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Xu HF, Yu C, Bai Y, Zuo AW, Ye YT, Liu YR, Li ZK, Dai GZ, Chen M, Qiu BS. Red-light-dependent chlorophyll synthesis kindles photosynthetic recovery of chlorotic dormant cyanobacteria using a dark-operative enzyme. Curr Biol 2024:S0960-9822(24)01022-4. [PMID: 39146941 DOI: 10.1016/j.cub.2024.07.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024]
Abstract
Chlorosis dormancy resulting from nitrogen starvation and its resuscitation upon available nitrogen contributes greatly to the fitness of cyanobacterial population under nitrogen-fluctuating environments. The reinstallation of the photosynthetic machinery is a key process for resuscitation from a chlorotic dormant state; however, the underlying regulatory mechanism is still elusive. Here, we reported that red light is essential for re-greening chlorotic Synechocystis sp. PCC 6803 (a non-diazotrophic cyanobacterium) after nitrogen supplement under weak light conditions. The expression of dark-operative protochlorophyllide reductase (DPOR) governed by the transcriptional factor RpaB was strikingly induced by red light in chlorotic cells, and its deficient mutant lost the capability of resuscitation from a dormant state, indicating DPOR catalyzing chlorophyll synthesis is a key step in the photosynthetic recovery of dormant cyanobacteria. Although light-dependent protochlorophyllide reductase is widely considered as a master switch in photomorphogenesis, this study unravels the primitive DPOR as a spark to activate the photosynthetic recovery of chlorotic dormant cyanobacteria. These findings provide new insight into the biological significance of DPOR in cyanobacteria and even some plants thriving in extreme environments.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Chen Yu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Yang Bai
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Ai-Wei Zuo
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Ying-Tong Ye
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Yan-Ru Liu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Zheng-Ke Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Guo-Zheng Dai
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Min Chen
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Bao-Sheng Qiu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China.
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2
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Domínguez-Lobo MT, Roldán M, Gutiérrez-Diánez AM, Florencio FJ, Muro-Pastor MI. Double blocking of carbon metabolism causes a large increase of Calvin-Benson cycle compounds in cyanobacteria. PLANT PHYSIOLOGY 2024; 195:1491-1505. [PMID: 38377468 PMCID: PMC11142378 DOI: 10.1093/plphys/kiae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/08/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024]
Abstract
Carbon-flow-regulator A (CfrA) adapts carbon flux to nitrogen conditions in nondiazotrophic cyanobacteria. Under nitrogen deficiency, CfrA leads to the storage of excess carbon, which cannot combine with nitrogen, mainly as glycogen. cfrA overexpression from the arsenite-inducible, nitrogen-independent ParsB promoter allows analysis of the metabolic effects of CfrA accumulation. Considering that the main consequence of cfrA overexpression is glycogen accumulation, we examined carbon distribution in response to cfrA expression in Synechocystis sp. PCC 6803 strains impaired in synthesizing this polymer. We carried out a comparative phenotypic analysis to evaluate cfrA overexpression in the wild-type strain and in a mutant of ADP-glucose pyrophosphorylase (ΔglgC), which is unable to synthesize glycogen. The accumulation of CfrA in the wild-type background caused a photosynthetic readjustment although growth was not affected. However, in a ΔglgC strain, growth decreased depending on CfrA accumulation and photosynthesis was severely affected. An elemental analysis of the H, C, and N content of cells revealed that cfrA expression in the wild-type caused an increase in the C/N ratio, due to decreased nitrogen assimilation. Metabolomic study indicated that these cells store sucrose and glycosylglycerol, in addition to the previously described glycogen accumulation. However, cells deficient in glycogen synthesis accumulated large amounts of Calvin-Benson cycle intermediates as cfrA was expressed. These cells also showed increased levels of some amino acids, mainly alanine, serine, valine, isoleucine, and leucine. The findings suggest that by controlling cfrA expression, in different conditions and strains, we could change the distribution of fixed carbon, with potential biotechnological benefits.
