsR Family of Transcriptional Repressors Regulates Metallothionein in Anabaena sp. Strain PCC 7120. Front Microbiol 2022; 12:782363. [PMID: 35095796 PMCID: PMC8790569 DOI: 10.3389/fmicb.2021.782363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
Metallothioneins (MTs) are cysteine-rich, metal-sequestering cytosolic proteins that play a key role in maintaining metal homeostasis and detoxification. We had previously characterized NmtA, a MT from the heterocystous, nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 and demonstrated its role in providing protection against cadmium toxicity. In this study, we illustrate the regulation of Anabaena NmtA by AzuR (Alr0831) belonging to the SmtB/ArsR family of transcriptional repressors. There is currently no experimental evidence for any functional role of AzuR. It is observed that azuR is located within the znuABC operon but in the opposite orientation and remotely away from the nmtA locus. Sequence analysis of AzuR revealed a high degree of sequence identity with Synechococcus SmtB and a distinct α5 metal binding site similar to that of SmtB. In order to characterize AzuR, we overexpressed it in Escherichia coli and purified it by chitin affinity chromatography. Far-UV circular dichroism spectroscopy indicated that the recombinant AzuR protein possessed a properly folded structure. Glutaraldehyde cross-linking and size-exclusion chromatography revealed that AzuR exists as a dimer of ∼28 kDa in solution. Analysis of its putative promoter region [100 bp upstream of nmtA open reading frame (ORF)] identified the presence of a 12–2–12 imperfect inverted repeat as the cis-acting element important for repressor binding. Electrophoretic mobility shift assays (EMSAs) showed concentration-dependent binding of recombinant dimeric AzuR with the promoter indicating that NmtA is indeed a regulatory target of AzuR. Binding of AzuR to DNA was disrupted in the presence of metal ions like Zn2+, Cd2+, Cu2+, Co2+, Ni2+, Pb2+, and Mn2+. The metal-dependent dissociation of protein–DNA complexes suggested the negative regulation of metal-inducible nmtA expression by AzuR. Overexpression of azuR in its native strain Anabaena 7120 enhanced the susceptibility to cadmium stress significantly. Overall, we propose a negative regulation of Anabaena MT by an α5 SmtB/ArsR metalloregulator AzuR.
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Affiliation(s)
- T V Divya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
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25
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Abstract
Anabaena sp. PCC7120 (hereafter Anabaena 7120) is a nitrogen-fixing, filamentous cyanobacterium. Given its diverse metabolism, it serves as an excellent model organism, particularly for studying cell differentiation, nitrogen fixation, photosynthesis, production of high-value chemicals, and synthetic biology. Gene knockout is a common approach to assess the function of gene products through assessing phenotypic loss of function. In the method described here, a double crossover approach is used to inactivate a target gene or target genes in Anabaena 7120. This method involves replicating the gene(s) from the wild-type genomic DNA and inserting them into an integrative plasmid vector. An internal portion of the genes may be removed and replaced with a GFP-Spectinomycin (gfp-sp) cassette. The plasmid is then introduced into Anabaena 7120 where a double crossover event occurs between the wild-type chromosome and the cargo plasmid, effectively replacing the wild-type gene with the disrupted gene from the plasmid. The gfp-sp cassette combined with the sacB gene serve as positive selection to identify double crossover mutants (Cai and Wolk (1990), 172(6):3138-3145, J. Bacteriol). Finally, the functional genes are cloned into another replicating plasmid vector to produce a cargo plasmid, which is conjugatively introduced into the mutant for a complementation test. By comparing the phenotypes among the wild-type, mutant, and complement, one should see a loss of function in the mutant which is recovered in the complement, thereby defining the function of the target gene. The double crossover approach described here for Anabaena PCC 7120 may be broadly applicable to the study of gene function in cyanobacteria and other prokaryotic organisms.
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Affiliation(s)
- Jaimie Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Liping Gu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.
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26
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Sengupta A, Liu D, Pakrasi HB. CRISPR-Cas mediated genome engineering of cyanobacteria. Methods Enzymol 2022; 676:403-432. [DOI: 10.1016/bs.mie.2022.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Gibbons J, Gu L, Qiu Y, Zhou R. Single Crossover to Inactivate Target Gene in Cyanobacteria. Methods Mol Biol 2022; 2489:289-298. [PMID: 35524056 DOI: 10.1007/978-1-0716-2273-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Anabaena sp. PCC 7120 (hereafter Anabaena 7120) is a model cyanobacterium for studying pathways such as photosynthesis and nitrogen fixation along with many other metabolic pathways common to plants. In addition, since Anabaena 7120 forms specialized N2-fixing cells, called heterocysts, to perform uniquely solar-powered, oxic nitrogen fixation under fixed-nitrogen depleted conditions, this cyanobacterium provides the unique opportunity to study cellular differentiation in bacteria. Since more than 155,810 sequenced prokaryotic genomes are currently available (Zhang et al., Microbiome 8(1):134, 2020), target gene inactivation, combined with analyses of the corresponding mutant's phenotype, has become a powerful tool to assess gene function through detecting a loss-of-function in the knockout mutant. In the method described here, a single crossover approach is used to knockout a target gene in Anabaena 7120. The method requires inserting an internal fragment of the target gene into the cyanobacterial integration vector pZR606 to create a knockout plasmid, and then is introduced to Anabaena 7120 via conjugative transformation. A single crossover, occurring via homologous recombination, disrupts the target gene, creating 3'- and 5'-deleted fragments (Fig. 1). The mutant containing the inactivated gene can then be studied to determine any loss of function, thereby defining the gene's function. This gene inactivation approach is based on an integrative vector pZR606 (Chen et al., Appl Microbiol Biotechnol 99:1779-1793, 2015), which may be broadly applied to gene inactivation in other cyanobacterial species as well as other prokaryotic organisms.
