1
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Muth-Pawlak D, Kakko L, Kallio P, Aro EM. Interplay between photosynthetic electron flux and organic carbon sinks in sucrose-excreting Synechocystis sp. PCC 6803 revealed by omics approaches. Microb Cell Fact 2024; 23:188. [PMID: 38951789 PMCID: PMC11218172 DOI: 10.1186/s12934-024-02462-6] [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: 04/16/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Advancing the engineering of photosynthesis-based prokaryotic cell factories is important for sustainable chemical production and requires a deep understanding of the interplay between bioenergetic and metabolic pathways. Rearrangements in photosynthetic electron flow to increase the efficient use of the light energy for carbon fixation must be balanced with a strong carbon sink to avoid photoinhibition. In the cyanobacterium Synechocystis sp. PCC 6803, the flavodiiron protein Flv3 functions as an alternative electron acceptor of photosystem I and represents an interesting engineering target for reorganizing electron flow in attempts to enhance photosynthetic CO2 fixation and increase production yield. RESULTS We have shown that inactivation of Flv3 in engineered sucrose-excreting Synechocystis (S02:Δflv3) induces a transition from photoautotrophic sucrose production to mixotrophic growth sustained by sucrose re-uptake and the formation of intracellular carbon sinks such as glycogen and polyhydroxybutyrate. The growth of S02:Δflv3 exceeds that of the sucrose-producing strain (S02) and demonstrates unforeseen proteomic and metabolomic changes over the course of the nine-day cultivation. In the absence of Flv3, a down-regulation of proteins related to photosynthetic light reactions and CO2 assimilation occurred concomitantly with up-regulation of those related to glycolytic pathways, before any differences in sucrose production between S02 and S02:Δflv3 strains were observed. Over time, increased sucrose degradation in S02:Δflv3 led to the upregulation of respiratory pathway components, such as the plastoquinone reductase complexes NDH-11 and NDH-2 and the terminal respiratory oxidases Cyd and Cox, which transfer electrons to O2. While glycolytic metabolism is significantly up-regulated in S02:Δflv3 to provide energy for the cell, the accumulation of intracellular storage compounds and the increase in respiration serve as indirect sinks for photosynthetic electrons. CONCLUSIONS Our results show that the presence of strong carbon sink in the engineered sucrose-producing Synechocystis S02 strain, operating under high light, high CO2 and salt stress, cannot compensate for the lack of Flv3 by directly balancing the light transducing source and carbon fixing sink reactions. Instead, the cells immediately sense the imbalance, leading to extensive reprogramming of cellular bioenergetic, metabolic and ion transport pathways that favor mixotrophic growth rather than enhancing photoautotrophic sucrose production.
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Affiliation(s)
- Dorota Muth-Pawlak
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland.
| | - Lauri Kakko
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland
| | - Pauli Kallio
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland
| | - Eva-Mari Aro
- Department of Life Technologies, Molecular Plant Biology, University of Turku, Turku, FIN-20014, Finland
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2
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Liu Y, Ge H, Lu D. Functional proteomics reveals that Slr0237 is a SigE-regulated glycogen debranching enzyme pivotal for glycogen breakdown. Proteomics 2024:e2300222. [PMID: 38581091 DOI: 10.1002/pmic.202300222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
The group 2 σ factor for RNA polymerase SigE plays important role in regulating central carbon metabolism in cyanobacteria. However, the regulation of SigE for these pathways at a proteome level remains unknown. Using a sigE-deficient strain (ΔsigE) of Synechocystis sp. PCC 6803 and quantitative proteomics, we found that SigE depletion induces differential protein expression for sugar catabolic pathways including glycolysis, oxidative pentose phosphate (OPP) pathway, and glycogen catabolism. Two glycogen debranching enzyme homologues Slr1857 and Slr0237 are found differentially expressed in ΔsigE. Glycogen determination indicated that Δslr0237 accumulated glycogen under photomixotrophic condition but was unable to utilize these reserves in the dark, whereas Δslr1857 accumulates and utilizes glycogen in a similar way as the WT strain does in the same condition. These results suggest that Slr0237 plays the major role as the glycogen debranching enzyme in Synechocystis.
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Affiliation(s)
- Ye Liu
- Science & Technology Department of Sichuan Province, Chengdu, Sichuan, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
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3
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Huang C, Duan X, Ge H, Xiao Z, Zheng L, Wang G, Dong J, Wang Y, Zhang Y, Huang X, An H, Xu W, Wang Y. Parallel Proteomic Comparison of Mutants With Altered Carbon Metabolism Reveals Hik8 Regulation of P II Phosphorylation and Glycogen Accumulation in a Cyanobacterium. Mol Cell Proteomics 2023; 22:100582. [PMID: 37225018 PMCID: PMC10315926 DOI: 10.1016/j.mcpro.2023.100582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023] Open
Abstract
Carbon metabolism is central to photosynthetic organisms and involves the coordinated operation and regulation of numerous proteins. In cyanobacteria, proteins involved in carbon metabolism are regulated by multiple regulators including the RNA polymerase sigma factor SigE, the histidine kinases Hik8, Hik31 and its plasmid-borne paralog Slr6041, and the response regulator Rre37. To understand the specificity and the cross-talk of such regulations, we simultaneously and quantitatively compared the proteomes of the gene knockout mutants for the regulators. A number of proteins showing differential expression in one or more mutants were identified, including four proteins that are unanimously upregulated or downregulated in all five mutants. These represent the important nodes of the intricate and elegant regulatory network for carbon metabolism. Moreover, serine phosphorylation of PII, a key signaling protein sensing and regulating in vivo carbon/nitrogen (C/N) homeostasis through reversible phosphorylation, is massively increased with a concomitant significant decrease in glycogen content only in the hik8-knockout mutant, which also displays impaired dark viability. An unphosphorylatable PII S49A substitution restored the glycogen content and rescued the dark viability of the mutant. Together, our study not only establishes the quantitative relationship between the targets and the corresponding regulators and elucidated their specificity and cross-talk but also unveils that Hik8 regulates glycogen accumulation through negative regulation of PII phosphorylation, providing the first line of evidence that links the two-component system with PII-mediated signal transduction and implicates them in the regulation of carbon metabolism.
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Affiliation(s)
- Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Gaojie Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jinghui Dong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongyu An
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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4
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Tang J, Yao D, Zhou H, Wang M, Daroch M. Distinct Molecular Patterns of Two-Component Signal Transduction Systems in Thermophilic Cyanobacteria as Revealed by Genomic Identification. BIOLOGY 2023; 12:biology12020271. [PMID: 36829548 PMCID: PMC9953108 DOI: 10.3390/biology12020271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Two-component systems (TCSs) play crucial roles in sensing and responding to environmental signals, facilitating the acclimation of cyanobacteria to hostile niches. To date, there is limited information on the TCSs of thermophilic cyanobacteria. Here, genome-based approaches were used to gain insights into the structure and architecture of the TCS in 17 well-described thermophilic cyanobacteria, namely strains from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. The results revealed a fascinating complexity and diversity of the TCSs. A distinct composition of TCS genes existed among these thermophilic cyanobacteria. A majority of TCS genes were classified as orphan, followed by the paired and complex cluster. A high proportion of histidine kinases (HKs) were predicted to be cytosolic subcellular localizations. Further analyses suggested diversified domain architectures of HK and response regulators (RRs), putatively in association with various functions. Comparative and evolutionary genomic analyses indicated that the horizontal gene transfer, as well as duplications events, might be involved in the evolutionary history of TCS genes in Thermostichus and Thermosynechococcus strains. A comparative analysis between thermophilic and mesophilic cyanobacteria indicated that one HK cluster and one RR cluster were uniquely shared by all the thermophilic cyanobacteria studied, while two HK clusters and one RR cluster were common to all the filamentous thermophilic cyanobacteria. These results suggested that these thermophile-unique clusters may be related to thermal characters and morphology. Collectively, this study shed light on the TCSs of thermophilic cyanobacteria, which may confer the necessary regulatory flexibility; these findings highlight that the genomes of thermophilic cyanobacteria have a broad potential for acclimations to environmental fluctuations.