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Affiliation(s)
| | - Miguel Roldán
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| | - Alba María Gutiérrez-Diánez
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| | - Francisco Javier Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| | - María Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
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3
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Liu Y, Cheng YY, Thompson J, Zhou Z, Vivas EI, Warren MF, Rey FE, Anantharaman K, Venturelli OS. Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.10.523442. [PMID: 37986770 PMCID: PMC10659395 DOI: 10.1101/2023.01.10.523442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The arginine dihydrolase pathway (arc operon) present in a subset of diverse human gut species enables arginine catabolism. This specialized metabolic pathway can alter environmental pH and nitrogen availability, which in turn could shape gut microbiota inter-species interactions. By exploiting synthetic control of gene expression, we investigated the role of the arc operon in probiotic Escherichia coli Nissle 1917 on human gut community assembly and health-relevant metabolite profiles in vitro and in the murine gut. By stabilizing environmental pH, the arc operon reduced variability in community composition across different initial pH perturbations. The abundance of butyrate producing bacteria were altered in response to arc operon activity and butyrate production was enhanced in a physiologically relevant pH range. While the presence of the arc operon altered community dynamics, it did not impact production of short chain fatty acids. Dynamic computational modeling of pH-mediated interactions reveals the quantitative contribution of this mechanism to community assembly. In sum, our framework to quantify the contribution of molecular pathways and mechanism modalities on microbial community dynamics and functions could be applied more broadly.
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Affiliation(s)
- Yiyi Liu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
- Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew F. Warren
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
| | | | - Ophelia S. Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Bacteriology, University of Wisconsin-Madison, WI 53706
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4
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Zhou J, Xu S, Li H, Xi H, Cheng W, Yang C. A Ribulose-5-phosphate Shunt from the Calvin-Benson Cycle to Methylerythritol Phosphate Pathway for Enhancing Photosynthetic Terpenoid Production. ACS Synth Biol 2024; 13:876-887. [PMID: 38362836 DOI: 10.1021/acssynbio.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cyanobacteria are attractive hosts for photosynthetic terpenoid production, using CO2 as the sole carbon source. Although the methylerythritol phosphate (MEP) pathway is superior to the mevalonate pathway for cyanobacterial terpenoid synthesis, the first reaction of the MEP pathway, which is catalyzed by 1-deoxy-d-xylulose-5-phosphate (DXP) synthase, involves complex regulation and carbon loss. Here, we constructed a direct route linking ribulose-5-phosphate (Ru5P) in the Calvin-Benson (CB) cycle with DXP in the MEP pathway in a cyanobacterium to increase the terpenoid yield from CO2 and bypass the DXS-targeted regulations. By employing the adaptive laboratory evolution, we identified new RibB variants including RibB 90-92del with a high activity of synthesizing DXP from Ru5P. These RibB variants were introduced into Synechococcus elongatus, resulting in the significantly increased photosynthetic production of isopentenol. The 13C tracer experiments demonstrated a direct carbon flow from Ru5P in the CB cycle to the MEP pathway; thus, this direct route was denoted as the Ru5P shunt. The strain harboring the Ru5P shunt produced 105.2 mg L-1 of isopentenol with an average rate of 17.5 mg L-1 d-1 under continuous light conditions, which is higher than those ever reported for five-carbon alcohol production by photoautotrophic microorganisms. Utilization of the Ru5P shunt in cyanobacterial cells also improved the pinene production, which demonstrates that this shunt can be used to enhance the photosynthetic production of diverse terpenoids.
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Affiliation(s)
- Jie Zhou
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suxian Xu
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huachao Xi
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Cheng
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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5
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Katayama N, Osanai T. Arginine inhibits the arginine biosynthesis rate-limiting enzyme and leads to the accumulation of intracellular aspartate in Synechocystis sp. PCC 6803. PLANT MOLECULAR BIOLOGY 2024; 114:27. [PMID: 38478146 PMCID: PMC10937788 DOI: 10.1007/s11103-024-01416-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/02/2024] [Indexed: 03/17/2024]
Abstract
Cyanobacteria are oxygen-evolving photosynthetic prokaryotes that affect the global carbon and nitrogen turnover. Synechocystis sp. PCC 6803 (Synechocystis 6803) is a model cyanobacterium that has been widely studied and can utilize and uptake various nitrogen sources and amino acids from the outer environment and media. l-arginine is a nitrogen-rich amino acid used as a nitrogen reservoir in Synechocystis 6803, and its biosynthesis is strictly regulated by feedback inhibition. Argininosuccinate synthetase (ArgG; EC 6.3.4.5) is the rate-limiting enzyme in arginine biosynthesis and catalyzes the condensation of citrulline and aspartate using ATP to produce argininosuccinate, which is converted to l-arginine and fumarate through argininosuccinate lyase (ArgH). We performed a biochemical analysis of Synechocystis 6803 ArgG (SyArgG) and obtained a Synechocystis 6803 mutant overexpressing SyArgG and ArgH of Synechocystis 6803 (SyArgH). The specific activity of SyArgG was lower than that of other arginine biosynthesis enzymes and SyArgG was inhibited by arginine, especially among amino acids and organic acids. Both arginine biosynthesis enzyme-overexpressing strains grew faster than the wild-type Synechocystis 6803. Based on previous reports and our results, we suggest that SyArgG is the rate-limiting enzyme in the arginine biosynthesis pathway in cyanobacteria and that arginine biosynthesis enzymes are similarly regulated by arginine in this cyanobacterium. Our results contribute to elucidating the regulation of arginine biosynthesis during nitrogen metabolism.