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Affiliation(s)
- Jaimie Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Liping Gu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yeyan Qiu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.
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28
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The Molecular Toolset and Techniques Required to Build Cyanobacterial Cell Factories. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022. [DOI: 10.1007/10_2022_210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Bandyopadhyay A, Ye Z, Benedikty Z, Trtilek M, Pakrasi HB. Antenna Modification Leads to Enhanced Nitrogenase Activity in a High Light-Tolerant Cyanobacterium. mBio 2021; 12:e0340821. [PMID: 34933453 PMCID: PMC8689445 DOI: 10.1128/mbio.03408-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/11/2023] Open
Abstract
Biological nitrogen fixation is an energy-intensive process that contributes significantly toward supporting life on this planet. Among nitrogen-fixing organisms, cyanobacteria remain unrivaled in their ability to fuel the energetically expensive nitrogenase reaction with photosynthetically harnessed solar energy. In heterocystous cyanobacteria, light-driven, photosystem I (PSI)-mediated ATP synthesis plays a key role in propelling the nitrogenase reaction. Efficient light transfer to the photosystems relies on phycobilisomes (PBS), the major antenna protein complexes. PBS undergo degradation as a natural response to nitrogen starvation. Upon nitrogen availability, these proteins are resynthesized back to normal levels in vegetative cells, but their occurrence and function in heterocysts remain inconclusive. Anabaena 33047 is a heterocystous cyanobacterium that thrives under high light, harbors larger amounts of PBS in its heterocysts, and fixes nitrogen at higher rates compared to other heterocystous cyanobacteria. To assess the relationship between PBS in heterocysts and nitrogenase function, we engineered a strain that retains large amounts of the antenna proteins in its heterocysts. Intriguingly, under high light intensities, the engineered strain exhibited unusually high rates of nitrogenase activity compared to the wild type. Spectroscopic analysis revealed altered PSI kinetics in the mutant with increased cyclic electron flow around PSI, a route that contributes to ATP generation and nitrogenase activity in heterocysts. Retaining higher levels of PBS in heterocysts appears to be an effective strategy to enhance nitrogenase function in cyanobacteria that are equipped with the machinery to operate under high light intensities. IMPORTANCE The function of phycobilisomes, the large antenna protein complexes in heterocysts has long been debated. This study provides direct evidence of the involvement of these proteins in supporting nitrogenase activity in Anabaena 33047, a heterocystous cyanobacterium that has an affinity for high light intensities. This strain was previously known to be recalcitrant to genetic manipulation and, hence, despite its many appealing traits, remained largely unexplored. We developed a genetic modification system for this strain and generated a ΔnblA mutant that exhibited resistance to phycobilisome degradation upon nitrogen starvation. Physiological characterization of the strain indicated that PBS degradation is not essential for acclimation to nitrogen deficiency and retention of PBS is advantageous for nitrogenase function.
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Affiliation(s)
| | - Zi Ye
- Department of Biology, Washington University, St. Louis, Missouri, USA
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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30
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Huang M, Zhang JY, Zeng X, Zhang CC. c-di-GMP Homeostasis Is Critical for Heterocyst Development in Anabaena sp. PCC 7120. Front Microbiol 2021; 12:793336. [PMID: 34925302 PMCID: PMC8682488 DOI: 10.3389/fmicb.2021.793336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/09/2021] [Indexed: 12/04/2022] Open
Abstract
c-di-GMP is a ubiquitous bacterial signal regulating various physiological process. Anabaena PCC 7120 (Anabaena) is a filamentous cyanobacterium able to form regularly-spaced heterocysts for nitrogen fixation, in response to combined-nitrogen deprivation in 24h. Anabaena possesses 16 genes encoding proteins for c-di-GMP metabolism, and their functions are poorly characterized, except all2874 (cdgS) whose deletion causes a decrease in heterocyst frequency 48h after nitrogen starvation. We demonstrated here that c-di-GMP levels increased significantly in Anabaena after combined-nitrogen starvation. By inactivating each of the 16 genes, we found that the deletion of all1175 (cdgSH) led to an increase of heterocyst frequency 24h after nitrogen stepdown. A double mutant ΔcdgSHΔcdgS had an additive effect over the single mutants in regulating heterocyst frequency, indicating that the two genes acted at different time points for heterocyst spacing. Biochemical and genetic data further showed that the functions of CdgSH and CdgS in the setup or maintenance of heterocyst frequency depended on their opposing effects on the intracellular levels of c-di-GMP. Finally, we demonstrated that heterocyst differentiation was completely inhibited when c-di-GMP levels became too high or too low. Together, these results indicate that the homeostasis of c-di-GMP level is important for heterocyst differentiation in Anabaena.