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Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Dan Yao
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Mingcheng Wang
- School of Food and Bioengineering, Chengdu University, Chengdu 610106, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Road, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-0755-2603-2184
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5
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Muth-Pawlak D, Kreula S, Gollan PJ, Huokko T, Allahverdiyeva Y, Aro EM. Patterning of the Autotrophic, Mixotrophic, and Heterotrophic Proteomes of Oxygen-Evolving Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2022; 13:891895. [PMID: 35694301 PMCID: PMC9175036 DOI: 10.3389/fmicb.2022.891895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Proteomes of an oxygenic photosynthetic cyanobacterium, Synechocystis sp. PCC 6803, were analyzed under photoautotrophic (low and high CO2, assigned as ATLC and ATHC), photomixotrophic (MT), and light-activated heterotrophic (LAH) conditions. Allocation of proteome mass fraction to seven sub-proteomes and differential expression of individual proteins were analyzed, paying particular attention to photosynthesis and carbon metabolism–centered sub-proteomes affected by the quality and quantity of the carbon source and light regime upon growth. A distinct common feature of the ATHC, MT, and LAH cultures was low abundance of inducible carbon-concentrating mechanisms and photorespiration-related enzymes, independent of the inorganic or organic carbon source. On the other hand, these cells accumulated a respiratory NAD(P)H dehydrogenase I (NDH-11) complex in the thylakoid membrane (TM). Additionally, in glucose-supplemented cultures, a distinct NDH-2 protein, NdbA, accumulated in the TM, while the plasma membrane-localized NdbC and terminal oxidase decreased in abundance in comparison to both AT conditions. Photosynthetic complexes were uniquely depleted under the LAH condition but accumulated under the ATHC condition. The MT proteome displayed several heterotrophic features typical of the LAH proteome, particularly including the high abundance of ribosome as well as amino acid and protein biosynthesis machinery-related components. It is also noteworthy that the two equally light-exposed ATHC and MT cultures allocated similar mass fractions of the total proteome to the seven distinct sub-proteomes. Unique trophic condition-specific expression patterns were likewise observed among individual proteins, including the accumulation of phosphate transporters and polyphosphate polymers storing energy surplus in highly energetic bonds under the MT condition and accumulation under the LAH condition of an enzyme catalyzing cyanophycin biosynthesis. It is concluded that the rigor of cell growth in the MT condition results, to a great extent, by combining photosynthetic activity with high intracellular inorganic carbon conditions created upon glucose breakdown and release of CO2, besides the direct utilization of glucose-derived carbon skeletons for growth. This combination provides the MT cultures with excellent conditions for growth that often exceeds that of mere ATHC.
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6
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Biochemical elucidation of citrate accumulation in Synechocystis sp. PCC 6803 via kinetic analysis of aconitase. Sci Rep 2021; 11:17131. [PMID: 34429477 PMCID: PMC8385029 DOI: 10.1038/s41598-021-96432-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/04/2021] [Indexed: 12/03/2022] Open
Abstract
A unicellular cyanobacterium Synechocystis sp. PCC 6803 possesses a unique tricarboxylic acid (TCA) cycle, wherein the intracellular citrate levels are approximately 1.5–10 times higher than the levels of other TCA cycle metabolite. Aconitase catalyses the reversible isomerisation of citrate and isocitrate. Herein, we biochemically analysed Synechocystis sp. PCC 6803 aconitase (SyAcnB), using citrate and isocitrate as the substrates. We observed that the activity of SyAcnB for citrate was highest at pH 7.7 and 45 °C and for isocitrate at pH 8.0 and 53 °C. The Km value of SyAcnB for citrate was higher than that for isocitrate under the same conditions. The Km value of SyAcnB for isocitrate was 3.6-fold higher than the reported Km values of isocitrate dehydrogenase for isocitrate. Therefore, we suggest that citrate accumulation depends on the enzyme kinetics of SyAcnB, and 2-oxoglutarate production depends on the chemical equilibrium in this cyanobacterium.
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7
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Neumann N, Doello S, Forchhammer K. Recovery of Unicellular Cyanobacteria from Nitrogen Chlorosis: A Model for Resuscitation of Dormant Bacteria. Microb Physiol 2021; 31:78-87. [PMID: 33878759 DOI: 10.1159/000515742] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/06/2021] [Indexed: 11/19/2022]
Abstract
Nitrogen starvation induces developmental transitions in cyanobacteria. Whereas complex multicellular cyanobacteria of the order Nostocales can differentiate specialized cells that perform nitrogen fixation in the presence of oxygenic photosynthesis, non-diazotrophic unicellular strains, such as Synechococcus elongatus or Synechocystis PCC 6803, undergo a transition into a dormant non-growing state. Due to loss of pigments during this acclimation, the process is termed chlorosis. Cells maintain viability in this state for prolonged periods of time, until they encounter a useable nitrogen source, which triggers a highly coordinated awakening process, termed resuscitation. The minimal set of cellular activity that maintains the viability of cells during chlorosis and ensures efficient resuscitation represents the organism's equivalent of the BIOS, the basic input/output system of a computer, that helps "booting" the operation system after switching on. This review summarizes the recent research in the resuscitation of cyanobacteria, representing a powerful model for the awakening of dormant bacteria.
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Affiliation(s)
- Niels Neumann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Sofia Doello
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
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8
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Srivastava A, Varshney RK, Shukla P. Sigma Factor Modulation for Cyanobacterial Metabolic Engineering. Trends Microbiol 2020; 29:266-277. [PMID: 33229204 DOI: 10.1016/j.tim.2020.10.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022]
Abstract
Sigma (σ) factors are key regulatory proteins that control the transcription initiation in prokaryotes. In response to environmental or developmental cues, σ factors initiate the transcription of necessary genes responsible for maintaining a life-sustaining metabolic balance. Due to the significant role of σ factors in bacterial metabolism, their rational engineering for commercial metabolite production in photoautotrophic, cyanobacterial cells is a desirable venture. As cyanobacterial genomes typically encode multiple σ factors, effective execution of metabolic engineering efforts largely relies on uncovering the complicated gene regulatory network and further characterization of the members of σ factor regulatory circuits. This review outlines the prospects of σ factor in metabolic engineering of cyanobacteria, summarizes the challenges in the path towards an efficient strain construction and highlights the genomic context of putative regulators of cyanobacterial σ factors.
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Affiliation(s)
- Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak-124001, Haryana, India.
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9
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Forchhammer K, Selim KA. Carbon/nitrogen homeostasis control in cyanobacteria. FEMS Microbiol Rev 2020; 44:33-53. [PMID: 31617886 PMCID: PMC8042125 DOI: 10.1093/femsre/fuz025] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023] Open
Abstract
Carbon/nitrogen (C/N) balance sensing is a key requirement for the maintenance of cellular homeostasis. Therefore, cyanobacteria have evolved a sophisticated signal transduction network targeting the metabolite 2-oxoglutarate (2-OG), the carbon skeleton for nitrogen assimilation. It serves as a status reporter for the cellular C/N balance that is sensed by transcription factors NtcA and NdhR and the versatile PII-signaling protein. The PII protein acts as a multitasking signal-integrating regulator, combining the 2-OG signal with the energy state of the cell through adenyl-nucleotide binding. Depending on these integrated signals, PII orchestrates metabolic activities in response to environmental changes through binding to various targets. In addition to 2-OG, other status reporter metabolites have recently been discovered, mainly indicating the carbon status of the cells. One of them is cAMP, which is sensed by the PII-like protein SbtB. The present review focuses, with a main emphasis on unicellular model strains Synechoccus elongatus and Synechocystis sp. PCC 6803, on the physiological framework of these complex regulatory loops, the tight linkage to metabolism and the molecular mechanisms governing the signaling processes.
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Affiliation(s)
- Karl Forchhammer
- Lehrstuhl für Mikrobiologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Khaled A Selim
- Lehrstuhl für Mikrobiologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
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10
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Guyet U, Nguyen NA, Doré H, Haguait J, Pittera J, Conan M, Ratin M, Corre E, Le Corguillé G, Brillet-Guéguen L, Hoebeke M, Six C, Steglich C, Siegel A, Eveillard D, Partensky F, Garczarek L. Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803. Front Microbiol 2020; 11:1707. [PMID: 32793165 PMCID: PMC7393227 DOI: 10.3389/fmicb.2020.01707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.