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Affiliation(s)
- Noriaki Katayama
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, 214-8571, Kawasaki, Kanagawa, Japan
| | - Takashi Osanai
- School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, 214-8571, Kawasaki, Kanagawa, Japan.
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6
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Kugler A, Stensjö K. Machine learning predicts system-wide metabolic flux control in cyanobacteria. Metab Eng 2024; 82:171-182. [PMID: 38395194 DOI: 10.1016/j.ymben.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Metabolic fluxes and their control mechanisms are fundamental in cellular metabolism, offering insights for the study of biological systems and biotechnological applications. However, quantitative and predictive understanding of controlling biochemical reactions in microbial cell factories, especially at the system level, is limited. In this work, we present ARCTICA, a computational framework that integrates constraint-based modelling with machine learning tools to address this challenge. Using the model cyanobacterium Synechocystis sp. PCC 6803 as chassis, we demonstrate that ARCTICA effectively simulates global-scale metabolic flux control. Key findings are that (i) the photosynthetic bioproduction is mainly governed by enzymes within the Calvin-Benson-Bassham (CBB) cycle, rather than by those involve in the biosynthesis of the end-product, (ii) the catalytic capacity of the CBB cycle limits the photosynthetic activity and downstream pathways and (iii) ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a major, but not the most, limiting step within the CBB cycle. Predicted metabolic reactions qualitatively align with prior experimental observations, validating our modelling approach. ARCTICA serves as a valuable pipeline for understanding cellular physiology and predicting rate-limiting steps in genome-scale metabolic networks, and thus provides guidance for bioengineering of cyanobacteria.
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Affiliation(s)
- Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden.
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7
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Kraus A, Spät P, Timm S, Wilson A, Schumann R, Hagemann M, Maček B, Hess WR. Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria. Nat Commun 2024; 15:1911. [PMID: 38429292 PMCID: PMC10907346 DOI: 10.1038/s41467-024-46253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.
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Affiliation(s)
- Alexander Kraus
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Philipp Spät
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Stefan Timm
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Amy Wilson
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Rhena Schumann
- Biological Station Zingst, University of Rostock, D-18374, Zingst, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany.
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8
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Kiss É, Talbot J, Adams NBP, Opekar S, Moos M, Pilný J, Kvasov T, Schneider E, Koník P, Šimek P, Sobotka R. Chlorophyll biosynthesis under the control of arginine metabolism. Cell Rep 2023; 42:113265. [PMID: 37864789 PMCID: PMC10783636 DOI: 10.1016/j.celrep.2023.113265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/11/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023] Open
Abstract
In natural environments, photosynthetic organisms adjust their metabolism to cope with the fluctuating availability of combined nitrogen sources, a growth-limiting factor. For acclimation, the dynamic degradation/synthesis of tetrapyrrolic pigments, as well as of the amino acid arginine, is pivotal; however, there has been no evidence that these processes could be functionally coupled. Using co-immunopurification and spectral shift assays, we found that in the cyanobacterium Synechocystis sp. PCC 6803, the arginine metabolism-related ArgD and CphB enzymes form protein complexes with Gun4, an essential protein for chlorophyll biosynthesis. Gun4 binds ArgD with high affinity, and the Gun4-ArgD complex accumulates in cells supplemented with ornithine, a key intermediate of the arginine pathway. Elevated ornithine levels restricted de novo synthesis of tetrapyrroles, which arrested the recovery from nitrogen deficiency. Our data reveal a direct crosstalk between tetrapyrrole biosynthesis and arginine metabolism that highlights the importance of balancing photosynthetic pigment synthesis with nitrogen homeostasis.
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Affiliation(s)
- Éva Kiss
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Jana Talbot
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Nathan B P Adams
- NanoTemper Technologies, Floessegasse 4, 81369 Munich, Germany; Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Stanislav Opekar
- Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Martin Moos
- Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Jan Pilný
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Tatjana Kvasov
- NanoTemper Technologies, Floessegasse 4, 81369 Munich, Germany
| | | | - Peter Koník
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Petr Šimek
- Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Roman Sobotka
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology, The Czech Academy of Sciences, 37901 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic.