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Affiliation(s)
- Min Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.,Institut AMU-WUT, Aix-Marseille University and Wuhan University of Technology, Wuhan, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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31
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Chavan AG, Swan JA, Heisler J, Sancar C, Ernst DC, Fang M, Palacios JG, Spangler RK, Bagshaw CR, Tripathi S, Crosby P, Golden SS, Partch CL, LiWang A. Reconstitution of an intact clock reveals mechanisms of circadian timekeeping. Science 2021; 374:eabd4453. [PMID: 34618577 DOI: 10.1126/science.abd4453] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Archana G Chavan
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jeffrey A Swan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Joel Heisler
- Department of Chemistry and Biochemistry, University of California, Merced, CA 95343, USA
| | - Cigdem Sancar
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dustin C Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph G Palacios
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Clive R Bagshaw
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Priya Crosby
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, CA 95343, USA.,Department of Chemistry and Biochemistry, University of California, Merced, CA 95343, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, CA 95343, USA.,Health Sciences Research Institute, University of California, Merced, CA 95343, USA
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32
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Wongpayak P, Meesungnoen O, Saejang S, Subsoontorn P. A highly effective and self-transmissible CRISPR antimicrobial for elimination of target plasmids without antibiotic selection. PeerJ 2021; 9:e11996. [PMID: 34567840 PMCID: PMC8428258 DOI: 10.7717/peerj.11996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023] Open
Abstract
The use of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) for sequence-specific elimination of bacteria or resistance genes is a powerful tool for combating antibiotic resistance. However, this approach requires efficient delivery of CRISPR/Cas DNA cassette(s) into the targeted bacterial population. Compared to phage transduction, plasmid conjugation can deliver DNA to a broader host range but often suffers from low delivery efficiency. Here, we developed multi-plasmid conjugation systems for efficient CRISPR/Cas delivery, target DNA elimination and plasmid replacement. The CRISPR/Cas system, delivered via a broad-host-range R1162 mobilizable plasmid, specifically eliminated the targeted plasmid in recipient cells. A self-transmissible RK2 helper plasmid facilitated the spread of mobilizable CRISPR/Cas. The replacement of the target plasmid with another plasmid from the same compatibility group helped speed up target plasmid elimination especially when the target plasmid was also mobilizable. Together, we showed that up to 100% of target plasmid from the entire recipient population could be replaced even at a low (1:180) donor-to-recipient ratio and in the absence of transconjugant selection. Such an ability to modify genetic content of microbiota efficiently in the absence of selection will be critical for future development of CRISPR antimicrobials as well as genetic tools for in situ microbiome engineering.
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Affiliation(s)
- Panjaporn Wongpayak
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
| | | | - Somchai Saejang
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
| | - Pakpoom Subsoontorn
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
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33
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Racharaks R, Arnold W, Peccia J. Development of CRISPR-Cas9 knock-in tools for free fatty acid production using the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. J Microbiol Methods 2021; 189:106315. [PMID: 34454980 DOI: 10.1016/j.mimet.2021.106315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022]
Abstract
Synechococcus elongatus UTEX 2973 has one of the fastest measured doubling time of cyanobacteria making it an important candidate for metabolic engineering. Traditional genetic engineering methods, which rely on homologous recombination, however, are inefficient, labor-intensive, and time-consuming due to the oligoploidy or polyploidy nature of cyanobacteria and the reliance on unique antibiotic resistance markers. CRISPR-Cas9 has emerged as an effective and versatile editing platform in a wide variety of organisms, but its application for cyanobacterial engineering is limited by the inherent toxicity of Cas9 resulting in poor transformation efficiencies. Here, we demonstrated that a single-plasmid CRISPR-Cas9 system, pCRISPOmyces-2, can effectively knock-in a truncated thioesterase gene from Escherichia coli to generate free fatty acid (FFA) producing mutants of Syn2973. To do so, three parameters were evaluated on the effect of generating recipient colonies after conjugation with pCRISPOmyces-2-based plasmids: 1) a modified conjugation protocol termed streaked conjugation, 2) the deletion of the gene encoding RecJ exonuclease, and 3) single guide RNA (sgRNA) sequence. With the use of the streaked conjugation protocol and a ΔrecJ mutant strain of Syn2973, the conjugation efficiency for the pCRISPomyces-2 plasmid could be improved by 750-fold over the wildtype (WT) for a conjugation efficiency of 2.0 × 10-6 transconjugants/recipient cell. While deletion of the RecJ exonuclease alone increased the conjugation efficiency by 150-fold over the WT, FFA generation was impaired in FFA-producing mutants with the ΔrecJ background, and the large number of poor FFA-producing isolates indicated the potential increase in spontaneous mutation rates. The sgRNA sequence was found to be critical in achieving the desired CRISPR-Cas9-mediated knock-in mutation as the sgRNA impacts conjugation efficiency, likelihood of homogenous recombinants, and free fatty acid production in engineered strains.
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Affiliation(s)
- Ratanachat Racharaks
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Wyatt Arnold
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA.
