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Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:microorganisms11020455. [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
- Correspondence:
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2
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Saw JH, Cardona T, Montejano G. Complete Genome Sequencing of a Novel Gloeobacter Species from a Waterfall Cave in Mexico. Genome Biol Evol 2021; 13:6446517. [PMID: 34850891 PMCID: PMC8691054 DOI: 10.1093/gbe/evab264] [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] [Accepted: 11/24/2021] [Indexed: 12/18/2022] Open
Abstract
Only two complete genomes of the cyanobacterial genus Gloeobacter from two very different regions of the world currently exist. Here, we present the complete genome sequence of a third member of the genus isolated from a waterfall cave in Mexico. Analysis of the average nucleotide identities (ANIs) between published Gloeobacter genomes revealed that the complete genome of this new member is only 92.7% similar to Gloeobacter violaceus and therefore we determined it to be a new species. We propose to name this new species Gloeobacter morelensis after the location in Mexico where it was isolated. The complete genome consists of one circular chromosome (4,921,229 bp), one linear plasmid (172,328 bp), and one circular plasmid (8,839 bp). Its genome is the largest of all completely sequenced genomes of Gloeobacter species. Pangenomic comparisons revealed that G. morelensis encodes 759 genes not shared with other Gloeobacter species. Despite being more closely related to G. violaceus, it features an extremely divergent psbA gene encoding an atypical D1 core subunit of Photosystem II previously only found within the genome of Gloeobacter kilaueensis. In addition, we detected evidence of concerted evolution of psbA genes encoding identical D1 in all three Gloeobacter genomes, a characteristic that seems widespread in cyanobacteria and may therefore be traced back to their last common ancestor.
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Affiliation(s)
- Jimmy H Saw
- Department of Biological Sciences, The George Washington University, District of Columbia, USA
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Gustavo Montejano
- Facultad de Ciencias, Laboratorio de Ficología, National Autonomous University of Mexico, Ciudad de México, Mexico
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Rahmatpour N, Hauser DA, Nelson JM, Chen PY, Villarreal A JC, Ho MY, Li FW. A novel thylakoid-less isolate fills a billion-year gap in the evolution of Cyanobacteria. Curr Biol 2021; 31:2857-2867.e4. [PMID: 33989529 DOI: 10.1016/j.cub.2021.04.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/02/2021] [Accepted: 04/16/2021] [Indexed: 12/31/2022]
Abstract
Cyanobacteria have played pivotal roles in Earth's geological history, especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution has been limited by their extremely lopsided tree of life-the vast majority of extant diversity belongs to Phycobacteria (or "crown Cyanobacteria"), while its sister lineage, Gloeobacteria, is depauperate and contains only two closely related species of Gloeobacter and a metagenome-assembled genome. Here, we describe a new cultured member of Gloeobacteria, Anthocerotibacter panamensis, isolated from a tropical hornwort. Anthocerotibacter diverged from Gloeobacter over 1.4 Ga ago and has low 16S rDNA identities with environmental samples. Our ultrastructural, physiological, and genomic analyses revealed that this species possesses a unique combination of traits that are exclusively shared with either Gloeobacteria or Phycobacteria. For example, similar to Gloeobacter, it lacks thylakoids and circadian clock genes, but the carotenoid biosynthesis pathway is typical of Phycobacteria. Furthermore, Anthocerotibacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerotibacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency. Given its key phylogenetic position, distinct trait combination, and availability as a culture, Anthocerotibacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.
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Affiliation(s)
| | | | | | - Pa Yu Chen
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Juan Carlos Villarreal A
- Department of Biology, Laval University, Quebec City, QC, Canada; Smithsonian Tropical Research Institute, Panama City, Panama
| | - Ming-Yang Ho
- Department of Life Science, National Taiwan University, Taipei, Taiwan; Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA; Plant Biology Section, Cornell University, Ithaca, NY, USA.