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9
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Xi H, Nie X, Gao F, Liang X, Li H, Zhou H, Cai Y, Yang C. A bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine. SCIENCE ADVANCES 2023; 9:eadj9075. [PMID: 37878710 PMCID: PMC10599626 DOI: 10.1126/sciadv.adj9075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/22/2023] [Indexed: 10/27/2023]
Abstract
Spermidine, a ubiquitous polyamine, is known to be required for critical physiological functions in bacteria. Two principal pathways are known for spermidine biosynthesis, both of which involve aminopropylation of putrescine. Here, we identified a spermidine biosynthetic pathway via a previously unknown metabolite, carboxyaminopropylagmatine (CAPA), in a model cyanobacterium Synechocystis sp. PCC 6803 through an approach combining 13C and 15N tracers, metabolomics, and genetic and biochemical characterization. The CAPA pathway starts with reductive condensation of agmatine and l-aspartate-β-semialdehyde into CAPA by a previously unknown CAPA dehydrogenase, followed by decarboxylation of CAPA to form aminopropylagmatine, and ends with conversion of aminopropylagmatine to spermidine by an aminopropylagmatine ureohydrolase. Thus, the pathway does not involve putrescine and depends on l-aspartate-β-semialdehyde as the aminopropyl group donor. Genomic, biochemical, and metagenomic analyses showed that the CAPA-pathway genes are widespread in 15 different phyla of bacteria distributed in marine, freshwater, and other ecosystems.
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Affiliation(s)
- Huachao Xi
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqun Nie
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fang Gao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Hu Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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10
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Liang J, Chen Z, Yin P, Hu H, Cheng W, Shang J, Yang Y, Yuan Z, Pan J, Yin Y, Li W, Chen X, Gao X, Qiu B, Wang B. Efficient Semi-Artificial Photosynthesis of Ethylene by a Self-Assembled InP-Cyanobacterial Biohybrid System. CHEMSUSCHEM 2023; 16:e202300773. [PMID: 37381086 DOI: 10.1002/cssc.202300773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Biomanufacturing of ethylene is particularly important for modern society. Cyanobacterial cells are able to photosynthesize various valuable chemicals. A promising platform for next-generation biomanufacturing, the semiconductor-cyanobacterial hybrid systems are capable of enhancing the solar-to-chemical conversion efficiency. Herein, the native ethylene-producing capability of a filamentous cyanobacterium Nostoc sphaeroides is confirmed experimentally. The self-assembly characteristic of N. sphaeroides is exploited to facilitate its interaction with InP nanomaterial, and the resulting biohybrid system gave rise to further elevated photosynthetic ethylene production. Based on chlorophyll fluorescence measurement and metabolic analysis, the InP nanomaterial-augmented photosystem I activity and enhanced ethylene production metabolism of biohybrid cells are confirmed, the mechanism underlying the material-cell energy transduction as well as nanomaterial-modulated photosynthetic light and dark reactions are established. This work not only demonstrates the potential application of semiconductor-N. sphaeroides biohybrid system as a good platform for sustainable ethylene production but also provides an important reference for future studies to construct and optimize nano-cell biohybrid systems for efficient solar-driven valuable chemical production.
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Affiliation(s)
- Jun Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Zhen Chen
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Panqing Yin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Haitao Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Wenbo Cheng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, P. R. China
| | - Jinlong Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Yiwen Yang
- College of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, Jiangxi, 332000, P.R. China
| | - Zuwen Yuan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Jinlong Pan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Yongqi Yin
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Weizhi Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Xiongwen Chen
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, P. R. China
| | - Xiang Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Baosheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, P. R. China
| | - Bo Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
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11
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Ran Z, Du Z, Miao G, Zheng M, Luo L, Pang X, Wei L, Li D, Ma W. Identification of a c-type heme oxygenase and its function during acclimation of cyanobacteria to nitrogen fluctuations. Commun Biol 2023; 6:944. [PMID: 37714932 PMCID: PMC10504260 DOI: 10.1038/s42003-023-05315-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
The mechanisms of acclimating to a nitrogen-fluctuating environment are necessary for the survival of aquatic cyanobacteria in their natural habitats, but our understanding is still far from complete. Here, the synthesis of phycobiliprotein is confirmed to be much earlier than that of photosystem components during recovery from nitrogen chlorosis and an unknown protein Ssr1698 is discovered to be involved in this synthetic process. The unknown protein is further identified as a c-type heme oxygenase (cHO) in tetrapyrrole biosynthetic pathway and catalyzes the opening of heme ring to form biliverdin IXα, which is required for phycobilin production and ensuing phycobiliprotein synthesis. In addition, the cHO-dependent phycobiliprotein is found to be vital for the growth of cyanobacterial cells during chlorosis and regreening through its nitrogen-storage and light-harvesting functions, respectively. Collectively, the cHO expressed preferentially during recovery from nitrogen chlorosis is identified in photosynthetic organisms and the dual function of this enzyme-dependent phycobiliprotein is proposed to be an important mechanism for acclimation of aquatic cyanobacteria to a nitrogen-fluctuating environment.