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McGuffie MJ, Barrick JE. pLannotate: engineered plasmid annotation. Nucleic Acids Res 2021; 49:W516-W522. [PMID: 34019636 PMCID: PMC8262757 DOI: 10.1093/nar/gkab374] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Engineered plasmids are widely used in the biological sciences. Since many plasmids contain DNA sequences that have been reused and remixed by researchers for decades, annotation of their functional elements is often incomplete. Missing information about the presence, location, or precise identity of a plasmid feature can lead to unintended consequences or failed experiments. Many engineered plasmids contain sequences—such as recombinant DNA from all domains of life, wholly synthetic DNA sequences, and engineered gene expression elements—that are not predicted by microbial genome annotation pipelines. Existing plasmid annotation tools have limited feature libraries and do not detect incomplete fragments of features that are present in many plasmids for historical reasons and may impact their newly designed functions. We created the open source pLannotate web server so users can quickly and comprehensively annotate plasmid features. pLannotate is powered by large databases of genetic parts and proteins. It employs a filtering algorithm to display only the most relevant feature matches and also reports feature fragments. Finally, pLannotate displays a graphical map of the annotated plasmid, explains the provenance of each feature prediction, and allows results to be downloaded in a variety of formats. The webserver for pLannotate is accessible at: http://plannotate.barricklab.org/
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Affiliation(s)
- Matthew J McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, 2500 Speedway A5000, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, 2500 Speedway A5000, Austin, TX 78712, USA
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Yunus IS, Wang Z, Sattayawat P, Muller J, Zemichael FW, Hellgardt K, Jones PR. Improved Bioproduction of 1-Octanol Using Engineered Synechocystis sp. PCC 6803. ACS Synth Biol 2021; 10:1417-1428. [PMID: 34003632 DOI: 10.1021/acssynbio.1c00029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
1-Octanol has gained interest as a chemical precursor for both high and low value commodities including fuel, solvents, surfactants, and fragrances. By harnessing the power from sunlight and CO2 as carbon source, cyanobacteria has recently been engineered for renewable production of 1-octanol. The productivity, however, remained low. In the present work, we report efforts to further improve the 1-octanol productivity. Different N-terminal truncations were evaluated on three thioesterases from different plant species, resulting in several candidate thioesterases with improved activity and selectivity toward octanoyl-ACP. The structure/function trials suggest that current knowledge and/or state-of-the art computational tools are insufficient to determine the most appropriate cleavage site for thioesterases in Synechocystis. Additionally, by tuning the inducer concentration and light intensity, we further improved the 1-octanol productivity, reaching up to 35% (w/w) carbon partitioning and a titer of 526 ± 5 mg/L 1-octanol in 12 days. Long-term cultivation experiments demonstrated that the improved strain can be stably maintained for at least 30 days and/or over ten times serial dilution. Surprisingly, the improved strain was genetically stable in contrast to earlier strains having lower productivity (and hence a reduced chance of reaching toxic product concentrations). Altogether, improved enzymes and environmental conditions (e.g., inducer concentration and light intensity) substantially increased the 1-octanol productivity. When cultured under continuous conditions, the bioproduction system reached an accumulative titer of >3.5 g/L 1-octanol over close to 180 days.
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Affiliation(s)
- Ian Sofian Yunus
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Zhixuan Wang
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Pachara Sattayawat
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jonathan Muller
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Fessehaye W. Zemichael
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Klaus Hellgardt
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Patrik R. Jones
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
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Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria. mBio 2021; 12:e0087321. [PMID: 34060332 PMCID: PMC8262939 DOI: 10.1128/mbio.00873-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The mechanisms driving cyanobacterial harmful algal blooms (HABs) like those caused by Microcystis aeruginosa remain elusive, but improved defense against viral predation has been implicated for success in eutrophic environments. Our genus-level analyses of 139,023 genomes revealed that HAB-forming cyanobacteria carry vastly more restriction modification systems per genome (RMPG) than nearly all other prokaryotic genera, suggesting that viral defense is a cornerstone of their ecological success. In contrast, picocyanobacteria that numerically dominate nutrient-poor systems have the fewest RMPG within the phylum Cyanobacteria. We used classic resource competition models to explore the hypothesis that nutrient enrichments drive ecological selection for high RMPG due to increased host-phage contact rate. These classic models, agnostic to the mechanism of defense, explain how nutrient loading can select for increased RMPG but, importantly, fail to explain the extreme accumulation of these defense systems. However, extreme accumulation of RMPG can be achieved in a novel “memory” model that accounts for a unique activity of restriction modification systems: the accidental methylation of viral DNA by the methyltransferase. The methylated virus “remembers” the RM defenses of its former host and can evade these defenses if they are present in the next host. This viral memory leads to continual RM system devaluation; RMs accumulate extensively because the benefit of each addition is diminished. Our modeling leads to the hypothesis that nutrient loading and virion methylation drive the extreme accumulation of RMPG in HAB-forming cyanobacteria. Finally, our models suggest that hosts with different RMPG values can coexist when hosts have unique sets of RM systems.
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Roh H, Lee JS, Choi HI, Sung YJ, Choi SY, Woo HM, Sim SJ. Improved CO 2-derived polyhydroxybutyrate (PHB) production by engineering fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 for potential utilization of flue gas. BIORESOURCE TECHNOLOGY 2021; 327:124789. [PMID: 33556769 DOI: 10.1016/j.biortech.2021.124789] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Industrial application of cyanobacterial poly-β-hydroxybutyrate (PHB) production from CO2 is currently challenged by slow growth rate and low photoautotrophic PHB productivity of existing cyanobacteria species. Herein, a novel PHB-producing cyanobacterial strain was developed by harnessing fast-growing cyanobacteria Synechococcus elongatus UTEX 2973 with introduction of heterologous phaCAB genes. Under photoautotrophic condition, the engineered strain produced 420 mg L-1 (16.7% of dry cell weight) with the highest specific productivity of 75.2 mg L-1 d-1. When compared with a native PHB producer Synechocystis PCC 6803 under nitrogen deprivation, the engineered strain exhibited 2.4-fold higher PHB productivity. The performance of the engineered strain was further demonstrated in large scale cultivation using photobioreactor and outdoor cultivation employing industrial flue gas as the sole carbon source. This study can provide a promising solution to address petroleum-based plastic waste and contribute to CO2 mitigation.
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Affiliation(s)
- Hyejin Roh
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Jeong Seop Lee
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Hong Il Choi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Young Joon Sung
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Sun Young Choi
- SOL inc, 2BK Tower 2F, 28 Beopwon-ro 11-gil, Songpa-gu, Seoul, Seoul 0583, South Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, South Korea; BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, South Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.
