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Koch M, Noonan AJC, Qiu Y, Dofher K, Kieft B, Mottahedeh S, Shastri M, Hallam SJ. The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential. Front Bioeng Biotechnol 2022; 10:932695. [PMID: 36046667 PMCID: PMC9420970 DOI: 10.3389/fbioe.2022.932695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].
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Affiliation(s)
- Moritz Koch
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Avery J. C. Noonan
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | - Yilin Qiu
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Kalen Dofher
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Steven J. Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Steven J. Hallam,
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In silico insight of cell-death-related proteins in photosynthetic cyanobacteria. Arch Microbiol 2022; 204:511. [PMID: 35864385 DOI: 10.1007/s00203-022-03130-2] [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: 10/08/2021] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/02/2022]
Abstract
Cyanobacteria are a large group of ubiquitously found photosynthetic prokaryotes that are constantly exposed to different kinds of stressors of varying intensities and seem to overcome these in a precise and regulated manner. However, a high dose and duration of given stress induce cell death in a few select cyanobacteria, mainly to protect other cells (altruism). Despite the recent findings for the presence of biochemical and molecular hallmarks of cell death in cyanobacteria, it is yet a sketchily understood phenomenon. Regulation of metacaspase-like genes during Programmed Cell Death suggests it to be a genetically controlled mechanism like other eukaryotes. In addition to providing a comprehensive understanding of the current status of cell death in cyanobacteria, this review has used in silico analyses to directly compare the existence of some important molecular players operating in the intrinsic and extrinsic apoptotic pathways. Phylogenetic trees for all sequences indicate a cluster with a common ancestry and also a divergence from sequences of eukaryotic origin. To the best of our knowledge, such a comparison (except for orthocaspases) has not been attempted earlier and hopes to encourage workers in the field to investigate this altruistic phenomenon in detail.
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Yegorov Y, Sendersky E, Zilberman S, Nagar E, Waldman Ben-Asher H, Shimoni E, Simkovsky R, Golden SS, LiWang A, Schwarz R. A Cyanobacterial Component Required for Pilus Biogenesis Affects the Exoproteome. mBio 2021; 12:e03674-20. [PMID: 33727363 PMCID: PMC8092324 DOI: 10.1128/mbio.03674-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/02/2021] [Indexed: 12/23/2022] Open
Abstract
Protein secretion as well as the assembly of bacterial motility appendages are central processes that substantially contribute to fitness and survival. This study highlights distinctive features of the mechanism that serves these functions in cyanobacteria, which are globally prevalent photosynthetic prokaryotes that significantly contribute to primary production. Our studies of biofilm development in the cyanobacterium Synechococcus elongatus uncovered a novel component required for the biofilm self-suppression mechanism that operates in this organism. This protein, which is annotated as "hypothetical," is denoted EbsA (essential for biofilm self-suppression A) here. EbsA homologs are highly conserved and widespread in diverse cyanobacteria but are not found outside this clade. We revealed a tripartite complex of EbsA, Hfq, and the ATPase homolog PilB (formerly called T2SE) and demonstrated that each of these components is required for the assembly of the hairlike type IV pili (T4P) appendages, for DNA competence, and affects the exoproteome in addition to its role in biofilm self-suppression. These data are consistent with bioinformatics analyses that reveal only a single set of genes in S. elongatus to serve pilus assembly or protein secretion; we suggest that a single complex is involved in both processes. A phenotype resulting from the impairment of the EbsA homolog in the cyanobacterium Synechocystis sp. strain PCC 6803 implies that this feature is a general cyanobacterial trait. Moreover, comparative exoproteome analyses of wild-type and mutant strains of S. elongatus suggest that EbsA and Hfq affect the exoproteome via a process that is independent of PilB, in addition to their involvement in a T4P/secretion machinery.IMPORTANCE Cyanobacteria, environmentally prevalent photosynthetic prokaryotes, contribute ∼25% of global primary production. Cyanobacterial biofilms elicit biofouling, thus leading to substantial economic losses; however, these microbial assemblages can also be beneficial, e.g., in wastewater purification processes and for biofuel production. Mechanistic aspects of cyanobacterial biofilm development were long overlooked, and genetic and molecular information emerged only in recent years. The importance of this study is 2-fold. First, it identifies novel components of cyanobacterial biofilm regulation, thus contributing to the knowledge of these processes and paving the way for inhibiting detrimental biofilms or promoting beneficial ones. Second, the data suggest that cyanobacteria may employ the same complex for the assembly of the motility appendages, type 4 pili, and protein secretion. A shared pathway was previously shown in only a few cases of heterotrophic bacteria, whereas numerous studies demonstrated distinct systems for these functions. Thus, our study broadens the understanding of pilus assembly/secretion in diverse bacteria and furthers the aim of controlling the formation of cyanobacterial biofilms.