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Affiliation(s)
- Zhaoxing Ran
- School of Ecological and Environmental Sciences, East China Normal University, 200241, Shanghai, China
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Zhenyu Du
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Gengkai Miao
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Mei Zheng
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Ligang Luo
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Xiaoqin Pang
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China
| | - Lanzhen Wei
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China.
| | - Dezhi Li
- School of Ecological and Environmental Sciences, East China Normal University, 200241, Shanghai, China.
- Key Laboratory of Urbanization and Ecological Restoration of Shanghai, 200241, Shanghai, China.
- Institute of Eco-Chongming (IEC), 20 Cuiniao Rd, Chenjia Zhen, Chongming, 202162, Shanghai, China.
- Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, 3663 N. Zhongshan Road, 200062, Shanghai, China.
| | - Weimin Ma
- College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China.
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12
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Nie M, Wang J, Zhang K. A novel strategy for L-arginine production in engineered Escherichia coli. Microb Cell Fact 2023; 22:138. [PMID: 37495979 PMCID: PMC10373293 DOI: 10.1186/s12934-023-02145-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND L-arginine is an important amino acid with applications in diverse industrial and pharmaceutical fields. N-acetylglutamate, synthesized from L-glutamate and acetyl-CoA, is a precursor of the L-arginine biosynthetic branch in microorganisms. The enzyme that produces N-acetylglutamate, N-acetylglutamate synthase, is allosterically inhibited by L-arginine. L-glutamate, as a central metabolite, provides carbon backbone for diverse biological compounds besides L-arginine. When glucose is the sole carbon source, the theoretical maximum carbon yield towards L-arginine is 96.7%, but the experimental highest yield was 51%. The gap of L-arginine yield indicates the regulation complexity of carbon flux and energy during the L-arginine biosynthesis. Besides endogenous biosynthesis, N-acetylglutamate, the key precursor of L-arginine, can be obtained by chemical acylation of L-glutamate with a high yield of 98%. To achieve high-yield production of L-arginine, we demonstrated a novel approach by directly feeding precursor N-acetylglutamate to engineered Escherichia coli. RESULTS We reported a new approach for the high yield of L-arginine production in E. coli. Gene argA encoding N-acetylglutamate synthase was deleted to disable endogenous biosynthesis of N-acetylglutamate. The feasibility of external N-acetylglutamate towards L-arginine was verified via growth assay in argA- strain. To improve L-arginine production, astA encoding arginine N-succinyltransferase, speF encoding ornithine decarboxylase, speB encoding agmatinase, and argR encoding an arginine responsive repressor protein were disrupted. Based on overexpression of argDGI, argCBH operons, encoding enzymes of the L-arginine biosynthetic pathway, ~ 4 g/L L-arginine was produced in shake flask fermentation, resulting in a yield of 0.99 mol L-arginine/mol N-acetylglutamate. This strain was further engineered for the co-production of L-arginine and pyruvate by removing genes adhE, ldhA, poxB, pflB, and aceE, encoding enzymes involved in the conversion and degradation of pyruvate. The resulting strain was shown to produce 4 g/L L-arginine and 11.3 g/L pyruvate in shake flask fermentation. CONCLUSIONS Here, we developed a novel approach to avoid the strict regulation of L-arginine on ArgA and overcome the metabolism complexity in the L-arginine biosynthesis pathway. We achieve a high yield of L-arginine production from N-acetylglutamate in E. coli. Co-production pyruvate and L-arginine was used as an example to increase the utilization of input carbon sources.
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Affiliation(s)
- Mengzhen Nie
- Zhejiang University, Hangzhou, 310027 Zhejiang China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030 Zhejiang China
| | - Jingyu Wang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030 Zhejiang China
| | - Kechun Zhang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030 Zhejiang China
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13
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Zhang S, Sun J, Feng D, Sun H, Cui J, Zeng X, Wu Y, Luan G, Lu X. Unlocking the potentials of cyanobacterial photosynthesis for directly converting carbon dioxide into glucose. Nat Commun 2023; 14:3425. [PMID: 37296173 PMCID: PMC10256809 DOI: 10.1038/s41467-023-39222-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Glucose is the most abundant monosaccharide, serving as an essential energy source for cells in all domains of life and as an important feedstock for the biorefinery industry. The plant-biomass-sugar route dominates the current glucose supply, while the direct conversion of carbon dioxide into glucose through photosynthesis is not well studied. Here, we show that the potential of Synechococcus elongatus PCC 7942 for photosynthetic glucose production can be unlocked by preventing native glucokinase activity. Knocking out two glucokinase genes causes intracellular accumulation of glucose and promotes the formation of a spontaneous mutation in the genome, which eventually leads to glucose secretion. Without heterologous catalysis or transportation genes, glucokinase deficiency and spontaneous genomic mutation lead to a glucose secretion of 1.5 g/L, which is further increased to 5 g/L through metabolic and cultivation engineering. These findings underline the cyanobacterial metabolism plasticities and demonstrate their applications for supporting the direct photosynthetic production of glucose.