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Arbel-Goren R, Buonfiglio V, Di Patti F, Camargo S, Zhitnitsky A, Valladares A, Flores E, Herrero A, Fanelli D, Stavans J. Robust, coherent, and synchronized circadian clock-controlled oscillations along Anabaena filaments. eLife 2021; 10:64348. [PMID: 33749592 PMCID: PMC8064755 DOI: 10.7554/elife.64348] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/20/2021] [Indexed: 02/01/2023] Open
Abstract
Circadian clocks display remarkable reliability despite significant stochasticity in biomolecular reactions. We study the dynamics of a circadian clock-controlled gene at the individual cell level in Anabaena sp. PCC 7120, a multicellular filamentous cyanobacterium. We found significant synchronization and spatial coherence along filaments, clock coupling due to cell-cell communication, and gating of the cell cycle. Furthermore, we observed low-amplitude circadian oscillatory transcription of kai genes encoding the post-transcriptional core oscillatory circuit and high-amplitude oscillations of rpaA coding for the master regulator transducing the core clock output. Transcriptional oscillations of rpaA suggest an additional level of regulation. A stochastic one-dimensional toy model of coupled clock cores and their phosphorylation states shows that demographic noise can seed stochastic oscillations outside the region where deterministic limit cycles with circadian periods occur. The model reproduces the observed spatio-temporal coherence along filaments and provides a robust description of coupled circadian clocks in a multicellular organism.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Valentina Buonfiglio
- Dipartimento di Fisica e Astronomia, Università di Firenze, INFN and CSDC, Sesto Fiorentino, Italy
| | - Francesca Di Patti
- Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, Sesto Fiorentino, Italy
| | - Sergio Camargo
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Zhitnitsky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Duccio Fanelli
- Dipartimento di Fisica e Astronomia, Università di Firenze, INFN and CSDC, Sesto Fiorentino, Italy
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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Lin PC, Zhang F, Pakrasi HB. Enhanced limonene production in a fast-growing cyanobacterium through combinatorial metabolic engineering. Metab Eng Commun 2021; 12:e00164. [PMID: 33659180 PMCID: PMC7890178 DOI: 10.1016/j.mec.2021.e00164] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Terpenoids are a large and diverse group of natural products with commercial applications. Microbial production of terpenes is considered as a feasible approach for the stable supply of these complex hydrocarbons. Cyanobacteria, photosynthetic prokaryotes, are attractive hosts for sustainable bioproduction, because these autotrophs require only light and CO2 for growth. Despite cyanobacteria having been engineered to produce a variety of compounds, their productivities of terpenes are generally low. Further research is needed to determine the bottleneck reactions for enhancing terpene production in cyanobacteria. In this study, we engineered the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce a commercially-used terpenoid, limonene. We identified a beneficial mutation in the gene encoding geranylgeranyl pyrophosphate synthase crtE, leading to a 2.5-fold increase in limonene production. The engineered strain produced 16.4 mg L−1 of limonene at a rate of 8.2 mg L−1 day−1, which is 8-fold higher than limonene productivities previously reported in other cyanobacterial species. Furthermore, we employed a combinatorial metabolic engineering approach to optimize genes involved in the upstream pathway of limonene biosynthesis. By modulating the expression of genes encoding the enzymes in the MEP pathway and the geranyl pyrophosphate synthase, we showed that optimization of the expression level is critical to enhance limonene production in cyanobacteria. Engineering of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973 for limonene production. Identification of a beneficial mutation with 2.5-fold increase in limonene productivity. Pathway optimization for limonene biosynthesis.
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Affiliation(s)
- Po-Cheng Lin
- Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
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The Two TpsB-Like Proteins in Anabaena sp. Strain PCC 7120 Are Involved in Secretion of Selected Substrates. J Bacteriol 2021; 203:JB.00568-20. [PMID: 33257527 DOI: 10.1128/jb.00568-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/23/2020] [Indexed: 11/20/2022] Open
Abstract
The outer membrane of Gram-negative bacteria acts as an initial diffusion barrier that shields the cell from the environment. It contains many membrane-embedded proteins required for functionality of this system. These proteins serve as solute and lipid transporters or as machines for membrane insertion or secretion of proteins. The genome of Anabaena sp. strain PCC 7120 codes for two outer membrane transporters termed TpsB1 and TpsB2. They belong to the family of the two-partner secretion system proteins which are characteristic of pathogenic bacteria. Because pathogenicity of Anabaena sp. strain PCC 7120 has not been reported, the function of these two cyanobacterial TpsB proteins was analyzed. TpsB1 is encoded by alr1659, while TpsB2 is encoded by all5116 The latter is part of a genomic region containing 11 genes encoding TpsA-like proteins. However, tpsB2 is transcribed independently of a tpsA gene cluster. Bioinformatics analysis revealed the presence of at least 22 genes in Anabaena sp. strain PCC 7120 putatively coding for substrates of the TpsB system, suggesting a rather global function of the two TpsB proteins. Insertion of a plasmid into each of the two genes resulted in altered outer membrane integrity and antibiotic resistance. In addition, the expression of genes coding for the Clp and Deg proteases is dysregulated in these mutants. Moreover, for two of the putative substrates, a dependence of the secretion on functional TpsB proteins could be confirmed. We confirm the existence of a two-partner secretion system in Anabaena sp. strain PCC 7120 and predict a large pool of putative substrates.IMPORTANCE Cyanobacteria are important organisms for the ecosystem, considering their contribution to carbon fixation and oxygen production, while at the same time some species produce compounds that are toxic to their environment. As a consequence, cyanobacterial overpopulation might negatively impact the diversity of natural communities. Thus, a detailed understanding of cyanobacterial interaction with the environment, including other organisms, is required to define their impact on ecosystems. While two-partner secretion systems in pathogenic bacteria are well known, we provide a first description of the cyanobacterial two-partner secretion system.