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Affiliation(s)
- Yevgeni Yegorov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Shaul Zilberman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Susan S Golden
- Division 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
| | - Andy LiWang
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, California, USA
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Brilisauer K, Rapp J, Rath P, Schöllhorn A, Bleul L, Weiß E, Stahl M, Grond S, Forchhammer K. Cyanobacterial antimetabolite 7-deoxy-sedoheptulose blocks the shikimate pathway to inhibit the growth of prototrophic organisms. Nat Commun 2019; 10:545. [PMID: 30710081 PMCID: PMC6358636 DOI: 10.1038/s41467-019-08476-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/09/2019] [Indexed: 11/17/2022] Open
Abstract
Antimetabolites are small molecules that inhibit enzymes by mimicking physiological substrates. We report the discovery and structural elucidation of the antimetabolite 7-deoxy-sedoheptulose (7dSh). This unusual sugar inhibits the growth of various prototrophic organisms, including species of cyanobacteria, Saccharomyces, and Arabidopsis. We isolate bioactive 7dSh from culture supernatants of the cyanobacterium Synechococcus elongatus. A chemoenzymatic synthesis of 7dSh using S. elongatus transketolase as catalyst and 5-deoxy-d-ribose as substrate allows antimicrobial and herbicidal bioprofiling. Organisms treated with 7dSh accumulate 3-deoxy-d-arabino-heptulosonate 7-phosphate, which indicates that the molecular target is 3-dehydroquinate synthase, a key enzyme of the shikimate pathway, which is absent in humans and animals. The herbicidal activity of 7dSh is in the low micromolar range. No cytotoxic effects on mammalian cells have been observed. We propose that the in vivo inhibition of the shikimate pathway makes 7dSh a natural antimicrobial and herbicidal agent. Mother Nature is a valuable resource for the discovery of drug and agricultural chemicals. Here, the authors show that 7-deoxy-sedoheptulose produced by a cyanobacterium is an antimicrobial and herbicidal compound that acts through inhibition of 3-dehydroquniate synthase in the shikimate pathway.
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Affiliation(s)
- Klaus Brilisauer
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany.,Microbiology, Organismic Interactions, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Johanna Rapp
- Microbiology, Organismic Interactions, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Pascal Rath
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Anna Schöllhorn
- Microbiology, Organismic Interactions, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Lisa Bleul
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls Universität Tübingen, Eugenstraße 6, 72076, Tübingen, Germany
| | - Elisabeth Weiß
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karls Universität Tübingen, Eugenstraße 6, 72076, Tübingen, Germany
| | - Mark Stahl
- Center for Plant Molecular Biology, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
| | - Karl Forchhammer
- Microbiology, Organismic Interactions, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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Zer H, Margulis K, Georg J, Shotland Y, Kostova G, Sultan LD, Hess WR, Keren N. Resequencing of a mutant bearing an iron starvation recovery phenotype defines Slr1658 as a new player in the regulatory network of a model cyanobacterium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:235-245. [PMID: 29161470 DOI: 10.1111/tpj.13770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria. We set out to study the role of bacterioferritin co-migratory proteins during transitions in iron bioavailability in the cyanobacterium Synechocystis sp. PCC 6803 using knockout strains coupled with physiological and biochemical measurements. One of the mutants displayed slow recovery from iron limitation. However, we discovered that the cause of the phenotype was not the intended knockout but rather the serendipitous selection of a mutation in an unrelated locus, slr1658. Bioinformatics analysis suggested similarities to two-component systems and a possible regulatory role. Transcriptomic analysis of the recovery from iron limitation showed that the slr1658 mutation had an extensive effect on the expression of genes encoding regulatory proteins, proteins involved in the remodeling and degradation of the photosynthetic apparatus and proteins modulating electron transport. Most significantly, expression of the cyanobacterial homologue of the cyclic electron transport protein PGR5 was upregulated 1000-fold in slr1658 disruption mutants. pgr5 transcripts in the Δslr1658 mutant retained these high levels under a range of stress and recovery conditions. The results suggest that slr1658 is part of a regulatory operon that, among other aspects, affects the regulation of alternative electron flow. Disruption of its function has deleterious results under oxidative stress promoting conditions.