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Affiliation(s)
- Shanshan Zhang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiahui Sun
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dandan Feng
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Huili Sun
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jinyu Cui
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Xuexia Zeng
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Yannan Wu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Guodong Luan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning, 116023, China.
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Shandong Energy Institute, No. 189 Songling Road, Qingdao, Shandong, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, Dalian, Liaoning, 116023, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China.
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14
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Canizales S, Chen PH, Temmink H, Wijffels RH, Janssen M. Cyanobacteria cultivation on human urine for nutrients recovery. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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15
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Burkhardt M, Rapp J, Menzel C, Link H, Forchhammer K. The Global Influence of Sodium on Cyanobacteria in Resuscitation from Nitrogen Starvation. BIOLOGY 2023; 12:biology12020159. [PMID: 36829438 PMCID: PMC9952445 DOI: 10.3390/biology12020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Dormancy and resuscitation are key to bacterial survival under fluctuating environmental conditions. In the absence of combined nitrogen sources, the non-diazotrophic model cyanobacterium Synechocystis sp. PCC 6803 enters into a metabolically quiescent state during a process termed chlorosis. This state enables the cells to survive until nitrogen sources reappear, whereupon the cells resuscitate in a process that follows a highly orchestrated program. This coincides with a metabolic switch into a heterotrophic-like mode where glycogen catabolism provides the cells with reductant and carbon skeletons for the anabolic reactions that serve to re-establish a photosynthetically active cell. Here we show that the entire resuscitation process requires the presence of sodium, a ubiquitous cation that has a broad impact on bacterial physiology. The requirement for sodium in resuscitating cells persists even at elevated CO2 levels, a condition that, by contrast, relieves the requirement for sodium ions in vegetative cells. Using a multi-pronged approach, including the first metabolome analysis of Synechocystis cells resuscitating from chlorosis, we reveal the involvement of sodium at multiple levels. Not only does sodium play a role in the bioenergetics of chlorotic cells, as previously shown, but it is also involved in nitrogen compound assimilation, pH regulation, and synthesis of key metabolites.
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Affiliation(s)
- Markus Burkhardt
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Johanna Rapp
- CMFI, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Claudia Menzel
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Hannes Link
- CMFI, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Correspondence:
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16
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Yan X, Zhao F, Wang G, Wang Z, Zhou M, Zhang L, Wang G, Chen Y. Metabolomic Analysis of Microcystis aeruginosa After Exposure to the Algicide L-Lysine. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 110:12. [PMID: 36512146 DOI: 10.1007/s00128-022-03658-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
The widespread occurrence of cyanobacteria blooms damages the water ecosystem and threatens the safety of potable water and human health. Exogenous L-lysine significantly inhibits the growth of a dominant cyanobacteria Microcystis aeruginosa in freshwater. However, the molecular mechanism of how lysine inhibits the growth of M. aeruginosa is unclear. In this study, both non-target and target metabolomic analysis were performed to investigate the effects of algicide L-lysine. The results showed that 8 mg L- 1 lysine most likely disrupts the metabolism of amino acids, especially the arginine and proline metabolism. According to targeted amino acid metabolomics analysis, only 3 amino acids (L-arginine, ornithine, and citrulline), which belong to the ornithine-ammonia cycle (OAC) in arginine metabolic pathway, showed elevated levels. The intracellular concentrations of ornithine, citrulline, and arginine increased by 115%, 124%, and 19.4%, respectively. These results indicate that L-lysine may affect arginine metabolism and OAC to inhibit the growth of M. aeruginosa.