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Mustila H, Kugler A, Stensjö K. Isobutene production in Synechocystis sp. PCC 6803 by introducing α-ketoisocaproate dioxygenase from Rattus norvegicus. Metab Eng Commun 2021; 12:e00163. [PMID: 33552898 PMCID: PMC7856465 DOI: 10.1016/j.mec.2021.e00163] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/28/2022] Open
Abstract
Cyanobacteria can be utilized as a platform for direct phototrophic conversion of CO2 to produce several types of carbon-neutral biofuels. One promising compound to be produced photobiologically in cyanobacteria is isobutene. As a volatile compound, isobutene will quickly escape the cells without building up to toxic levels in growth medium or get caught in the membranes. Unlike liquid biofuels, gaseous isobutene may be collected from the headspace and thus avoid the costly extraction of a chemical from culture medium or from cells. Here we investigate a putative synthetic pathway for isobutene production suitable for a photoautotrophic host. First, we expressed α-ketoisocaproate dioxygenase from Rattus norvegicus (RnKICD) in Escherichia coli. We discovered isobutene formation with the purified RnKICD with the rate of 104.6 ± 9 ng (mg protein)-1 min-1 using α-ketoisocaproate as a substrate. We further demonstrate isobutene production in the cyanobacterium Synechocystis sp. PCC 6803 by introducing the RnKICD enzyme. Synechocystis strain heterologously expressing the RnKICD produced 91 ng l−1 OD750−1 h−1. Thus, we demonstrate a novel sustainable platform for cyanobacterial production of an important building block chemical, isobutene. These results indicate that RnKICD can be used to further optimize the synthetic isobutene pathway by protein and metabolic engineering efforts. Photosynthetic isobutene production is demonstrated in a cyanobacterium. A Synechocystis strain capable of continuous direct conversion of CO2 to isobutene. α-ketoisocaproate dioxygenase from R. norvegicus (RnKICD) is determined to form isobutene. RnKICD can convert α-ketoisocaproate to isobutene both in vitro and in vivo.
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Affiliation(s)
- Henna Mustila
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
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RNA Interference by Cyanobacterial Feeding Demonstrates the SCSG1 Gene Is Essential for Ciliogenesis during Oral Apparatus Regeneration in Stentor. Microorganisms 2021; 9:microorganisms9010176. [PMID: 33467569 PMCID: PMC7830263 DOI: 10.3390/microorganisms9010176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/17/2022] Open
Abstract
In the giant ciliate Stentor coeruleus, oral apparatus (OA) regeneration is an experimentally tractable regeneration paradigm that occurs via a series of morphological steps. OA regeneration is thought to be driven by a complex regulatory system that orchestrates the temporal expression of conserved and specific genes. We previously identified a S. coeruleus-specific gene (named SCSG1) that was significantly upregulated during the ciliogenesis stages of OA regeneration, with an expression peak at the stage of the first OA cilia appearance. We established a novel RNA interference (RNAi) method through cyanobacteria Synechocystis sp. PCC6803 feeding in S. coeruleus. The expression of SCSG1 gene was significantly knocked down by using this method and induced abnormal ciliogenesis of OA regeneration in S. coeruleus, suggesting that SCSG1 is essential for OA regeneration in S. coeruleus. This novel RNAi method by cyanobacterial feeding has potential utility for studying other ciliates.
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Taton A, Ecker A, Diaz B, Moss NA, Anderson B, Reher R, Leão TF, Simkovsky R, Dorrestein PC, Gerwick L, Gerwick WH, Golden JW. Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host. ACS Synth Biol 2020; 9:3364-3376. [PMID: 33180461 DOI: 10.1021/acssynbio.0c00431] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Filamentous marine cyanobacteria make a variety of bioactive molecules that are produced by polyketide synthases, nonribosomal peptide synthetases, and hybrid pathways that are encoded by large biosynthetic gene clusters. These cyanobacterial natural products represent potential drug leads; however, thorough pharmacological investigations have been impeded by the limited quantity of compound that is typically available from the native organisms. Additionally, investigations of the biosynthetic gene clusters and enzymatic pathways have been difficult due to the inability to conduct genetic manipulations in the native producers. Here we report a set of genetic tools for the heterologous expression of biosynthetic gene clusters in the cyanobacteria Synechococcus elongatus PCC 7942 and Anabaena (Nostoc) PCC 7120. To facilitate the transfer of gene clusters in both strains, we engineered a strain of Anabaena that contains S. elongatus homologous sequences for chromosomal recombination at a neutral site and devised a CRISPR-based strategy to efficiently obtain segregated double recombinant clones of Anabaena. These genetic tools were used to express the large 28.7 kb cryptomaldamide biosynthetic gene cluster from the marine cyanobacterium Moorena (Moorea) producens JHB in both model strains. S. elongatus did not produce cryptomaldamide; however, high-titer production of cryptomaldamide was obtained in Anabaena. The methods developed in this study will facilitate the heterologous expression of biosynthetic gene clusters isolated from marine cyanobacteria and complex metagenomic samples.
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Inactivation of Three RG(S/T)GR Pentapeptide-Containing Negative Regulators of HetR Results in Lethal Differentiation of Anabaena PCC 7120. Life (Basel) 2020; 10:life10120326. [PMID: 33291589 PMCID: PMC7761841 DOI: 10.3390/life10120326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 12/19/2022] Open
Abstract
The filamentous cyanobacterium Anabaena sp. PCC 7120 produces, during the differentiation of heterocysts, a short peptide PatS and a protein HetN, both containing an RGSGR pentapeptide essential for activity. Both act on the master regulator HetR to guide heterocyst pattern formation by controlling the binding of HetR to DNA and its turnover. A third small protein, PatX, with an RG(S/T)GR motif is present in all HetR-containing cyanobacteria. In a nitrogen-depleted medium, inactivation of patX does not produce a discernible change in phenotype, but its overexpression blocks heterocyst formation. Mutational analysis revealed that PatX is not required for normal intercellular signaling, but it nonetheless is required when PatS is absent to prevent rapid ectopic differentiation. Deprivation of all three negative regulators—PatS, PatX, and HetN—resulted in synchronous differentiation. However, in a nitrogen-containing medium, such deprivation leads to extensive fragmentation, cell lysis, and aberrant differentiation, while either PatX or PatS as the sole HetR regulator can establish and maintain a semiregular heterocyst pattern. These results suggest that tight control over HetR by PatS and PatX is needed to sustain vegetative growth and regulated development. The mutational analysis has been interpreted in light of the opposing roles of negative regulators of HetR and the positive regulator HetL.
