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Turunen O, Saleem T, Kurkela J, Kallio P, Tyystjärvi T. Engineering RNA polymerase to construct biotechnological host strains of cyanobacteria. PHYSIOLOGIA PLANTARUM 2024; 176:e14263. [PMID: 38528669 DOI: 10.1111/ppl.14263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Application of cyanobacteria for bioproduction, bioremediation and biotransformation is being increasingly explored. Photoautotrophs are carbon-negative by default, offering a direct pathway to reducing emissions in production systems. More robust and versatile host strains are needed for constructing production strains that would function as efficient and carbon-neutral cyanofactories. We have tested if the engineering of sigma factors, regulatory units of the bacterial RNA polymerase, could be used to generate better host strains of the model cyanobacterium Synechocystis sp. PCC 6803. Overexpressing the stress-responsive sigB gene under the strong psbA2 promoter (SigB-oe) led to improved tolerance against heat, oxidative stress and toxic end-products. By targeting transcription initiation in the SigB-oe strain, we could simultaneously activate a wide spectrum of cellular protective mechanisms, including carotenoids, the HspA heat shock protein, and highly activated non-photochemical quenching. Yellow fluorescent protein was used to test the capacity of the SigB-oe strain to produce heterologous proteins. In standard conditions, the SigB-oe strain reached a similar production as the control strain, but when cultures were challenged with oxidative stress, the production capacity of SigB-oe surpassed the control strain. We also tested the production of growth-rate-controlled host strains via manipulation of RNA polymerase, but post-transcriptional regulation prevented excessive overexpression of the primary sigma factor SigA, and overproduction of the growth-restricting SigC factor was lethal. Thus, more research is needed before cyanobacteria growth can be manipulated by engineering RNA polymerase.
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Affiliation(s)
- Otso Turunen
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Tayyab Saleem
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Juha Kurkela
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Pauli Kallio
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Taina Tyystjärvi
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
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2
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Srivastava A, Thapa S, Chakdar H, Babele PK, Shukla P. Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications. Crit Rev Biotechnol 2024; 44:63-77. [PMID: 36137567 DOI: 10.1080/07388551.2022.2117682] [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: 04/09/2022] [Revised: 07/09/2022] [Accepted: 08/06/2022] [Indexed: 11/03/2022]
Abstract
Cyanobacteria safeguard their photosynthetic machinery from oxidative damage caused by adverse environmental factors such as high-intensity light. Together with many photoprotective compounds, they contain myxoxanthophylls, a rare group of glycosidic carotenoids containing a high number of conjugated double bonds. These carotenoids have been shown to: have strong photoprotective effects, contribute to the integrity of the thylakoid membrane, and upregulate in cyanobacteria under a variety of stress conditions. However, their metabolic potential has not been fully utilized in the stress biology of cyanobacteria and the pharmaceutical industry due to a lack of mechanistic understanding and their insufficient biosynthesis. This review summarizes current knowledge on: biological function, genetic regulation, biotechnological production, and pharmaceutical potential of myxoxanthophyll, with a focus on strain engineering and parameter optimization strategies for increasing their cellular content. The summarized knowledge can be utilized in cyanobacterial metabolic engineering to improve the stress tolerance of useful strains and enhance the commercial-scale synthesis of myxoxanthophyll for pharmaceutical uses.
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Affiliation(s)
- Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, United States of America
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, India
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Hasegawa H, Kobayashi I, Bairagi N, Watanabe S, Tanaka K. DnaK2 Mediates a Negative Feedback Regulation of the Heat Shock Responsive Hik2-Rre1 Two-Component System in the Cyanobacterium Synechococcus Elongatus PCC 7942. PLANT & CELL PHYSIOLOGY 2024; 65:120-127. [PMID: 37856257 DOI: 10.1093/pcp/pcad129] [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: 04/01/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
The two-component system (TCS) is a conserved signal transduction module in bacteria. The Hik2-Rre1 system is responsible for transcriptional activation upon high-temperature shift as well as plastoquinone-related redox stress in the cyanobacterium Synechococcus elongatus PCC 7942. As heat-induced de novo protein synthesis was previously shown to be required to quench the heat-activated response, we investigated the underlying mechanism in this study. We found that the heat-inducible transcription activation was alleviated by the overexpression of dnaK2, which is an essential homolog of the highly conserved HSP70 chaperone and whose expression is induced under the control of the Hik2-Rre1 TCS. Phosphorylation of Rre1 correlated with transcription of the regulatory target hspA. The redox stress response was found to be similarly repressed by dnaK2 overexpression. Considered together with the previous information, we propose a negative feedback mechanism of the Hik2-Rre1-dependent stress response that maintains the cellular homeostasis mediated by DnaK2.