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Affiliation(s)
- Xiangjuan Yan
- School of Environment, Nanjing Normal University, 210023, Nanjing, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, 210023, Nanjing, China
| | - Fei Zhao
- School of Environment, Nanjing Normal University, 210023, Nanjing, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, 210023, Nanjing, China
| | - Guosheng Wang
- School of Environment, Nanjing Normal University, 210023, Nanjing, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, 210023, Nanjing, China
| | - Zhen Wang
- School of Environment, Nanjing Normal University, 210023, Nanjing, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, 210023, Nanjing, China
| | - Mingxi Zhou
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 37005, Ceske Budejovice, Czech Republic
| | - Limin Zhang
- School of Environment, Nanjing Normal University, 210023, Nanjing, China
- Green Economy Development Institute, Nanjing University of Finance and Economics, 210023, Nanjing, China
| | - Guoxiang Wang
- School of Environment, Nanjing Normal University, 210023, Nanjing, China
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, 210023, Nanjing, China
| | - Yanshan Chen
- School of Environment, Nanjing Normal University, 210023, Nanjing, China.
- Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, 210023, Nanjing, China.
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17
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The ornithine-urea cycle involves fumaric acid biosynthesis in Aureobasidium pullulans var. aubasidani, a green and eco-friendly process for fumaric acid production. Synth Syst Biotechnol 2022; 8:33-45. [DOI: 10.1016/j.synbio.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022] Open
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18
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Tian B, Chen M, Liu L, Rui B, Deng Z, Zhang Z, Shen T. 13C metabolic flux analysis: Classification and characterization from the perspective of mathematical modeling and application in physiological research of neural cell. Front Mol Neurosci 2022; 15:883466. [PMID: 36157075 PMCID: PMC9493264 DOI: 10.3389/fnmol.2022.883466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
13C metabolic flux analysis (13C-MFA) has emerged as a forceful tool for quantifying in vivo metabolic pathway activity of different biological systems. This technology plays an important role in understanding intracellular metabolism and revealing patho-physiology mechanism. Recently, it has evolved into a method family with great diversity in experiments, analytics, and mathematics. In this review, we classify and characterize the various branch of 13C-MFA from a unified perspective of mathematical modeling. By linking different parts in the model to each step of its workflow, the specific technologies of 13C-MFA are put into discussion, including the isotope labeling model (ILM), isotope pattern measuring technique, optimization algorithm and statistical method. Its application in physiological research in neural cell has also been reviewed.
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Affiliation(s)
- Birui Tian
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, China
| | - Meifeng Chen
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Lunxian Liu
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Bin Rui
- Eurofins Lancaster Laboratories Professional Scientific Services, Lancaster, PA, United States
| | - Zhouhui Deng
- China Guizhou Science Data Center Gui’an Supercomputing Center, Guiyang, China
| | - Zhengdong Zhang
- College of Mathematics and Information Science, Guiyang University, Guiyang, China
- *Correspondence: Zhengdong Zhang,
| | - Tie Shen
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Key Laboratory of Plant Physiology and Development Regulation, School of Life Science, Guizhou Normal University, Guiyang, China
- Tie Shen,
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19
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Katayama N, Osanai T. Arginine inhibition of the argininosuccinate lyases is conserved among three orders in cyanobacteria. PLANT MOLECULAR BIOLOGY 2022; 110:13-22. [PMID: 35583703 DOI: 10.1007/s11103-022-01280-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
This study revealed different catalytic efficiencies of cyanobacterial argininosuccinate lyases in non-nitrogen-fixing and nitrogen-fixing cyanobacteria, demonstrating that L-arginine inhibition of L-argininosuccinate lyase is conserved among enzymes of three cyanobacterial orders. Arginine is a nitrogen-rich amino acid that uses a nitrogen reservoir, and its biosynthesis is strictly controlled by feedback inhibition. Argininosuccinate lyase (EC 4.3.2.1) is the final enzyme in arginine biosynthesis that catalyzes the conversion of argininosuccinate to L-arginine and fumarate. Cyanobacteria synthesize intracellular cyanophycin, which is a nitrogen reservoir composed of aspartate and arginine. Arginine is an important source of nitrogen for cyanobacteria. We expressed and purified argininosuccinate lyases, ArgHs, from Synechocystis sp. PCC 6803, Nostoc sp. PCC 7120, and Arthrospira platensis NIES-39. The catalytic efficiency of the Nostoc sp. PCC 7120 ArgH was 2.8-fold higher than those of Synechocystis sp. PCC 6803 and Arthrospira platensis NIES-39. All three ArgHs were inhibited in the presence of arginine, and their inhibitory effects were lowered at pH 7.0, compared to those at pH 8.0. These results indicate that arginine inhibition of ArgH is widely conserved among the three cyanobacterial orders. The current results demonstrate the conserved regulation of enzymes in the cyanobacterial aspartase/fumarase superfamily.