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45
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Wang Z, Chen Q, Zhang J, Guan T, Chen Y, Shi W. Critical roles of cyanobacteria as reservoir and source for antibiotic resistance genes. ENVIRONMENT INTERNATIONAL 2020; 144:106034. [PMID: 32777621 DOI: 10.1016/j.envint.2020.106034] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
The widespread occurrence of antibiotic resistance genes (ARGs) throughout aquatic environments has raised global concerns for public health, but understanding of the emergence and propagation of ARGs in diverse environmental media remains limited. This study investigated the occurrence and spatio-temporal patterns of six classes of ARGs in cyanobacteria isolated from Taihu Lake. Tetracycline and sulfonamide resistance genes were identified as dominant ARGs. The abundance of ARGs in cyanobacteria was significantly higher in the bloom period than in the non-bloom period. The contribution and persistence of ARGs were higher in extracellular DNA (eDNA) than in intracellular DNA (iDNA) from cyanobacteria. Cyanobacteria-associated eDNA carrying ARGs was more stable at lower temperature. The relative abundances of ARGs in Microcystis and Synechococcus, the dominant genera of cyanobacterial blooms in Taihu Lake, were significantly higher than those in other cyanobacterial strains. The conjugative transfer efficiency for bacterial assimilation of ARGs in cyanobacteria was facilitated by increasing temperature and cyanobacterial cell concentration. Our results demonstrated that cyanobacteria could act as a significant reservoir and source for the acquisition and dissemination of ARGs in aquatic environments, hence the definition of negative ecological effects of cyanobacterial blooms was expanded.
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Affiliation(s)
- Zhiyuan Wang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Qiuwen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China.
| | - Jianyun Zhang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Tiesheng Guan
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Yuchen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Wenqing Shi
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
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Schirmacher AM, Hanamghar SS, Zedler JAZ. Function and Benefits of Natural Competence in Cyanobacteria: From Ecology to Targeted Manipulation. Life (Basel) 2020; 10:E249. [PMID: 33105681 PMCID: PMC7690421 DOI: 10.3390/life10110249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023] Open
Abstract
Natural competence is the ability of a cell to actively take up and incorporate foreign DNA in its own genome. This trait is widespread and ecologically significant within the prokaryotic kingdom. Here we look at natural competence in cyanobacteria, a group of globally distributed oxygenic photosynthetic bacteria. Many cyanobacterial species appear to have the genetic potential to be naturally competent, however, this ability has only been demonstrated in a few species. Reasons for this might be due to a high variety of largely uncharacterised competence inducers and a lack of understanding the ecological context of natural competence in cyanobacteria. To shed light on these questions, we describe what is known about the molecular mechanisms of natural competence in cyanobacteria and analyse how widespread this trait might be based on available genomic datasets. Potential regulators of natural competence and what benefits or drawbacks may derive from taking up foreign DNA are discussed. Overall, many unknowns about natural competence in cyanobacteria remain to be unravelled. A better understanding of underlying mechanisms and how to manipulate these, can aid the implementation of cyanobacteria as sustainable production chassis.
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Affiliation(s)
| | | | - Julie A. Z. Zedler
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (A.M.S.); (S.S.H.)
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Molecular organizations and function of iron-stress-induced-A protein family in Anabaena sp. PCC 7120. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148327. [PMID: 33069682 DOI: 10.1016/j.bbabio.2020.148327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 11/22/2022]
Abstract
Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions, and surround photosystem I (PSI) trimer with a ring formation. A cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, it is unknown how the IsiAs are associated with PSI. Here we report on molecular organizations and function of the IsiAs in this cyanobacterium. A deletion mutant of the isiA1 gene was constructed, and the four types of thylakoids were prepared from the wild-type (WT) and ΔisiA1 cells under iron-replete (+Fe) and iron-deficient (-Fe) conditions. Immunoblotting analysis exhibits a clear expression of the IsiA1 in the WT-Fe. The PSI-IsiA1 supercomplex is found in the WT-Fe, and excitation-energy transfer from IsiA1 to PSI is verified by time-resolved fluorescence analyses. Instead of the IsiA1, both IsiA2 and IsiA3 are bound to PSI monomer in the ΔisiA1-Fe. These findings provide insights into multiple-expression system of the IsiA family in this cyanobacterium.