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Affiliation(s)
- Hazuki Hasegawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Ikki Kobayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Nachiketa Bairagi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
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Koskinen S, Kurkela J, Linhartová M, Tyystjärvi T. The genome sequence of Synechocystis sp. PCC 6803 substrain GT-T and its implications for the evolution of PCC 6803 substrains. FEBS Open Bio 2023; 13:701-712. [PMID: 36792971 PMCID: PMC10068330 DOI: 10.1002/2211-5463.13576] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Synechocystis sp. PCC 6803 is a model cyanobacterium, glucose-tolerant substrains of which are commonly used as laboratory strains. In recent years, it has become evident that 'wild-type' strains used in different laboratories show some differences in their phenotypes. We report here the chromosome sequence of our Synechocystis sp. PCC 6803 substrain, named substrain GT-T. The chromosome sequence of GT-T was compared to those of two other commonly used laboratory substrains, GT-S and PCC-M. We identified 11 specific mutations in the GT-T substrain, whose physiological consequences are discussed. We also provide an update on evolutionary relationships between different Synechocystis sp. PCC 6803 substrains.
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Affiliation(s)
- Satu Koskinen
- Department of Life Sciences/Molecular Plant Biology, University of Turku, Finland
| | - Juha Kurkela
- Department of Life Sciences/Molecular Plant Biology, University of Turku, Finland
| | - Markéta Linhartová
- Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Taina Tyystjärvi
- Department of Life Sciences/Molecular Plant Biology, University of Turku, Finland
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Kariyazono R, Osanai T. Identification of the genome-wide distribution of cyanobacterial group-2 sigma factor SigE, accountable for its regulon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:548-561. [PMID: 35092706 DOI: 10.1111/tpj.15687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Ryo Kariyazono
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
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Roles of Close Homologues SigB and SigD in Heat and High Light Acclimation of the Cyanobacterium Synechocystis sp. PCC 6803. Life (Basel) 2022; 12:life12020162. [PMID: 35207450 PMCID: PMC8875361 DOI: 10.3390/life12020162] [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: 12/22/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 11/18/2022] Open
Abstract
Acclimation of cyanobacterium Synechocystis sp. PCC6803 to suboptimal conditions is largely dependent on adjustments of gene expression, which is highly controlled by the σ factor subunits of RNA polymerase (RNAP). The SigB and SigD σ factors are close homologues. Here we show that the sigB and sigD genes are both induced in high light and heat stresses. Comparison of transcriptomes of the control strain (CS), ΔsigB, ΔsigD, ΔsigBCE (containing SigD as the only functional group 2 σ factor), and ΔsigCDE (SigB as the only functional group 2 σ factor) strains in standard, high light, and high temperature conditions revealed that the SigB and SigD factors regulate different sets of genes and SigB and SigD regulons are highly dependent on stress conditions. The SigB regulon is bigger than the SigD regulon at high temperature, whereas, in high light, the SigD regulon is bigger than the SigB regulon. Furthermore, our results show that favoring the SigB or SigD factor by deleting other group 2 σ factors does not lead to superior acclimation to high light or high temperature, indicating that all group 2 σ factors play roles in the acclimation processes.