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Affiliation(s)
- Ulysse Guyet
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ngoc A Nguyen
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Hugo Doré
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Julie Haguait
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Justine Pittera
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Maël Conan
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Morgane Ratin
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Erwan Corre
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Gildas Le Corguillé
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France.,CNRS, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Mark Hoebeke
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Christophe Six
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | | | - Anne Siegel
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Damien Eveillard
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Frédéric Partensky
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Laurence Garczarek
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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11
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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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12
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Arisaka S, Terahara N, Oikawa A, Osanai T. Increased polyhydroxybutyrate levels by ntcA overexpression in Synechocystis sp. PCC 6803. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101565] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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13
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Katayama N, Takeya M, Osanai T. Biochemical characterisation of fumarase C from a unicellular cyanobacterium demonstrating its substrate affinity, altered by an amino acid substitution. Sci Rep 2019; 9:10629. [PMID: 31337820 PMCID: PMC6650407 DOI: 10.1038/s41598-019-47025-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/09/2019] [Indexed: 01/14/2023] Open
Abstract
The tricarboxylic acid cycle produces NADH for oxidative phosphorylation and fumarase [EC 4.2.1.2] is a critical enzyme in this cycle, catalysing the reversible conversion of fumarate and L-malate. Fumarase is applied to industrial L-malate production as a biocatalyst. L-malate is used in a wide range of industries such as food and beverage, pharmacy chemistry. Although the biochemical properties of fumarases have been studied in many organisms, they have not been investigated in cyanobacteria. In this study, the optimum pH and temperature of Synechocystis 6803 fumarase C (SyFumC) were 7.5 and 30 °C, respectively. The Km of SyFumC for L-malate was higher than for fumarate. Furthermore, SyFumC activity was strongly inhibited by citrate and succinate, consistent with fumarases in other organisms. Substitution of alanine by glutamate at position 314 of SyFumC changed the kcat for fumarate and L-malate. In addition, the inhibitory effects of citrate and succinate on SyFumC activity were alleviated. Phylogenetic analysis revealed cyanobacterial fumarase clades divided in non-nitrogen-fixing cyanobacteria and nitrogen-fixing cyanobacteria. SyFumC was thus biochemically characterised, including identification of an amino acid residue important for substrate affinity and enzymatic activity.
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Affiliation(s)
- Noriaki Katayama
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Masahiro Takeya
- 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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14
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Georg J, Rosana ARR, Chamot D, Migur A, Hess WR, Owttrim GW. Inactivation of the RNA helicase CrhR impacts a specific subset of the transcriptome in the cyanobacterium Synechocystis sp. PCC 6803. RNA Biol 2019; 16:1205-1214. [PMID: 31234711 PMCID: PMC6693541 DOI: 10.1080/15476286.2019.1621622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083), whose expression is regulated by abiotic stresses that alter the redox potential of the photosynthetic electron transport chain, including temperature downshift. Despite its proposed effect on RNA metabolism and its known relevance in cold-stress adaptation, the reported impact of a CrhR knockout on the cold adaption of the transcriptome only identified eight affected genes. Here, we utilized a custom designed microarray to assess the impact of the absence of CrhR RNA helicase activity on the transcriptome, independent of cold stress. CrhR truncation impacts an RNA subset comprising ~10% of the ncRNA and also ~10% of the mRNA transcripts. While equal numbers of mRNAs showed increased as well as decreased abundance, more than 90% of the ncRNAs showed enhanced expression in the absence of CrhR, indicative of a negative effect on ncRNA transcription or stability. We further tested the effect of CrhR on the stability of strongly responding RNAs that identify examples of post-transcriptional and transcriptional regulation. The data suggest that CrhR impacts multiple aspects of RNA metabolism in Synechocystis.
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Affiliation(s)
- Jens Georg
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | | | - Danuta Chamot
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
| | - Anzhela Migur
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Wolfgang R Hess
- a Faculty of Biology, University of Freiburg , Freiburg , Germany.,c Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg , Germany
| | - George W Owttrim
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
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15
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Sawa N, Tatsuke T, Ogawa A, Hirokawa Y, Osanai T, Hanai T. Modification of carbon metabolism in Synechococcus elongatus PCC 7942 by cyanophage-derived sigma factors for bioproduction improvement. J Biosci Bioeng 2019; 127:256-264. [DOI: 10.1016/j.jbiosc.2018.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022]
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16
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Shimmori Y, Kanesaki Y, Nozawa M, Yoshikawa H, Ehira S. Transcriptional Activation of Glycogen Catabolism and the Oxidative Pentose Phosphate Pathway by NrrA Facilitates Cell Survival Under Nitrogen Starvation in the Cyanobacterium Synechococcus sp. Strain PCC 7002. PLANT & CELL PHYSIOLOGY 2018; 59:1225-1233. [PMID: 29566230 DOI: 10.1093/pcp/pcy059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria respond to nitrogen deprivation by changing cellular metabolism. Glycogen is accumulated within cells to assimilate excess carbon and energy during nitrogen starvation, and inhibition of glycogen synthesis results in impaired nitrogen response and decreased ability to survive. In spite of glycogen accumulation, genes related to glycogen catabolism are up-regulated by nitrogen deprivation. In this study, we found that glycogen catabolism was also involved in acclimation to nitrogen deprivation in the cyanobacterium Synechococcus sp. PCC 7002. The glgP2 gene, encoding glycogen phosphorylase, was induced by nitrogen deprivation, and its expression was regulated by the nitrogen-regulated response regulator A (NrrA), which is a highly conserved transcriptional regulator in cyanobacteria. Activation of glycogen phosphorylase under nitrogen-deprived conditions was abolished by disruption of the nrrA gene, and survival of the nrrA mutant declined. In addition, a glgP2 mutant was highly susceptible to nitrogen starvation. NrrA also regulated expression of the tal-zwf-opcA operon, encoding enzymes of the oxidative pentose phosphate (OPP) pathway, and inactivation of glucose-6-phosphate dehydrogenase, the first enzyme of the OPP pathway, decreased the ability to survive under nitrogen starvation. It was concluded that NrrA facilitates cell survival by activating glycogen degradation and the OPP pathway under nitrogen-deprived conditions.
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Affiliation(s)
- Yuka Shimmori
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Masafumi Nozawa
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | | | - Shigeki Ehira
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
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17
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Esteves-Ferreira AA, Inaba M, Fort A, Araújo WL, Sulpice R. Nitrogen metabolism in cyanobacteria: metabolic and molecular control, growth consequences and biotechnological applications. Crit Rev Microbiol 2018. [DOI: 10.1080/1040841x.2018.1446902] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alberto A. Esteves-Ferreira
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Masami Inaba
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Antoine Fort
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Wagner L. Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Ronan Sulpice
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
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18
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Production of Bioplastic Compounds by Genetically Manipulated and Metabolic Engineered Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:155-169. [DOI: 10.1007/978-981-13-0854-3_7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Takeya M, Iijima H, Sukigara H, Osanai T. Cluster-Level Relationships of Genes Involved in Carbon Metabolism in Synechocystis sp. PCC 6803: Development of a Novel Succinate-Producing Strain. PLANT & CELL PHYSIOLOGY 2018; 59:72-81. [PMID: 29069477 DOI: 10.1093/pcp/pcx162] [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: 08/09/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
We quantified the transcript levels of 44 genes related to sugar catabolism in strains with altered primary carbon metabolism and discovered a consistent expression pattern among succinate-producing mutants. To identify factors that determine the expression pattern, we calculated Pearson's correlation coefficients, using the transcript data. Correlation analysis revealed positive and negative correlations among genes encoding sugar catabolic enzymes. On the basis of this analysis, we found that the mutant overexpressing both rre37 (encoding an OmpR-type response regulator) and sigE (encoding an RNA polymerase sigma factor) produced increased levels of succinate under dark, anaerobic conditions, with a maximum productivity of 420 mg l-1.
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Affiliation(s)
- Masahiro Takeya
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, 1-1-1, Higashimita, Tamaku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Hiroko Iijima
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, 1-1-1, Higashimita, Tamaku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Haruna Sukigara
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, 1-1-1, Higashimita, Tamaku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Takashi Osanai
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, 1-1-1, Higashimita, Tamaku, Kawasaki, Kanagawa, 214-8571 Japan
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20
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Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ, Futschik ME. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res 2017; 45:11800-11820. [PMID: 29036481 PMCID: PMC5714215 DOI: 10.1093/nar/gkx860] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.