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Raven JA. Chloride involvement in the synthesis, functioning and repair of the photosynthetic apparatus in vivo. THE NEW PHYTOLOGIST 2020; 227:334-342. [PMID: 32170958 DOI: 10.1111/nph.16541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
Cl- has long been known as a micronutrient for oxygenic photosynthetic resulting from its role an essential cofactor for photosystem II (PSII). Evidence on the in vivo Cl- distribution in Spinacia oleracea leaves and chloroplasts shows that sufficient Cl- is present for the involvement in PSII function, as indicated by in vitro studies on, among other organisms, S. oleracea PsII. There is also sufficient Cl- to function, with K+ , in parsing the H+ electrochemical potential difference (proton motive force) across the illuminated thylakoid membrane into electrical potential difference and pH difference components. However, recent in vitro work on PSII from S. oleracea shows that oxygen evolving complex (OEC) synthesis, and resynthesis after photodamage, requires significantly higher Cl- concentrations than would satisfy the function of assembled PSII O2 evolution of the synthesised PSII with the OEC. The low Cl- affinity of OEC (re-)assembly could be a component limiting the rate of OEC (re-)assembly.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Climate Change Cluster, University of Technology, Ultimo, Sydney, NSW, 2007, Australia
- School of Biological Science, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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A phylogenetically novel cyanobacterium most closely related to Gloeobacter. ISME JOURNAL 2020; 14:2142-2152. [PMID: 32424249 PMCID: PMC7368068 DOI: 10.1038/s41396-020-0668-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 01/01/2023]
Abstract
Clues to the evolutionary steps producing innovations in oxygenic photosynthesis may be preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Vampirovibrionia (formerly Melainabacteria) and the thylakoid-containing Cyanobacteria. However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter. Here, we describe nearly complete, metagenome-assembled genomes (MAGs) of an uncultured organism phylogenetically placed near Gloeobacter, for which we propose the name Candidatus Aurora vandensis {Au’ro.ra. L. fem. n. aurora, the goddess of the dawn in Roman mythology; van.de’nsis. N.L. fem. adj. vandensis of Lake Vanda, Antarctica}. The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many accessory subunits associated with the photosystems in other species either are missing from the MAG or are poorly conserved. The MAG also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Additional characterization of this organism is expected to inform models of the evolution of oxygenic photosynthesis.
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Cardona T, Murray JW, Rutherford AW. Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria. Mol Biol Evol 2015; 32:1310-28. [PMID: 25657330 PMCID: PMC4408414 DOI: 10.1093/molbev/msv024] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages toward the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria.
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Affiliation(s)
- Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James W Murray
- Department of Life Sciences, Imperial College London, London, United Kingdom
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Kihara S, Hartzler DA, Savikhin S. Oxygen concentration inside a functioning photosynthetic cell. Biophys J 2014; 106:1882-9. [PMID: 24806920 PMCID: PMC4017319 DOI: 10.1016/j.bpj.2014.03.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/13/2014] [Accepted: 03/12/2014] [Indexed: 11/23/2022] Open
Abstract
The excess oxygen concentration in the photosynthetic membranes of functioning oxygenic photosynthetic cells was estimated using classical diffusion theory combined with experimental data on oxygen production rates of cyanobacterial cells. The excess oxygen concentration within the plesiomorphic cyanobacterium Gloeobactor violaceus is only 0.025 μM, or four orders of magnitude lower than the oxygen concentration in air-saturated water. Such a low concentration suggests that the first oxygenic photosynthetic bacteria in solitary form could have evolved ∼2.8 billion years ago without special mechanisms to protect them against reactive oxygen species. These mechanisms instead could have been developed during the following ∼500 million years while the oxygen level in the Earth's atmosphere was slowly rising. Excess oxygen concentrations within individual cells of the apomorphic cyanobacteria Synechocystis and Synechococcus are 0.064 and 0.25 μM, respectively. These numbers suggest that intramembrane and intracellular proteins in isolated oxygenic photosynthetic cells are not subjected to excessively high oxygen levels. The situation is different for closely packed colonies of photosynthetic cells. Calculations show that the excess concentration within colonies that are ∼40 μm or larger in diameter can be comparable to the oxygen concentration in air-saturated water, suggesting that species forming colonies require protection against reactive oxygen species even in the absence of oxygen in the surrounding atmosphere.