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Cross-Activation of Two Nitrogenase Gene Clusters by CnfR1 or CnfR2 in the Cyanobacterium Anabaena variabilis. Microbiol Spectr 2021; 9:e0106021. [PMID: 34612667 PMCID: PMC8510180 DOI: 10.1128/spectrum.01060-21] [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] [Indexed: 11/20/2022] Open
Abstract
In Anabaena variabilis, the nif1 genes, which are activated by CnfR1, produce a Mo-nitrogenase that is expressed only in heterocysts. Similarly, the nif2 genes, which are activated by CnfR2, make a Mo-nitrogenase that is expressed only in anaerobic vegetative cells. However, CnfR1, when it was expressed in anaerobic vegetative cells under the control of the cnfR2 promoter or from the Co2+-inducible coaT promoter, activated the expression of both nifB1 and nifB2. Activation of nifB2, but not nifB1, by CnfR1 required NtcA. Thus, expression of the nif1 system requires no heterocyst-specific factor other than CnfR1. In contrast, CnfR2, when it was expressed in heterocysts under the control of the cnfR1 promoter or from the coaT promoter, did not activate the expression of nifB1 or nifB2. Thus, activation of the nif2 system in anaerobic vegetative cells by CnfR2 requires additional factors absent in heterocysts. CnfR2 made from the coaT promoter activated nifB2 expression in anaerobic vegetative cells grown with fixed nitrogen; however, oxygen inhibited CnfR2 activation of nifB2 expression. In contrast, activation of nifB1 and nifB2 by CnfR1 was unaffected by oxygen. CnfR1, which does not activate the nifB2 promoter in heterocysts, activated the expression of the entire nif2 gene cluster from a nifB2::nifB1::nifB2 hybrid promoter in heterocysts, producing functional Nif2 nitrogenase in heterocysts. However, activity was poor compared to the normal Nif1 nitrogenase. Expression of the nif2 cluster in anaerobic vegetative cells of Nostoc sp. PCC 7120, a strain lacking the nif2 nitrogenase, resulted in expression of the nif2 genes but weak nitrogenase activity. IMPORTANCE Cyanobacterial nitrogen fixation is important in the global nitrogen cycle, in oceanic productivity, and in many plant and fungal symbioses. While the proteins that mediate nitrogen fixation have been well characterized, the regulation of this complex and expensive process is poorly understood in cyanobacteria. Using a genetic approach, we have characterized unique and overlapping functions for two homologous transcriptional activators CnfR1 and CnfR2 that activate two distinct nitrogenases in a single organism. We found that CnfR1 is promiscuous in its ability to activate both nitrogenase systems, whereas CnfR2 depends on additional cellular factors; thus, it activates only one nitrogenase system.
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Kurkela J, Fredman J, Salminen TA, Tyystjärvi T. Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase. Mol Microbiol 2021; 115:1-11. [PMID: 32920946 DOI: 10.1111/mmi.14603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
The conserved omega (ω) subunit of RNA polymerase (RNAP) is the only nonessential subunit of bacterial RNAP core. The small ω subunit (7 kDa-11.5 kDa) contains three conserved α helices, and helices α2 and α3 contain five fully conserved amino acids of ω. Four conserved amino acids stabilize the correct folding of the ω subunit and one is located in the vicinity of the β' subunit of RNAP. Otherwise ω shows high variation between bacterial taxa, and although the main interaction partner of ω is always β', many interactions are taxon-specific. ω-less strains show pleiotropic phenotypes, and based on in vivo and in vitro results, a few roles for the ω subunits have been described. Interactions of the ω subunit with the β' subunit are important for the RNAP core assembly and integrity. In addition, the ω subunit plays a role in promoter selection, as ω-less RNAP cores recruit fewer primary σ factors and more alternative σ factors than intact RNAP cores in many species. Furthermore, the promoter selection of an ω-less RNAP holoenzyme bearing the primary σ factor seems to differ from that of an intact RNAP holoenzyme.
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Affiliation(s)
- Juha Kurkela
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Fredman
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Tiina A Salminen
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
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Thiel T. Organization and regulation of cyanobacterial nif gene clusters: implications for nitrogenase expression in plant cells. FEMS Microbiol Lett 2020; 366:5470946. [PMID: 31062027 DOI: 10.1093/femsle/fnz077] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/11/2019] [Indexed: 12/16/2022] Open
Abstract
For over 50 years scientists have considered the possibility of engineering a plant with nitrogen fixation capability, freeing farmers from their dependence on nitrogen fertilizers. With the development of the tools of synthetic biology, more progress has been made toward this goal in the last 5 years than in the previous five decades. Most of the effort has focused on nitrogenase genes from Klebsiella oxytoca, which has complex gene regulation. There may be advantages in using nitrogenase genes from cyanobacteria, which comprise large polycistronic gene clusters that may be easier to manipulate and eventually express in a plant. The fact that some diatoms have a cyanobacterial nitrogen fixing organelle further supports the idea that a cyanobacterial nitrogenase gene cluster may function in a newly-engineered, cyanobacterial-based plant organelle, a nitroplast. This review describes recent attempts to express the nif genes from Anabaena variabilis ATCC 29413, Leptolyngbya boryana dg5 and Cyanothece sp. ATCC 51142 in heterologous cyanobacteria in the context of the organization of the nitrogenase genes and their regulation by the transcription factor CnfR via its highly conserved binding sites.