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Affiliation(s)
- Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Laboratory of Intracellular Bacterial Pathogens, Department of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Rocío Robles-Rengel
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Miguel A Hernández-Prieto
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.,School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth PL6 8BU, UK
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21
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Gao X, Sun T, Wu L, Chen L, Zhang W. Co-overexpression of response regulator genes slr1037 and sll0039 improves tolerance of Synechocystis sp. PCC 6803 to 1-butanol. BIORESOURCE TECHNOLOGY 2017; 245:1476-1483. [PMID: 28533065 DOI: 10.1016/j.biortech.2017.04.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 05/22/2023]
Abstract
In this study, two response regulator (RR) encoding genes slr1037 as well as sll0039 were co-overexpressed in Synechocystis sp. PCC 6803 by metabolic engineering and the 1-butanol tolerance was successfully improved by 133%. Aiming to explore the possible mechanisms for the enhancing 1-butanol tolerance, a quantitative iTRAQ-LC-MS/MS proteomics approach was then employed, identifying 216 up-regulated and 99 down-regulated proteins compared to wild type after 1-butanol treatment. This study mapped the potential target genes regulated by Slr1037 and Sll0039 and demonstrated the feasibility of engineering response regulators for modifying the biofuel tolerance in cyanobacteria.
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Affiliation(s)
- Xinyan Gao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Lina Wu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China.
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, PR China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, PR China
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22
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Ehira S, Shimmori Y, Watanabe S, Kato H, Yoshikawa H, Ohmori M. The nitrogen-regulated response regulator NrrA is a conserved regulator of glycogen catabolism in β-cyanobacteria. Microbiology (Reading) 2017; 163:1711-1719. [DOI: 10.1099/mic.0.000549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shigeki Ehira
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Yuka Shimmori
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hiroaki Kato
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masayuki Ohmori
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
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Immethun CM, DeLorenzo DM, Focht CM, Gupta D, Johnson CB, Moon TS. Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803. Biotechnol Bioeng 2017; 114:1561-1569. [PMID: 28244586 DOI: 10.1002/bit.26275] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/19/2017] [Accepted: 02/19/2017] [Indexed: 02/04/2023]
Abstract
Many under-developed organisms possess important traits that can boost the effectiveness and sustainability of microbial biotechnology. Photoautotrophic cyanobacteria can utilize the energy captured from light to fix carbon dioxide for their metabolic needs while living in environments not suited for growing crops. Various value-added compounds have been produced by cyanobacteria in the laboratory; yet, the products' titers and yields are often not industrially relevant and lag behind what have been accomplished in heterotrophic microbes. Genetic tools for biological process control are needed to take advantage of cyanobacteria's beneficial qualities, as tool development also lags behind what has been created in common heterotrophic hosts. To address this problem, we developed a suite of sensors that regulate transcription in the model cyanobacterium Synechocystis sp. PCC 6803 in response to metabolically relevant signals, including light and the cell's nitrogen status, and a family of sensors that respond to the inexpensive chemical, l-arabinose. Increasing the number of available tools enables more complex and precise control of gene expression. Expanding the synthetic biology toolbox for this cyanobacterium also improves our ability to utilize this important under-developed organism in biotechnology. Biotechnol. Bioeng. 2017;114: 1561-1569. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Cheryl M Immethun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Drew M DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Caroline M Focht
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Dinesh Gupta
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Charles B Johnson
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
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24
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Transcriptome and proteome analysis of nitrogen starvation responses in Synechocystis 6803 ΔglgC, a mutant incapable of glycogen storage. ALGAL RES 2017. [DOI: 10.1016/j.algal.2016.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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25
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Mo H, Xie X, Zhu T, Lu X. Effects of global transcription factor NtcA on photosynthetic production of ethylene in recombinant Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:145. [PMID: 28592994 PMCID: PMC5460508 DOI: 10.1186/s13068-017-0832-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/26/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cyanobacteria are considered potential photosynthetic microbial cell factories for biofuel and biochemical production. Ethylene, one of the most important organic chemicals, has been successfully synthesized in cyanobacteria by introducing an exogenous ethylene-forming enzyme (Efe). However, it remains challenging to significantly improve the biosynthetic efficiency of cyanobacterial ethylene. Genetic modification of transcription factors is a powerful strategy for reprogramming cellular metabolism toward target products. In cyanobacteria, nitrogen control A (NtcA), an important global transcription regulator of primary carbon/nitrogen metabolism, is expected to play a crucial role in ethylene biosynthesis. RESULTS The partial deletion of ntcA (MH021) enhanced ethylene production by 23%, while ntcA overexpression (MH023) in a single-copy efe recombinant Synechocystis (XX76) reduced ethylene production by 26%. Compared to XX76, the Efe protein content increased 1.5-fold in MH021. This result may be due to the release of the negative regulation of NtcA on promoter P cpcB , which controls efe expression. Glycogen content showed a 23% reduction in MH021, and the ratio of intracellular succinate to 2-oxoglutarate (2-OG) increased 4.8-fold. In a four-copy efe recombinant strain with partially deleted ntcA and a modified tricarboxylic acid (TCA) cycle (MH043), a peak specific ethylene production rate of 2463 ± 219 μL L-1 h-1 OD730-1 was achieved, which is higher than previously reported. CONCLUSIONS The effects of global transcription factor NtcA on ethylene synthesis in genetically engineered Synechocystis sp. PCC 6803 were evaluated, and the partial deletion of ntcA enhanced ethylene production in both single-copy and multi-copy efe recombinant Synechocystis strains. Increased Efe expression, accelerated TCA cycling, and redirected carbon flux from glycogen probably account for this improvement. The results show great potential for improving ethylene synthetic efficiency in cyanobacteria by modulating global regulation factors.
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Affiliation(s)
- Huilin Mo
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoman Xie
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tao Zhu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
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26
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Klotz A, Georg J, Bučinská L, Watanabe S, Reimann V, Januszewski W, Sobotka R, Jendrossek D, Hess W, Forchhammer K. Awakening of a Dormant Cyanobacterium from Nitrogen Chlorosis Reveals a Genetically Determined Program. Curr Biol 2016; 26:2862-2872. [DOI: 10.1016/j.cub.2016.08.054] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/22/2016] [Indexed: 01/09/2023]
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27
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Damrow R, Maldener I, Zilliges Y. The Multiple Functions of Common Microbial Carbon Polymers, Glycogen and PHB, during Stress Responses in the Non-Diazotrophic Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2016; 7:966. [PMID: 27446007 PMCID: PMC4914499 DOI: 10.3389/fmicb.2016.00966] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/03/2016] [Indexed: 12/31/2022] Open
Abstract
Classical microbial carbon polymers such as glycogen and polyhydroxybutyrate (PHB) have a crucial impact as both a sink and a reserve under macronutrient stress conditions. Most microbial species exclusively synthesize and degrade either glycogen or PHB. A few bacteria such as the phototrophic model organism Synechocystis sp. PCC 6803 surprisingly produce both physico-chemically different polymers under conditions of high C to N ratios. For the first time, the function and interrelation of both carbon polymers in non-diazotrophic cyanobacteria are analyzed in a comparative physiological study of single- and double-knockout mutants (ΔglgC; ΔphaC; ΔglgC/ΔphaC), respectively. Most of the observed phenotypes are explicitly related to the knockout of glycogen synthesis, highlighting the metabolic, energetic, and structural impact of this process whenever cells switch from an active, photosynthetic 'protein status' to a dormant 'glycogen status'. The carbon flux regulation into glycogen granules is apparently crucial for both phycobilisome degradation and thylakoid layer disassembly in the presence of light. In contrast, PHB synthesis is definitely not involved in this primary acclimation response. Moreover, the very weak interrelations between the two carbon-polymer syntheses indicate that the regulation and role of PHB synthesis in Synechocystis sp. PCC 6803 is different from glycogen synthesis.