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Affiliation(s)
- Shigeharu Kihara
- Department of Physics, Purdue University, West Lafayette, Indiana
| | | | - Sergei Savikhin
- Department of Physics, Purdue University, West Lafayette, Indiana.
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Molecular environments of divinyl chlorophylls in Prochlorococcus and Synechocystis: Differences in fluorescence properties with chlorophyll replacement. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:471-81. [DOI: 10.1016/j.bbabio.2011.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 02/22/2011] [Accepted: 02/28/2011] [Indexed: 11/21/2022]
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Shimada Y, Suzuki H, Tsuchiya T, Tomo T, Noguchi T, Mimuro M. Effect of a Single-Amino Acid Substitution of the 43 kDa Chlorophyll Protein on the Oxygen-Evolving Reaction of the Cyanobacterium Synechocystis sp. PCC 6803: Analysis of the Glu354Gln Mutation. Biochemistry 2009; 48:6095-103. [DOI: 10.1021/bi900317a] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuichiro Shimada
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroyuki Suzuki
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Tohru Tsuchiya
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tatsuya Tomo
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Takumi Noguchi
- Institute of Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Mamoru Mimuro
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
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Raven JA. Functional evolution of photochemical energy transformations in oxygen-producing organisms. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:505-515. [PMID: 32688665 DOI: 10.1071/fp09087] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 04/21/2009] [Indexed: 05/21/2023]
Abstract
Chlorophyll a is the photochemical agent accounting for most oxygenic photosynthesis, that is, over 99.9% of photosynthetic primary activity on Earth. The spectral and energetic properties of chlorophyll a can, at least in part, be rationalised in terms of the solar spectral output and the energetics of oxygen production and carbon dioxide reduction with two photochemical reactions. The long wavelength limit on in vivo chlorophyll a absorption is probably close to the energetic limit: longer wavelengths could not support a high rate and efficiency of oxygenic photosynthesis. Retinal, a β-carotene derivative that is the chromophore of rhodopsin, acts not only as a sensory pigment, but also as an ion-pumping photochemical transducer. Both sensory and energy-transforming rhodopsins occur in oxygenic phototrophs, although the extent of expression and the function of the latter are not well understood.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, UK. Email
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12
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Mimuro M, Tomo T, Tsuchiya T. Two unique cyanobacteria lead to a traceable approach of the first appearance of oxygenic photosynthesis. PHOTOSYNTHESIS RESEARCH 2008; 97:167-176. [PMID: 18568415 DOI: 10.1007/s11120-008-9311-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Accepted: 05/08/2008] [Indexed: 05/26/2023]
Abstract
The evolutionary route from anoxygenic photosynthetic bacteria to oxygenic cyanobacteria is discontinuous in terms of photochemical/photophysical reaction systems. It is difficult to describe this transition process simply because there are no recognized intermediary organisms between the two bacterial groups. Gloeobacter violaceus PCC 7421 might be a model organism that is suitable for analysis because it still possesses primordial characteristics such as the absence of thylakoid membranes. Whole genome analysis and biochemical and biophysical surveys of G. violaceus have favored the hypothesis that it is an intermediary organism. On the other hand, species differentiation is an evolutionary process that could be driven by changes in a small number of genes, and this process might give fair information more in details by monitoring of those genes. Comparative studies of genes, including those in Acaryochloris marina MBIC 11017, have provided information relevant to species differentiation; in particular, the acquisition of a new pigment, chlorophyll d, and changes in amino acid sequences have been informative. Here, based on experimental evidence from these two species, we discuss some of the evolutionary pathways for the appearance and differentiation of cyanobacteria.
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Affiliation(s)
- Mamoru Mimuro
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan.
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