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Affiliation(s)
- Teresa Thiel
- Department of Biology, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA
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Cyanobacterial sigma factors: Current and future applications for biotechnological advances. Biotechnol Adv 2020; 40:107517. [DOI: 10.1016/j.biotechadv.2020.107517] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 11/15/2022]
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Valev D, Kurkela J, Tyystjärvi E, Tyystjärvi T. Testing the Potential of Regulatory Sigma Factor Mutants for Wastewater Purification or Bioreactor Run in High Light. Curr Microbiol 2020; 77:1590-1599. [PMID: 32266454 PMCID: PMC7334282 DOI: 10.1007/s00284-020-01973-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 03/27/2020] [Indexed: 11/25/2022]
Abstract
It is shown that a freshly inoculated culture of the model cyanobacterium Synechocystis sp. PCC 6803 consumed almost all phosphate and 50% of nitrate within 6 days from the nutrient-rich BG-11 growth medium, indicating potential of cyanobacteria to purify wastewaters. Synechocystis sp. PCC 6803 control strain also collected nutrients efficiently from a landfill leachate wastewater KA2 (5.9-6.9 mM ammonium and 0.073-0.077 mM phosphate). Wastewaters might induce oxidative stress to microalgae, which prompted us to test growth of sigma factor inactivation strains, as ΔsigBCE and ΔsigCDE strains show superior growth in chemically induced oxidative stress. All cyanobacterial strains, including a stress-sensitive strain ΔsigBCDE, grew well in KA2 for four days, indicating that KA2 did not cause immediate oxidative stress. Completely arrested growth and bleaching of ΔsigBCDE cells after one week in KA2 wastewater point to the importance of group 2 sigma factor-mediated changes in gene expression during wastewater treatment. The growth of ΔsigBCD was arrested early in un-buffered and Hepes buffered (pH 7.5) KA2. In ΔsigBCD, all phosphate transporter genes are upregulated in standard conditions, and ΔsigBCD cells showed growth defects in low-phosphate BG-11 medium. ΔsigBCD cells removed phosphate slower from KA2 than the control strain, but phosphate supplementation of KA2 did not improve growth of ΔsigBCD. The ΔsigBCE strain showed superior growth in a laboratory-scale bioreactor in bright light and removed phosphate even slightly more efficiently than the control strain if KA2 was Hepes buffered although ΔsigBCE grew slowly in un-buffered KA2 and in low-phosphate BG-11 medium. The results indicate that engineering expression of regulatory group 2 sigma factor(s) might be useful for practical applications.
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Affiliation(s)
- Dimitar Valev
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014, Turku, Finland
| | - Juha Kurkela
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014, Turku, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014, Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, 20014, Turku, Finland.
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Transcription in cyanobacteria: a distinctive machinery and putative mechanisms. Biochem Soc Trans 2019; 47:679-689. [DOI: 10.1042/bst20180508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 02/03/2023]
Abstract
Abstract
Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. The vast majority of bacterial species encode at least one of these highly conserved factors and so their absence in cyanobacteria is intriguing. Additionally, the largest subunit of bacterial RNAP has undergone a split in cyanobacteria to form two subunits and the SI3 insertion within the integral trigger loop element is roughly 3.5 times larger than in Escherichia coli. The Rho termination factor also appears to be absent, leaving cyanobacteria to rely solely on an intrinsic termination mechanism. Furthermore, cyanobacteria must be able to respond to environment signals such as light intensity and tightly synchronise gene expression and other cell activities to a circadian rhythm.