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Affiliation(s)
- Hagit Zer
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Ketty Margulis
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Yoram Shotland
- Department of Chemical Engineering, Shamoon College of Engineering, Beer Sheva, 84100, Israel
| | - Gergana Kostova
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Laure D Sultan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, D-79104, Freiburg, Germany
| | - Nir Keren
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
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Bezryadina A, Hansson T, Gautam R, Wetzel B, Siggins G, Kalmbach A, Lamstein J, Gallardo D, Carpenter EJ, Ichimura A, Morandotti R, Chen Z. Nonlinear Self-Action of Light through Biological Suspensions. PHYSICAL REVIEW LETTERS 2017; 119:058101. [PMID: 28949726 DOI: 10.1103/physrevlett.119.058101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Indexed: 05/12/2023]
Abstract
It is commonly thought that biological media cannot exhibit an appreciable nonlinear optical response. We demonstrate, for the first time to our knowledge, a tunable optical nonlinearity in suspensions of cyanobacteria that leads to robust propagation and strong self-action of a light beam. By deliberately altering the host environment of the marine bacteria, we show experimentally that nonlinear interaction can result in either deep penetration or enhanced scattering of light through the bacterial suspension, while the viability of the cells remains intact. A theoretical model is developed to show that a nonlocal nonlinearity mediated by optical forces (including both gradient and forward-scattering forces) acting on the bacteria explains our experimental observations.
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Affiliation(s)
- Anna Bezryadina
- Department of Physics and Astronomy, San Francisco State University, San Francisco, California 94132, USA
| | - Tobias Hansson
- Institut National de la Recherche Scientifique, Université du Québec, Varennes, Québec J3X 1S2, Canada
| | - Rekha Gautam
- Department of Physics and Astronomy, San Francisco State University, San Francisco, California 94132, USA
| | - Benjamin Wetzel
- Institut National de la Recherche Scientifique, Université du Québec, Varennes, Québec J3X 1S2, Canada
- School of Mathematical and Physical Sciences, University of Sussex, Sussex House, Falmer, Brighton BN1 9RH, United Kingdom
| | - Graham Siggins
- Department of Physics and Astronomy, San Francisco State University, San Francisco, California 94132, USA
| | - Andrew Kalmbach
- Romberg Tiburon Center for Environmental Studies and Department of Biology, San Francisco State University, San Francisco, California 94132, USA
| | - Josh Lamstein
- Department of Physics and Astronomy, San Francisco State University, San Francisco, California 94132, USA
| | - Daniel Gallardo
- Department of Physics and Astronomy, San Francisco State University, San Francisco, California 94132, USA
| | - Edward J Carpenter
- Romberg Tiburon Center for Environmental Studies and Department of Biology, San Francisco State University, San Francisco, California 94132, USA
| | - Andrew Ichimura
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
| | - Roberto Morandotti
- Institut National de la Recherche Scientifique, Université du Québec, Varennes, Québec J3X 1S2, Canada
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- National Research University of Information Technologies, Mechanics and Optics, St Petersburg 197101, Russia
| | - Zhigang Chen
- Department of Physics and Astronomy, San Francisco State University, San Francisco, California 94132, USA
- TEDA Applied Physics Institute and School of Physics, Nankai University, Tianjin 300457, China
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Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth. mBio 2016; 7:mBio.00949-16. [PMID: 27460798 PMCID: PMC4981716 DOI: 10.1128/mbio.00949-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Harnessing the metabolic potential of photosynthetic microbes for next-generation biotechnology objectives requires detailed scientific understanding of the physiological constraints and regulatory controls affecting carbon partitioning between biomass, metabolite storage pools, and bioproduct synthesis. We dissected the cellular mechanisms underlying the remarkable physiological robustness of the euryhaline unicellular cyanobacterium Synechococcus sp. strain PCC 7002 (Synechococcus 7002) and identify key mechanisms that allow cyanobacteria to achieve unprecedented photoautotrophic productivities (~2.5-h doubling time). Ultrafast growth of Synechococcus 7002 was supported by high rates of photosynthetic electron transfer and linked to significantly elevated transcription of precursor biosynthesis and protein translation machinery. Notably, no growth or photosynthesis inhibition signatures were observed under any of the tested experimental conditions. Finally, the ultrafast growth in Synechococcus 7002 was also linked to a 300% expansion of average cell volume. We hypothesize that this cellular adaptation is required at high irradiances to support higher cell division rates and reduce deleterious effects, corresponding to high light, through increased carbon and reductant sequestration. Efficient coupling between photosynthesis and productivity is central to the development of biotechnology based on solar energy. Therefore, understanding the factors constraining maximum rates of carbon processing is necessary to identify regulatory mechanisms and devise strategies to overcome productivity constraints. Here, we interrogate the molecular mechanisms that operate at a systems level to allow cyanobacteria to achieve ultrafast growth. This was done by considering growth and photosynthetic kinetics with global transcription patterns. We have delineated putative biological principles that allow unicellular cyanobacteria to achieve ultrahigh growth rates through photophysiological acclimation and effective management of cellular resource under different growth regimes.
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