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Koksharova OA, Popova AA, Plyuta VA, Khmel IA. Four New Genes of Cyanobacterium Synechococcus elongatus PCC 7942 Are Responsible for Sensitivity to 2-Nonanone. Microorganisms 2020; 8:microorganisms8081234. [PMID: 32823644 PMCID: PMC7464499 DOI: 10.3390/microorganisms8081234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022] Open
Abstract
Microbial volatile organic compounds (VOCs) are cell metabolites that affect many physiological functions of prokaryotic and eukaryotic organisms. Earlier we have demonstrated the inhibitory effects of soil bacteria volatiles, including ketones, on cyanobacteria. Cyanobacteria are very sensitive to ketone action. To investigate the possible molecular mechanisms of the ketone 2-nonanone influence on cyanobacterium Synechococcus elongatus PCC 7942, we applied a genetic approach. After Tn5-692 transposon mutagenesis, several 2-nonanone resistant mutants have been selected. Four different mutant strains were used for identification of the impaired genes (Synpcc7942_1362, Synpcc7942_0351, Synpcc7942_0732, Synpcc7942_0726) that encode correspondingly: 1) a murein-peptide ligase Mpl that is involved in the biogenesis of cyanobacteria cell wall; 2) a putative ABC transport system substrate-binding proteins MlaD, which participates in ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane by aberrantly localized phospholipids transport from outer to inner membranes of bacterial cells; 3) a conserved hypothetical protein that is encoding by gene belonging to phage gene cluster in Synechococcus elongatus PCC 7942 genome; 4) a protein containing the VRR-NUC (virus-type replication-repair nuclease) domain present in restriction-modification enzymes involved in replication and DNA repair. The obtained results demonstrated that 2-nonanone may have different targets in Synechococcus elongatus PCC 7942 cells. Among them are proteins involved in the biogenesis and functioning of the cyanobacteria cell wall (Synpcc7942_1362, Synpcc7942_0351, Synpcc7942_0732) and protein participating in stress response at DNA restriction-modification level (Synpcc7942_0726). This paper is the first report about the genes that encode protein products, which can be affected by 2-nonanone.
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Affiliation(s)
- Olga A. Koksharova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1-40, 119992 Moscow, Russia
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Square, 2, 123182 Moscow, Russia; (A.A.P.); (V.A.P.); (I.A.K.)
- Correspondence: ; Tel.: +7-917-534-7543
| | - Alexandra A. Popova
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Square, 2, 123182 Moscow, Russia; (A.A.P.); (V.A.P.); (I.A.K.)
- Winogradsky Institute of Microbiology, The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Prospekt 60 let Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Vladimir A. Plyuta
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Square, 2, 123182 Moscow, Russia; (A.A.P.); (V.A.P.); (I.A.K.)
| | - Inessa A. Khmel
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Square, 2, 123182 Moscow, Russia; (A.A.P.); (V.A.P.); (I.A.K.)
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Kurio Y, Koike Y, Kanesaki Y, Watanabe S, Ehira S. The CRP-family transcriptional regulator DevH regulates expression of heterocyst-specific genes at the later stage of differentiation in the cyanobacterium Anabaena sp. strain PCC 7120. Mol Microbiol 2020; 114:553-562. [PMID: 32564445 DOI: 10.1111/mmi.14558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022]
Abstract
Heterocysts are terminally differentiated cells of filamentous cyanobacteria, which are specialized for nitrogen fixation. Because nitrogenase is easily inactivated by oxygen, the intracellular environment of heterocysts is kept microoxic. In heterocysts, the oxygen-evolving photosystem II is inactivated, a heterocyst-specific envelope with an outer polysaccharide layer and an inner glycolipid layer is formed to limit oxygen entry, and oxygen consumption is activated. Heterocyst differentiation, which is accompanied by drastic morphological and physiological changes, requires strictly controlled gene expression systems. Here, we investigated the functions of a CRP-family transcriptional regulator, DevH, in the process of heterocyst differentiation. A devH-knockdown strain, devH-kd, was created by replacing the original promoter with the gifA promoter, which is repressed during heterocyst differentiation. Although devH-kd formed morphologically distinct cells with the heterocyst envelope polysaccharide layer, it was unable to grow diazotrophically. Genes involved in construction of the microoxic environment, such as cox operons and the hgl island, were not upregulated in devH-kd. Moreover, expression of the nif gene cluster was completely abolished. Although CnfR was expressed in devH-kd, the nif gene cluster was not induced even under microoxic conditions. Thus, DevH is necessary for the establishment of a microoxic environment and induction of nitrogenase in heterocysts.
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Affiliation(s)
- Yohei Kurio
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Yosuke Koike
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Shigeki Ehira
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
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50
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Liu D, Johnson VM, Pakrasi HB. A Reversibly Induced CRISPRi System Targeting Photosystem II in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synth Biol 2020; 9:1441-1449. [PMID: 32379958 DOI: 10.1021/acssynbio.0c00106] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cyanobacterium Synechocystis sp. PCC 6803 is used as a model organism to study photosynthesis, as it can utilize glucose as the sole carbon source to support its growth under heterotrophic conditions. CRISPR interference (CRISPRi) has been widely applied to repress the transcription of genes in a targeted manner in cyanobacteria. However, a robust and reversible induced CRISPRi system has not been explored in Synechocystis 6803 to knock down and recover the expression of a targeted gene. In this study, we built a tightly controlled chimeric promoter, P rhaBAD-RSW, in which a theophylline responsive riboswitch was integrated into a rhamnose-inducible promoter system. We applied this promoter to drive the expression of ddCpf1 (DNase-dead Cpf1 nuclease) in a CRISPRi system and chose the PSII reaction center gene psbD (D2 protein) to target for repression. psbD was specifically knocked down by over 95% of its native expression, leading to severely inhibited photosystem II activity and growth of Synechocystis 6803 under photoautotrophic conditions. Significantly, removal of the inducers rhamnose and theophylline reversed repression by CRISPRi. Expression of PsbD recovered following release of repression, coupled with increased photosystem II content and activity. This reversibly induced CRISPRi system in Synechocystis 6803 represents a new strategy for study of the biogenesis of photosynthetic complexes in cyanobacteria.
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Affiliation(s)
- Deng Liu
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Virginia M Johnson
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
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