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Hakkila K, Valev D, Antal T, Tyystjï Rvi E, Tyystjï Rvi T. Group 2 Sigma Factors are Central Regulators of Oxidative Stress Acclimation in Cyanobacteria. PLANT & CELL PHYSIOLOGY 2019; 60:436-447. [PMID: 30407607 DOI: 10.1093/pcp/pcy221] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/04/2018] [Indexed: 06/08/2023]
Abstract
Regulatory σ factors of the RNA polymerase (RNAP) adjust gene expression according to environmental cues when the cyanobacterium Synechocystis sp. PCC 6803 acclimates to suboptimal conditions. Here we show central roles of the non-essential group 2 σ factors in oxidative stress responses. Cells missing all group 2 σ factors fail to acclimate to chemically induced singlet oxygen, superoxide or H2O2 stresses, and lose pigments in high light. SigB and SigD are the major σ factors in oxidative stress, whereas SigC and SigE play only minor roles. The SigD factor is up-regulated in high light, singlet oxygen and H2O2 stresses, and overproduction of the SigD factor in the ΔsigBCE strain leads to superior growth of ΔsigBCE cells in those stress conditions. Superoxide does not induce the production of the SigD factor but instead SigB and SigC factors are moderately induced. The SigB factor alone in ΔsigCDE can support almost as fast growth in superoxide stress as the full complement of σ factors in the control strain, but an overdose of the stationary phase-related SigC factor causes growth arrest of ΔsigBDE in superoxide stress. A drastic decrease of the functional RNAP limits the transcription capacity of the cells in H2O2 stress, which explains why cyanobacteria are sensitive to H2O2. Formation of RNAP-SigB and RNAP-SigD holoenzymes is highly enhanced in H2O2 stress, and cells containing only SigB (ΔsigCDE) or SigD (ΔsigBCE) show superior growth in H2O2 stress.
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Affiliation(s)
- Kaisa Hakkila
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Dimitar Valev
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Taras Antal
- Biological Faculty, Moscow State University, Vorobyevi Gory, Moscow, Russia
| | - Esa Tyystjï Rvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Taina Tyystjï Rvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
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Koskinen S, Hakkila K, Kurkela J, Tyystjärvi E, Tyystjärvi T. Inactivation of group 2 σ factors upregulates production of transcription and translation machineries in the cyanobacterium Synechocystis sp. PCC 6803. Sci Rep 2018; 8:10305. [PMID: 29985458 PMCID: PMC6037674 DOI: 10.1038/s41598-018-28736-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/26/2018] [Indexed: 11/17/2022] Open
Abstract
We show that the formation of the RNAP holoenzyme with the primary σ factor SigA increases in the ΔsigBCDE strain of the cyanobacterium Synechocystis sp. PCC 6803 lacking all group 2 σ factors. The high RNAP-SigA holoenzyme content directly induces transcription of a particular set of housekeeping genes, including ones encoding transcription and translation machineries. In accordance with upregulated transcripts, ΔsigBCDE contain more RNAPs and ribosomal subunits than the control strain. Extra RNAPs are fully active, and the RNA content of ΔsigBCDE cells is almost tripled compared to that in the control strain. Although ΔsigBCDE cells produce extra rRNAs and ribosomal proteins, functional extra ribosomes are not formed, and translation activity and protein content remained similar in ΔsigBCDE as in the control strain. The arrangement of the RNA polymerase core genes together with the ribosomal protein genes might play a role in the co-regulation of transcription and translation machineries. Sequence logos were constructed to compare promoters of those housekeeping genes that directly react to the RNAP-SigA holoenzyme content and those ones that do not. Cyanobacterial strains with engineered transcription and translation machineries might provide solutions for construction of highly efficient production platforms for biotechnical applications in the future.
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Affiliation(s)
- Satu Koskinen
- Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Kaisa Hakkila
- Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Juha Kurkela
- Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry, University of Turku, FI-20014, Turku, Finland.
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15
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Stensjö K, Vavitsas K, Tyystjärvi T. Harnessing transcription for bioproduction in cyanobacteria. PHYSIOLOGIA PLANTARUM 2018; 162:148-155. [PMID: 28762505 DOI: 10.1111/ppl.12606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Sustainable production of biofuels and other valuable compounds is one of our future challenges. One tempting possibility is to use photosynthetic cyanobacteria as production factories. Currently, tools for genetic engineering of cyanobacteria are not good enough to exploit the full potential of cyanobacteria. A wide variety of expression systems will be required to adjust both the expression of heterologous enzyme(s) and metabolic routes to the best possible balance, allowing the optimal production of a particular substance. In bacteria, transcription, especially the initiation of transcription, has a central role in adjusting gene expression and thus also metabolic fluxes of cells according to environmental cues. Here we summarize the recent progress in developing tools for efficient cyanofactories, focusing especially on transcriptional regulation.
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Affiliation(s)
- Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Taina Tyystjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803. BMC Microbiol 2017; 17:229. [PMID: 29216826 PMCID: PMC5721685 DOI: 10.1186/s12866-017-1137-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
Background The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. Results Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation. Conclusions The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria. Electronic supplementary material The online version of this article (10.1186/s12866-017-1137-9) contains supplementary material, which is available to authorized users.