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Affiliation(s)
- Ramon Damrow
- Section of Plant Biochemistry, Institute of Biology, Humboldt-Universität zu Berlin Berlin, Germany
| | - Iris Maldener
- Section of Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen Tübingen, Germany
| | - Yvonne Zilliges
- Section of Plant Biochemistry, Institute of Biology, Humboldt-Universität zu BerlinBerlin, Germany; Section of Biophysics and Photosynthesis, Institute of Physics, Freie Universität BerlinBerlin, Germany
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Kawahara A, Sato Y, Saito Y, Kaneko Y, Takimura Y, Hagihara H, Hihara Y. Free fatty acid production in the cyanobacterium Synechocystis sp. PCC 6803 is enhanced by deletion of the cyAbrB2 transcriptional regulator. J Biotechnol 2016; 220:1-11. [DOI: 10.1016/j.jbiotec.2015.12.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/30/2015] [Accepted: 12/21/2015] [Indexed: 12/16/2022]
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Osanai T, Iijima H, Hirai MY. Understanding Sugar Catabolism in Unicellular Cyanobacteria Toward the Application in Biofuel and Biomaterial Production. Subcell Biochem 2016; 86:511-523. [PMID: 27023248 DOI: 10.1007/978-3-319-25979-6_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Synechocystis sp. PCC 6803 is a model species of the cyanobacteria that undergo oxygenic photosynthesis, and has garnered much attention for its potential biotechnological applications. The regulatory mechanism of sugar metabolism in this cyanobacterium has been intensively studied and recent omics approaches have revealed the changes in transcripts, proteins, and metabolites of sugar catabolism under different light and nutrient conditions. Several transcriptional regulators that control the gene expression of enzymes related to sugar catabolism have been identified in the past 10 years, including a sigma factor, transcription factors, and histidine kinases. The modification of these genes can lead to alterations in the primary metabolism as well as the levels of high-value products such as bioplastics and hydrogen. This review summarizes recent studies on sugar catabolism in Synechocystis sp. PCC 6803, emphasizing the importance of elucidating the molecular mechanisms of cyanobacterial metabolism for biotechnological applications.
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Affiliation(s)
- Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
| | - Hiroko Iijima
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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Osanai T, Shirai T, Iijima H, Nakaya Y, Okamoto M, Kondo A, Hirai MY. Genetic manipulation of a metabolic enzyme and a transcriptional regulator increasing succinate excretion from unicellular cyanobacterium. Front Microbiol 2015; 6:1064. [PMID: 26500619 PMCID: PMC4594341 DOI: 10.3389/fmicb.2015.01064] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 09/15/2015] [Indexed: 11/13/2022] Open
Abstract
Succinate is a building block compound that the U.S. Department of Energy (DOE) has declared as important in biorefineries, and it is widely used as a commodity chemical. Here, we identified the two genes increasing succinate production of the unicellular cyanobacterium Synechocystis sp. PCC 6803. Succinate was excreted under dark, anaerobic conditions, and its production level increased by knocking out ackA, which encodes an acetate kinase, and by overexpressing sigE, which encodes an RNA polymerase sigma factor. Glycogen catabolism and organic acid biosynthesis were enhanced in the mutant lacking ackA and overexpressing sigE, leading to an increase in succinate production reaching five times of the wild-type levels. Our genetic and metabolomic analyses thus demonstrated the effect of genetic manipulation of a metabolic enzyme and a transcriptional regulator on succinate excretion from this cyanobacterium with the data based on metabolomic technique.
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Affiliation(s)
- Takashi Osanai
- RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Department of Agricultural Chemistry, School of Agriculture, Meiji University Kawasaki, Japan
| | | | - Hiroko Iijima
- RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Department of Agricultural Chemistry, School of Agriculture, Meiji University Kawasaki, Japan
| | - Yuka Nakaya
- RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Biomass Engineering Program, RIKEN Yokohama, Japan
| | - Mami Okamoto
- Biomass Engineering Program, RIKEN Yokohama, Japan
| | - Akihiko Kondo
- Biomass Engineering Program, RIKEN Yokohama, Japan ; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University Kobe, Japan
| | - Masami Y Hirai
- RIKEN Center for Sustainable Resource Science Yokohama, Japan
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Iijima H, Shirai T, Okamoto M, Kondo A, Hirai MY, Osanai T. Changes in primary metabolism under light and dark conditions in response to overproduction of a response regulator RpaA in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2015; 6:888. [PMID: 26379657 PMCID: PMC4549654 DOI: 10.3389/fmicb.2015.00888] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/14/2015] [Indexed: 11/23/2022] Open
Abstract
The study of the primary metabolism of cyanobacteria in response to light conditions is important for environmental biology because cyanobacteria are widely distributed among various ecological niches. Cyanobacteria uniquely possess circadian rhythms, with central oscillators consisting from three proteins, KaiA, KaiB, and KaiC. The two-component histidine kinase SasA/Hik8 and response regulator RpaA transduce the circadian signal from KaiABC to control gene expression. Here, we generated a strain overexpressing rpaA in a unicellular cyanobacterium Synechocystis sp. PCC 6803. The rpaA-overexpressing strain showed pleiotropic phenotypes, including slower growth, aberrant degradation of an RNA polymerase sigma factor SigE after the light-to-dark transition, and higher accumulation of sugar catabolic enzyme transcripts under dark conditions. Metabolome analysis revealed delayed glycogen degradation, decreased sugar phosphates and organic acids in the tricarboxylic acid cycle, and increased amino acids under dark conditions. The current results demonstrate that in this cyanobacterium, RpaA is a regulator of primary metabolism and involved in adaptation to changes in light conditions.
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Affiliation(s)
- Hiroko Iijima
- School of Agriculture, Meiji University, Kawasaki Japan
| | - Tomokazu Shirai
- RIKEN, Center for Sustainable Resource Science, Yokohama Japan
| | - Mami Okamoto
- RIKEN, Center for Sustainable Resource Science, Yokohama Japan
| | - Akihiko Kondo
- RIKEN, Center for Sustainable Resource Science, Yokohama Japan ; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe Japan
| | | | - Takashi Osanai
- School of Agriculture, Meiji University, Kawasaki Japan ; RIKEN, Center for Sustainable Resource Science, Yokohama Japan
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One day of nitrogen starvation reveals the effect of sigE and rre37 overexpression on the expression of genes related to carbon and nitrogen metabolism in Synechocystis sp. PCC 6803. J Biosci Bioeng 2015; 120:128-34. [DOI: 10.1016/j.jbiosc.2014.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/19/2014] [Accepted: 12/20/2014] [Indexed: 01/08/2023]
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Okada K, Horii E, Nagashima Y, Mitsui M, Matsuura H, Fujiwara S, Tsuzuki M. Genes for a series of proteins that are involved in glucose catabolism are upregulated by the Hik8-cascade in Synechocystis sp. PCC 6803. PLANTA 2015; 241:1453-1462. [PMID: 25732003 DOI: 10.1007/s00425-015-2270-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
In summary, we could show the involvement of a Hik8-cascade in the expression of genes involved in the glycolytic and OPP pathways induced by GPL, and another signal pathway under photosynthetic conditions in Synechocystis . The Hik8-cascade under GPL conditions may regulate glucose degradation to produce some energy and carbon compounds. This cascade might be important for the supply of organic materials such as amino acids and nucleotides through enhancement of the rates of the glycolysis and OPP pathways. Histidine kinase Hik8 upregulates the expression of one of the important glycolytic genes, fbaA, via sll1330 under heterotrophic growth conditions (i.e., in the presence of glucose with an indispensable short period of light) in Synechocystis sp. PCC 6803. In this study, expression of the genes for the glycolytic and OPP pathways was investigated using the wild type, and disruption mutants of Hik8 and sll1330, to determine whether or not the Hik8-involving signal transduction system generally regulates glucose catabolism. In the wild type, all the genes for the glycolytic and OPP pathways were upregulated under the same conditions as for fbaA. Analyses of the disruption mutants suggested that the signal transduction system involving Hik8 and Sll1330 plays a key role in the upregulation of genes such as pfkA, pgmB, and glk, and also that Hik8 induces genes including gap1 and pgk independently of Sll1330. This complicated signal transduction cascade, designated as the Hik8-cascade, occurs under heterotrophic growth with light pulses. In addition, a disruption mutant of a putative histidine kinase, sll1334, exhibited growth and gene expression patterns that suggested it to be a negative regulator in the cascade. Possible histidine kinases and response regulators as candidates for other components in the cascade are discussed.
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Affiliation(s)
- Katsuhiko Okada
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan,
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Iijima H, Nakaya Y, Kuwahara A, Hirai MY, Osanai T. Seawater cultivation of freshwater cyanobacterium Synechocystis sp. PCC 6803 drastically alters amino acid composition and glycogen metabolism. Front Microbiol 2015; 6:326. [PMID: 25954257 PMCID: PMC4406197 DOI: 10.3389/fmicb.2015.00326] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/01/2015] [Indexed: 11/28/2022] Open
Abstract
Water use assessment is important for bioproduction using cyanobacteria. For eco-friendly reasons, seawater should preferably be used for cyanobacteria cultivation instead of freshwater. In this study, we demonstrated that the freshwater unicellular cyanobacterium Synechocystis sp. PCC 6803 could be grown in a medium based on seawater. The Synechocystis wild-type strain grew well in an artificial seawater (ASW) medium supplemented with nitrogen and phosphorus sources. The addition of HEPES buffer improved cell growth overall, although the growth in ASW medium was inferior to that in the synthetic BG-11 medium. The levels of proteins involved in sugar metabolism changed depending on the culture conditions. The biosynthesis of several amino acids including aspartate, glutamine, glycine, proline, ornithine, and lysine, was highly up-regulated by cultivation in ASW. Two types of natural seawater (NSW) were also made available for the cultivation of Synechocystis cells, with supplementation of both nitrogen and phosphorus sources. These results revealed the potential use of seawater for the cultivation of freshwater cyanobacteria, which would help to reduce freshwater consumption during biorefinery using cyanobacteria.