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Srivastava A, Brilisauer K, Rai AK, Ballal A, Forchhammer K, Tripathi AK. Down-Regulation of the Alternative Sigma Factor SigJ Confers a Photoprotective Phenotype to Anabaena PCC 7120. PLANT & CELL PHYSIOLOGY 2017; 58:287-297. [PMID: 27837096 DOI: 10.1093/pcp/pcw188] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Alternative sigma factors belonging to Group 3 are thought to play an important role in the adaptation of cyanobacteria to environmental challenges by altering expression of genes needed for coping with such stresses. In this study, the role of an alternative sigma factor, SigJ, was analyzed in the filamentous nitrogen-fixing cyanobacterium, Anabaena sp. PCC 7120 by knocking down the expression of the sigJ gene (alr0277) employing an antisense RNA-mediated approach. In the absence of any stress, the knock-down (KD0277) or the wild-type strain both grew similarly. Upon exposure to high-intensity light, KD0277 showed substantially reduced bleaching of its pigments, higher photosynthetic activity and consequently better survival than the wild type. KD0277 also showed an enhanced accumulation of two carotenoids, which were identified as myxoxanthophyll and keto-myxoxanthophyll. Further, KD0277 was more tolerant to ammonium-triggered photodamage than the wild type. Moreover, PSII was better protected against photodamage in KD0277 than in the wild type. Down-regulation of sigJ in Anabaena PCC 7120, however, reduced its ability to cope with desiccation. This study demonstrates that down-regulation of the sigJ gene in Anabaena PCC 7120 differentially affects its ability to tolerate two environmentally relevant stresses, i.e. high-intensity light and desiccation.
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Affiliation(s)
- Amit Srivastava
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Klaus Brilisauer
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle, Tübingen, Germany
| | - Ashutosh K Rai
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle, Tübingen, Germany
| | - Anil K Tripathi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Al-Haj L, Lui YT, Abed RMM, Gomaa MA, Purton S. Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects. Life (Basel) 2016; 6:life6040042. [PMID: 27916886 PMCID: PMC5198077 DOI: 10.3390/life6040042] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/13/2016] [Accepted: 11/25/2016] [Indexed: 12/24/2022] Open
Abstract
Cyanobacteria hold significant potential as industrial biotechnology (IB) platforms for the production of a wide variety of bio-products ranging from biofuels such as hydrogen, alcohols and isoprenoids, to high-value bioactive and recombinant proteins. Underpinning this technology, are the recent advances in cyanobacterial “omics” research, the development of improved genetic engineering tools for key species, and the emerging field of cyanobacterial synthetic biology. These approaches enabled the development of elaborate metabolic engineering programs aimed at creating designer strains tailored for different IB applications. In this review, we provide an overview of the current status of the fields of cyanobacterial omics and genetic engineering with specific focus on the current molecular tools and technologies that have been developed in the past five years. The paper concludes by giving insights on future commercial applications of cyanobacteria and highlights the challenges that need to be addressed in order to make cyanobacterial industrial biotechnology more feasible in the near future.
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Affiliation(s)
- Lamya Al-Haj
- Biology Department, College of Science, Sultan Qaboos University, Al-Khoud, P.O. Box 36, Muscat 123, Oman.
| | - Yuen Tin Lui
- Institute of Structural & Molecular Biology, University College London, London WC1E 6BT, UK.
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, Al-Khoud, P.O. Box 36, Muscat 123, Oman.
| | - Mohamed A Gomaa
- Biology Department, College of Science, Sultan Qaboos University, Al-Khoud, P.O. Box 36, Muscat 123, Oman.
| | - Saul Purton
- Institute of Structural & Molecular Biology, University College London, London WC1E 6BT, UK.