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Affiliation(s)
- Hiroko Iijima
- RIKEN Center for Sustainable Resource Science Yokohama, Japan
| | - Yuka Nakaya
- RIKEN Center for Sustainable Resource Science Yokohama, Japan
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science Yokohama, Japan
| | | | - Takashi Osanai
- RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Advanced Low Carbon Technology Research and Development Program (ALCA), Japan Science and Technology Agency Kawaguchi, Japan ; School of Agriculture, Meiji University Tokyo, Japan
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Sarkar D, Shimizu K. An overview on biofuel and biochemical production by photosynthetic microorganisms with understanding of the metabolism and by metabolic engineering together with efficient cultivation and downstream processing. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0045-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Aikawa S, Ho SH, Nakanishi A, Chang JS, Hasunuma T, Kondo A. Improving polyglucan production in cyanobacteria and microalgae via cultivation design and metabolic engineering. Biotechnol J 2015; 10:886-98. [DOI: 10.1002/biot.201400344] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 02/20/2015] [Accepted: 03/05/2015] [Indexed: 01/20/2023]
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Burnap RL, Hagemann M, Kaplan A. Regulation of CO2 Concentrating Mechanism in Cyanobacteria. Life (Basel) 2015; 5:348-71. [PMID: 25636131 PMCID: PMC4390856 DOI: 10.3390/life5010348] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/31/2022] Open
Abstract
In this chapter, we mainly focus on the acclimation of cyanobacteria to the changing ambient CO2 and discuss mechanisms of inorganic carbon (Ci) uptake, photorespiration, and the regulation among the metabolic fluxes involved in photoautotrophic, photomixotrophic and heterotrophic growth. The structural components for several of the transport and uptake mechanisms are described and the progress towards elucidating their regulation is discussed in the context of studies, which have documented metabolomic changes in response to changes in Ci availability. Genes for several of the transport and uptake mechanisms are regulated by transcriptional regulators that are in the LysR-transcriptional regulator family and are known to act in concert with small molecule effectors, which appear to be well-known metabolites. Signals that trigger changes in gene expression and enzyme activity correspond to specific "regulatory metabolites" whose concentrations depend on the ambient Ci availability. Finally, emerging evidence for an additional layer of regulatory complexity involving small non-coding RNAs is discussed.
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Affiliation(s)
- Robert L Burnap
- Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Martin Hagemann
- Institute Biosciences, Department Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, Rostock D-18059, Germany.
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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rre37 Overexpression alters gene expression related to the tricarboxylic acid cycle and pyruvate metabolism in Synechocystis sp. PCC 6803. ScientificWorldJournal 2014; 2014:921976. [PMID: 25614900 PMCID: PMC4295605 DOI: 10.1155/2014/921976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/22/2014] [Accepted: 11/23/2014] [Indexed: 11/23/2022] Open
Abstract
The tricarboxylic acid (TCA) cycle and pyruvate metabolism of cyanobacteria are unique and important from the perspectives of biology and biotechnology research. Rre37, a response regulator induced by nitrogen depletion, activates gene expression related to sugar catabolism. Our previous microarray analysis has suggested that Rre37 controls the transcription of genes involved in sugar catabolism, pyruvate metabolism, and the TCA cycle. In this study, quantitative real-time PCR was used to measure the transcript levels of 12 TCA cycle genes and 13 pyruvate metabolism genes. The transcripts of 6 genes (acnB, icd, ppc, pyk1, me, and pta) increased after 4 h of nitrogen depletion in the wild-type GT strain but the induction was abolished by rre37 overexpression. The repression of gene expression of fumC, ddh, and ackA caused by nitrogen depletion was abolished by rre37 overexpression. The expression of me was differently affected by rre37 overexpression, compared to the other 24 genes. These results indicate that Rre37 differently controls the genes of the TCA cycle and pyruvate metabolism, implying the key reaction of the primary in this unicellular cyanobacterium.
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Gunnelius L, Kurkela J, Hakkila K, Koskinen S, Parikainen M, Tyystjärvi T. The ω subunit of RNA polymerase is essential for thermal acclimation of the cyanobacterium Synechocystis sp. PCC 6803. PLoS One 2014; 9:e112599. [PMID: 25386944 PMCID: PMC4227741 DOI: 10.1371/journal.pone.0112599] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/09/2014] [Indexed: 01/26/2023] Open
Abstract
The rpoZ gene encodes the small ω subunit of RNA polymerase. A ΔrpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions (constant illumination at 40 µmol photons m−2 s−1; 32°C; ambient CO2) but was heat sensitive and died at 40°C. In the control strain, 71 genes were at least two-fold up-regulated and 91 genes down-regulated after a 24-h treatment at 40°C, while in ΔrpoZ 394 genes responded to heat. Only 62 of these heat-responsive genes were similarly regulated in both strains, and 80% of heat-responsive genes were unique for ΔrpoZ. The RNA polymerase core and the primary σ factor SigA were down-regulated in the control strain at 40°C but not in ΔrpoZ. In accordance with reduced RNA polymerase content, the total RNA content of mild-heat-stress-treated cells was lower in the control strain than in ΔrpoZ. Light-saturated photosynthetic activity decreased more in ΔrpoZ than in the control strain upon mild heat stress. The amounts of photosystem II and rubisco decreased at 40°C in both strains while PSI and the phycobilisome antenna protein allophycocyanin remained at the same level as in standard conditions. The phycobilisome rod proteins, phycocyanins, diminished during the heat treatment in ΔrpoZ but not in the control strain, and the nblA1 and nblA2 genes (encode NblA proteins required for phycobilisome degradation) were up-regulated only in ΔrpoZ. Our results show that the ω subunit of RNAP is essential in heat stress because it is required for heat acclimation of diverse cellular processes.
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Affiliation(s)
- Liisa Gunnelius
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Juha Kurkela
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Kaisa Hakkila
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Satu Koskinen
- Department of Biochemistry, University of Turku, Turku, Finland
| | | | - Taina Tyystjärvi
- Department of Biochemistry, University of Turku, Turku, Finland
- * E-mail:
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Integrated proteomic and metabolomic characterization of a novel two-component response regulator Slr1909 involved in acid tolerance in Synechocystis sp. PCC 6803. J Proteomics 2014; 109:76-89. [DOI: 10.1016/j.jprot.2014.06.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/13/2014] [Accepted: 06/22/2014] [Indexed: 11/17/2022]
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Osanai T, Oikawa A, Iijima H, Kuwahara A, Asayama M, Tanaka K, Ikeuchi M, Saito K, Hirai MY. Metabolomic analysis reveals rewiring of Synechocystis sp. PCC 6803 primary metabolism by ntcA overexpression. Environ Microbiol 2014; 16:3304-17. [PMID: 25039649 DOI: 10.1111/1462-2920.12554] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 06/30/2014] [Indexed: 11/26/2022]
Abstract
NtcA is a cAMP receptor protein-type transcription factor conserved among cyanobacteria and is essential for gene expression in response to nitrogen status. NtcA has been widely studied; however, no metabolomic analysis has been conducted using the ntcA mutant. Here, we generated a strain that overexpresses ntcA in Synechocystis sp. PCC 6803, named NOX10, and performed physiological, transcriptomic and metabolomic analyses. NOX10 grew faster than the wild-type strain under photoautotrophic conditions, but slower under light-activated heterotrophic conditions. Transcriptome analysis revealed that the expression of genes related to primary metabolism was altered by ntcA overexpression particularly under nitrogen-depleted conditions. Metabolomic analysis revealed that metabolite levels in sugar, purine/pyrimidine nucleotide, organic acid and amino acid metabolism were widely altered by ntcA overexpression. The protein levels of nitrogen-regulated transcriptional regulators were altered by ntcA overexpression during nitrogen starvation. These results demonstrate the alteration of primary metabolism by genetic engineering of NtcA, and they contribute to the current understanding of metabolic regulation of unicellular cyanobacteria.