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Tabatabai B, Arumanayagam AS, Enitan O, Mani A, Natarajan SS, Sitther V. Identification of a Halotolerant Mutant via In Vitro Mutagenesis in the Cyanobacterium Fremyella diplosiphon. Curr Microbiol 2016; 74:77-83. [DOI: 10.1007/s00284-016-1156-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/27/2016] [Indexed: 11/25/2022]
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Sinetova MA, Los DA. New insights in cyanobacterial cold stress responses: Genes, sensors, and molecular triggers. Biochim Biophys Acta Gen Subj 2016; 1860:2391-2403. [PMID: 27422804 DOI: 10.1016/j.bbagen.2016.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/16/2016] [Accepted: 07/09/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Cold stress strongly induces the expression of ~100 genes in cyanobacteria. Some of these genes are necessary to protect cellular functions by adjustment of membranes, as well as transcriptional and translational machineries. About a half of cold-induced genes are not functionally characterized. A part of cold-induced genes is under control of a two-component regulatory system, consisting of histidine kinase Hik33 and response regulator Rre26. The mechanism(s) that control another part of cold-inducible genes are still unknown. SCOPE OF REVIEW The aim of this review is to summarise the latest findings in cyanobacterial cold-stress responses including transcriptomics, cold sensing, and molecular triggers. MAJOR CONCLUSIONS A feedback loop between the membrane fluidity and transcription of genes for fatty acid desaturases operates via the transmembrane red-light-activated cold sensor Hik33, which perceives cold-induced membrane rigidification as a change in its thickness. The cold-induced kinase activity of Hik33 is facilitated by interaction with a small protein, Ssl3451 - the third contributor to a canonical two-component regulatory system, which may explain the ability of some cyanobacterial histidine kinases to interact with different response regulators under different stress conditions. Other regulatory systems that control cold-stress responses operate via Ser/Thr protein kinase, SpkE, and via temperature-dependent changes in DNA supercoiling. Transcriptomic analysis shows that universal triggers of stress responses are reactive oxygen species and changes in redox status of plastoquinone pool. GENERAL SIGNIFICANCE Deeper understanding of molecular mechanisms of temperature sensing and regulation of cold-stress responses in photosynthetic cells provide a background for generation of cold-resistant crops.
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Affiliation(s)
- Maria A Sinetova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russian Federation
| | - Dmitry A Los
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russian Federation.
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Antal T, Kurkela J, Parikainen M, Kårlund A, Hakkila K, Tyystjärvi E, Tyystjärvi T. Roles of Group 2 Sigma Factors in Acclimation of the Cyanobacterium Synechocystis sp. PCC 6803 to Nitrogen Deficiency. PLANT & CELL PHYSIOLOGY 2016; 57:1309-1318. [PMID: 27095737 DOI: 10.1093/pcp/pcw079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/10/2016] [Indexed: 06/05/2023]
Abstract
Acclimation of cyanobacteria to environmental conditions is mainly controlled at the transcriptional level, and σ factors of the RNA polymerase have a central role in this process. The model cyanobacterium Synechocystis sp. PCC 6803 has four non-essential group 2 σ factors (SigB, SigC, SigD and SigE) that regulate global metabolic responses to various adverse environmental conditions. Here we show that although none of the group 2 σ factors is essential for the major metabolic realignments induced by a short period of nitrogen starvation, the quadruple mutant without any group 2 σ factors and triple mutants missing both SigB and SigD grow slowly in BG-11 medium containing only 5% of the nitrate present in standard BG-11. These ΔsigBCDE, ΔsigBCD and ΔsigBDE strains lost PSII activity rapidly in low nitrogen and accumulated less glycogen than the control strain. An abnormally high glycogen content was detected in ΔsigBCE (SigD is active), while the carotenoid content became high in ΔsigCDE (SigB is active), indicating that SigB and SigD regulate the partitioning of carbon skeletons in low nitrogen. Long-term survival and recovery of the cells after nitrogen deficiency was strongly dependent on group 2 σ factors. The quadruple mutant and the ΔsigBDE strain (only SigC is active) recovered more slowly from nitrogen deficiency than the control strain, and ΔsigBCDE in particular lost viability during nitrogen starvation. Nitrogen deficiency-induced changes in the pigment content of the control strain recovered essentially in 1 d in nitrogen-replete medium, but little recovery occurred in ΔsigBCDE and ΔsigBDE.
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Affiliation(s)
- Taras Antal
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland Biological Faculty, Moscow State University, Vorobyevi Gory 119992, Moscow, Russia
| | - Juha Kurkela
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | | | - Anna Kårlund
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Kaisa Hakkila
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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Sinetova MA, Los DA. Systemic analysis of stress transcriptomics of Synechocystis reveals common stress genes and their universal triggers. MOLECULAR BIOSYSTEMS 2016; 12:3254-3258. [DOI: 10.1039/c6mb00551a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Systemic analysis of stress transcriptomics reveals that ROS and redox changes may universally trigger stress responses in Synechocystis (cyanobacteria).
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Affiliation(s)
- M. A. Sinetova
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow
- Russia
| | - D. A. Los
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow
- Russia
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