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Affiliation(s)
- Takashi Osanai
- RIKEN, Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
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Ehira S, Ohmori M. NrrA directly regulates expression of the fraF gene and antisense RNAs for fraE in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. Microbiology (Reading) 2014; 160:844-850. [DOI: 10.1099/mic.0.076703-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heterocystous cyanobacterium Anabaena sp. strain PCC 7120 grows as linear multicellular filaments that can contain hundreds of cells. Heterocysts, which are specialized cells for nitrogen fixation, are regularly intercalated among photosynthetic vegetative cells, and these cells are metabolically dependent on each other. Thus, multicellularity is essential for diazotrophic growth of heterocystous cyanobacteria. In Anabaena sp. strain PCC 7120, the fraF gene, which is required to limit filament length, is induced by nitrogen deprivation. The fraF transcripts extend to the fraE gene, which lies on the opposite DNA strand and could possess dual functionality, mRNAs for fraF and antisense RNAs for fraE. In the present study, we found that NrrA, a nitrogen-regulated response regulator, directly regulated expression of fraF. Induction of fraF by nitrogen deprivation was abolished by the nrrA disruption. NrrA specifically bound to the promoter region of fraF, and recognized an inverted repeat sequence. Thus, it is concluded that NrrA controls expression of mRNAs for fraF and antisense RNAs for fraE in response to nitrogen deprivation.
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Affiliation(s)
- Shigeki Ehira
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan
- Department of Biological Sciences, Graduate school of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Masayuki Ohmori
- Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan
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Osanai T, Oikawa A, Numata K, Kuwahara A, Iijima H, Doi Y, Saito K, Hirai MY. Pathway-level acceleration of glycogen catabolism by a response regulator in the cyanobacterium Synechocystis species PCC 6803. PLANT PHYSIOLOGY 2014; 164:1831-41. [PMID: 24521880 PMCID: PMC3982746 DOI: 10.1104/pp.113.232025] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/10/2014] [Indexed: 05/04/2023]
Abstract
Response regulators of two-component systems play pivotal roles in the transcriptional regulation of responses to environmental signals in bacteria. Rre37, an OmpR-type response regulator, is induced by nitrogen depletion in the unicellular cyanobacterium Synechocystis species PCC 6803. Microarray and quantitative real-time polymerase chain reaction analyses revealed that genes related to sugar catabolism and nitrogen metabolism were up-regulated by rre37 overexpression. Protein levels of GlgP(slr1367), one of the two glycogen phosphorylases, in the rre37-overexpressing strain were higher than those of the parental wild-type strain under both nitrogen-replete and nitrogen-depleted conditions. Glycogen amounts decreased to less than one-tenth by rre37 overexpression under nitrogen-replete conditions. Metabolome analysis revealed that metabolites of the sugar catabolic pathway and amino acids were altered in the rre37-overexpressing strain after nitrogen depletion. These results demonstrate that Rre37 is a pathway-level regulator that activates the metabolic flow from glycogen to polyhydroxybutyrate and the hybrid tricarboxylic acid and ornithine cycle, unraveling the mechanism of the transcriptional regulation of primary metabolism in this unicellular cyanobacterium.
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Affiliation(s)
- Takashi Osanai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan (T.O., A.O., K.N., A.K., H.I., Y.D., K.S., M.Y.H.)
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan (T.O.)
- Yamagata University, Faculty of Agriculture, Wakaba-machi, Tsuruoka-shi, Yamagata 997–8555, Japan (A.O.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260–8522, Japan (K.S.)
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan (T.O., A.O., K.N., A.K., H.I., Y.D., K.S., M.Y.H.)
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan (T.O.)
- Yamagata University, Faculty of Agriculture, Wakaba-machi, Tsuruoka-shi, Yamagata 997–8555, Japan (A.O.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260–8522, Japan (K.S.)
| | - Keiji Numata
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan (T.O., A.O., K.N., A.K., H.I., Y.D., K.S., M.Y.H.)
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan (T.O.)
- Yamagata University, Faculty of Agriculture, Wakaba-machi, Tsuruoka-shi, Yamagata 997–8555, Japan (A.O.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260–8522, Japan (K.S.)
| | - Ayuko Kuwahara
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan (T.O., A.O., K.N., A.K., H.I., Y.D., K.S., M.Y.H.)
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan (T.O.)
- Yamagata University, Faculty of Agriculture, Wakaba-machi, Tsuruoka-shi, Yamagata 997–8555, Japan (A.O.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260–8522, Japan (K.S.)
| | - Hiroko Iijima
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan (T.O., A.O., K.N., A.K., H.I., Y.D., K.S., M.Y.H.)
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan (T.O.)
- Yamagata University, Faculty of Agriculture, Wakaba-machi, Tsuruoka-shi, Yamagata 997–8555, Japan (A.O.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260–8522, Japan (K.S.)
| | - Yoshiharu Doi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan (T.O., A.O., K.N., A.K., H.I., Y.D., K.S., M.Y.H.)
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan (T.O.)
- Yamagata University, Faculty of Agriculture, Wakaba-machi, Tsuruoka-shi, Yamagata 997–8555, Japan (A.O.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260–8522, Japan (K.S.)
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa 230–0045, Japan (T.O., A.O., K.N., A.K., H.I., Y.D., K.S., M.Y.H.)
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan (T.O.)
- Yamagata University, Faculty of Agriculture, Wakaba-machi, Tsuruoka-shi, Yamagata 997–8555, Japan (A.O.); and
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260–8522, Japan (K.S.)
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Liu D, Yang C. The nitrogen-regulated response regulator NrrA controls cyanophycin synthesis and glycogen catabolism in the cyanobacterium Synechocystis sp. PCC 6803. J Biol Chem 2014; 289:2055-71. [PMID: 24337581 PMCID: PMC3900954 DOI: 10.1074/jbc.m113.515270] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 12/05/2013] [Indexed: 11/06/2022] Open
Abstract
The cellular metabolism in cyanobacteria is extensively regulated in response to changes of environmental nitrogen availability. Multiple regulators are involved in this process, including a nitrogen-regulated response regulator NrrA. However, the regulatory role of NrrA in most cyanobacteria remains to be elucidated. In this study, we combined a comparative genomic reconstruction of NrrA regulons in 15 diverse cyanobacterial species with detailed experimental characterization of NrrA-mediated regulation in Synechocystis sp. PCC 6803. The reconstructed NrrA regulons in most species included the genes involved in glycogen catabolism, central carbon metabolism, amino acid biosynthesis, and protein degradation. A predicted NrrA-binding motif consisting of two direct repeats of TG(T/A)CA separated by an 8-bp A/T-rich spacer was verified by in vitro binding assays with purified NrrA protein. The predicted target genes of NrrA in Synechocystis sp. PCC 6803 were experimentally validated by comparing the transcript levels and enzyme activities between the wild-type and nrrA-inactivated mutant strains. The effect of NrrA deficiency on intracellular contents of arginine, cyanophycin, and glycogen was studied. Severe impairments in arginine synthesis and cyanophycin accumulation were observed in the nrrA-inactivated mutant. The nrrA inactivation also resulted in a significantly decreased rate of glycogen degradation. Our results indicate that by directly up-regulating expression of the genes involved in arginine synthesis, glycogen degradation, and glycolysis, NrrA controls cyanophycin accumulation and glycogen catabolism in Synechocystis sp. PCC 6803. It is suggested that NrrA plays a role in coordinating the synthesis and degradation of nitrogen and carbon reserves in cyanobacteria.
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Affiliation(s)
- Deng Liu
- From the Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chen Yang
- From the Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Rre37 stimulates accumulation of 2-oxoglutarate and glycogen under nitrogen starvation in Synechocystis sp. PCC 6803. FEBS Lett 2013; 588:466-71. [PMID: 24374346 DOI: 10.1016/j.febslet.2013.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 11/21/2022]
Abstract
Rre37 (sll1330) in a cyanobacterium Synechocystis sp. PCC 6803 acts as a regulatory protein for sugar catabolic genes during nitrogen starvation. Low glycogen accumulation in Δrre37 was due to low expression of glycogen anabolic genes. In addition to low 2-oxoglutarate accumulation, normal upregulated expression of genes encoding glutamate synthases (gltD and gltB) as well as accumulation of metabolites in glycolysis (fructose-6-phosphate, fructose-1,6-bisphosphate, and glyceraldehyde-3-phosphate) and tricarboxylic acid (TCA) cycle (oxaloacetate, fumarate, succinate, and aconitate) were abolished by rre37 knockout. Rre37 regulates 2-oxoglutarate accumulation, glycogen accumulation through expression of glycogen anabolic genes, and TCA cycle metabolites accumulation.
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Nagarajan S, Srivastava S, Sherman LA. Essential role of the plasmid hik31 operon in regulating central metabolism in the dark in Synechocystis sp. PCC 6803. Mol Microbiol 2013; 91:79-97. [PMID: 24237382 DOI: 10.1111/mmi.12442] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2013] [Indexed: 12/13/2022]
Abstract
The plasmid hik31 operon (P3, slr6039-slr6041) is located on the pSYSX plasmid in Synechocystis sp. PCC 6803. A P3 mutant (ΔP3) had a growth defect in the dark and a pigment defect that was worsened by the addition of glucose. The glucose defect was from incomplete metabolism of the substrate, was pH dependent, and completely overcome by the addition of bicarbonate. Addition of organic carbon and nitrogen sources partly alleviated the defects of the mutant in the dark. Electron micrographs of the mutant revealed larger cells with division defects, glycogen limitation, lack of carboxysomes, deteriorated thylakoids and accumulation of polyhydroxybutyrate and cyanophycin. A microarray experiment over two days of growth in light-dark plus glucose revealed downregulation of several photosynthesis, amino acid biosynthesis, energy metabolism genes; and an upregulation of cell envelope and transport and binding genes in the mutant. ΔP3 had an imbalance in carbon and nitrogen levels and many sugar catabolic and cell division genes were negatively affected after the first dark period. The mutant suffered from oxidative and osmotic stress, macronutrient limitation, and an energy deficit. Therefore, the P3 operon is an important regulator of central metabolism and cell division in the dark.
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Affiliation(s)
- Sowmya Nagarajan
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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Osanai T, Numata K, Oikawa A, Kuwahara A, Iijima H, Doi Y, Tanaka K, Saito K, Hirai MY. Increased bioplastic production with an RNA polymerase sigma factor SigE during nitrogen starvation in Synechocystis sp. PCC 6803. DNA Res 2013; 20:525-35. [PMID: 23861321 PMCID: PMC3859321 DOI: 10.1093/dnares/dst028] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Because cyanobacteria directly harvest CO2 and light energy, their carbon metabolism is important for both basic and applied sciences. Here, we show that overexpression of the sigma factor sigE in Synechocystis sp. PCC 6803 widely changes sugar catabolism and increases production of the biodegradable polyester polyhydroxybutyrate (PHB) during nitrogen starvation. sigE overexpression elevates the levels of proteins implicated in glycogen catabolism, the oxidative pentose phosphate pathway, and polyhydroxyalkanoate biosynthesis. PHB accumulation is enhanced by sigE overexpression under nitrogen-limited conditions, yet the molecular weights of PHBs synthesized by the parental glucose-tolerant and sigE overexpression strain are similar. Although gene expression induced by nitrogen starvation is changed and other metabolites (such as GDP-mannose and citrate) accumulate under sigE overexpression, genetic engineering of this sigma factor altered the metabolic pathway from glycogen to PHB during nitrogen starvation.
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Affiliation(s)
- Takashi Osanai
- 1RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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48
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Wang J, Chen L, Huang S, Liu J, Ren X, Tian X, Qiao J, Zhang W. RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:89. [PMID: 23259593 PMCID: PMC3564720 DOI: 10.1186/1754-6834-5-89] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/04/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Fermentation production of biofuel ethanol consumes agricultural crops, which will compete directly with the food supply. As an alternative, photosynthetic cyanobacteria have been proposed as microbial factories to produce ethanol directly from solar energy and CO2. However, the ethanol productivity from photoautotrophic cyanobacteria is still very low, mostly due to the low tolerance of cyanobacterial systems to ethanol stress. RESULTS To build a foundation necessary to engineer robust ethanol-producing cyanobacterial hosts, in this study we applied a quantitative transcriptomics approach with a next-generation sequencing technology, combined with quantitative reverse-transcript PCR (RT-PCR) analysis, to reveal the global metabolic responses to ethanol in model cyanobacterial Synechocystis sp. PCC 6803. The results showed that ethanol exposure induced genes involved in common stress responses, transporting and cell envelope modification. In addition, the cells can also utilize enhanced polyhydroxyalkanoates (PHA) accumulation and glyoxalase detoxication pathway as means against ethanol stress. The up-regulation of photosynthesis by ethanol was also further confirmed at transcriptional level. Finally, we used gene knockout strains to validate the potential target genes related to ethanol tolerance. CONCLUSION RNA-Seq based global transcriptomic analysis provided a comprehensive view of cellular response to ethanol exposure. The analysis provided a list of gene targets for engineering ethanol tolerance in cyanobacterium Synechocystis.
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Affiliation(s)
- Jiangxin Wang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Lei Chen
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Siqiang Huang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Jie Liu
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Xiaoyue Ren
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Xiaoxu Tian
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Jianjun Qiao
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
| | - Weiwen Zhang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin, 300072, People's Republic of China
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Tabei Y, Okada K, Horii E, Mitsui M, Nagashima Y, Sakai T, Yoshida T, Kamiya A, Fujiwara S, Tsuzuki M. Two regulatory networks mediated by light and glucose involved in glycolytic gene expression in cyanobacteria. PLANT & CELL PHYSIOLOGY 2012; 53:1720-1727. [PMID: 22915573 DOI: 10.1093/pcp/pcs115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fructose 1,6-bisphosphate aldolase (FBA) is an enzyme involved in both glycolytic and photosynthetic reactions in photosynthetic organisms. In prokaryotes, the bidirectional reaction proceeds in the same cellular compartment, i.e. the cytoplasm. Expression of the FBA gene, fbaA, is induced through two independent pathways, stimulated by continuous light and by glucose plus pulsed light (GPL), in a cyanobactrium, Synechocystis sp. PCC 6803. Under GPL conditions, glucose can be replaced by glucose analogs that are not even metabolized in a cell. Analyses of transcripts in deletion mutants suggested that both a histidine kinase, Hik8, and a response regulator, Sll1330, played important roles as signal components in fbaA expression under GPL conditions, but not under photosynthetic conditions. Analysis of a transformant in which sll1330 expression was enhanced demonstrated that fbaA expression was induced at least partially even without glucose, but for its further induction a pulsed light stimulus was required. These results substantiated that there are two light-dependent regulatory pathways for aldolase gene expression in this cyanobacterium.
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Affiliation(s)
- Yosuke Tabei
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392 Japan
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Ehira S, Ohmori M. NrrA, a nitrogen-regulated response regulator protein, controls glycogen catabolism in the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. J Biol Chem 2011; 286:38109-38114. [PMID: 21926170 DOI: 10.1074/jbc.m111.289124] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium in which certain vegetative cells differentiate into heterocysts that are specialized cells for nitrogen fixation. Heterocysts are unable to carry out photosynthesis and depend on vegetative cells for carbohydrate to generate ATP and reductants required for nitrogen fixation. Thus, carbohydrate metabolism is very important for nitrogen fixation in the filamentous cyanobacteria; however, its regulatory mechanism remains unknown. In the present study, a nitrogen-regulated response regulator NrrA, which is a transcriptional regulator involved in heterocyst differentiation, was shown to control glycogen catabolism. The transcript levels of genes involved in glycogen catabolism, such as glgP1 and xfp-gap1-pyk1-talB operon, were decreased by the nrrA disruption. Moreover, glycogen accumulation and depression of nitrogenase activities were observed in this disruptant. NrrA bound specifically to the promoter region of glgP1, encoding a glycogen phosphorylase, and to the promoter region of sigE, encoding a group 2 σ factor of RNA polymerase. SigE activated expression of the xfp operon, encoding enzymes of glycolysis and the pentose phosphate pathway. It is concluded that NrrA controls not only heterocyst differentiation but also glycogen catabolism in Anabaena sp. strain PCC 7120.
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Affiliation(s)
- Shigeki Ehira
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo, Tokyo 112-8551, Japan
| | - Masayuki Ohmori
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo, Tokyo 112-8551, Japan.
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