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Affiliation(s)
- Noriaki Katayama
- 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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20
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Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. Nat Commun 2022; 13:5097. [PMID: 36042318 PMCID: PMC9427784 DOI: 10.1038/s41467-022-32834-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/08/2022] [Indexed: 11/23/2022] Open
Abstract
Cyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin synthetase (CphA1), and accumulates as a nitrogen reservoir during N2 fixation by most cyanobacteria. A recent structural study showed that three constituent domains of CphA1 function as two distinct catalytic sites and an oligomerization interface in cyanophycin synthesis. However, it remains unclear how the ATP-dependent addition of aspartate to cyanophycin is initiated at the catalytic site of the glutathione synthetase-like domain. Here, we report the cryogenic electron microscopy structures of CphA1, including a complex with aspartate, cyanophycin primer peptide, and ATP analog. These structures reveal the aspartate binding mode and phosphate-binding loop movement to the active site required for the reaction. Furthermore, structural and mutational data show a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction. CphA1 catalyzes the synthesis of cyanophycin polypeptide consisting of equimolar amounts of aspartate and arginine as a fixed nitrogen reservoir in cyanobacteria. Here, the authors solve the cryo-EM structures of CphA1, revealing the aspartate binding mode and protein dynamics required for cyanophycin elongation.
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21
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Metabolomics Analysis Coupled with Weighted Gene Co-Expression Network Analysis Unravels the Associations of Tricarboxylic Acid Cycle-Intermediates with Edible Pigments Produced by Monascus purpureus (Hong Qu). Foods 2022; 11:foods11142168. [PMID: 35885410 PMCID: PMC9320606 DOI: 10.3390/foods11142168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Monascus azaphilones pigments (MonAzPs) produced by microbial fermentation are widely used as food chemicals for coloring and supplying beneficial biological attributes. In this study, a fermentation perturbation strategy was implemented by separately adding different amino acids, and detecting the intracellular metabolome via UHPLC-Q-Orbitrap HRMS. With the aid of weighted gene co-expression network analysis, two metabolic intermediates, fumarate and malate, involved in the tricarboxylic acid cycle, were identified as the hub metabolites. Moreover, exogenous addition of fumarate or malate significantly promoted red pigment production, and reduced orange/yellow pigment production. The importance of the tricarboxylic acid cycle was further emphasized by detecting intracellular levels of ATP, NAD(P)H, and expression of oxidoreductase-coding genes located in the MonAzPs synthetic gene cluster, suggesting a considerable effect of the energy supply on MonAzPs synthesis. Collectively, metabolomics is a powerful approach to position the crucial metabolic regulatory factors, and facilitate the development of engineering strategies for targeted regulation, lower trial-and-error cost, and advance safe and controllable processes for fermented food chemistry industries.
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Luo H, Shen T, Xie X. Stochastic simulation of enzymatic kinetics for 13C isotope labeling at the single-cell scale. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-022-02262-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Zhang Y, Chen Y, Guo Y, Ma Y, Yang M, Fu R, Sun Y. Proteomics study on the changes in amino acid metabolism during broccoli senescence induced by elevated O2 storage. Food Res Int 2022; 157:111418. [DOI: 10.1016/j.foodres.2022.111418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/08/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022]
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Metabolic engineering of Aureobasidium melanogenum for the overproduction of putrescine by improved L-ornithine biosynthesis. Microbiol Res 2022; 260:127041. [PMID: 35483312 DOI: 10.1016/j.micres.2022.127041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/12/2022] [Accepted: 04/11/2022] [Indexed: 11/23/2022]
Abstract
Aureobasidium melanogenum HN6.2 is a high siderophore-producing yeast-like fungal strain. After blocking siderophore biosynthesis and attenuating the expression of the ornithine carbamoyltransferase gene (the OTC gene), the obtained D-LCFAO-cre strain produced 2.1 ± 0.02 mg of intracellular L-ornithine per mg of the protein. The overexpression of the L-ornithine decarboxylase gene (the SPE1-S gene) from Saccharomyces cerevisiae in the mutant D-LCFAO-cre could make the transformant E-SPE1-S synthesize 3.6 ± 0.1 of intracellular ornithine per mg of protein and produce 10.5 g/L of putrescine. The further overexpression of the ArgB/C gene encoding bifunctional acetylglutamate kinase/N-acetyl-gamma-glutamyl-phosphate reductase in the transformant E-SPE1-S caused the transformant E-SPE1-S-ArgB/C to accumulate L-ornithine (4.2 mg/mg protein) and to produce 21.3 g/L of putrescine. During fed-batch fermentation, the transformant E-SPE1-S-ArgB/C could produce 33.4 g/L of putrescine, the yield was 0.96 g/g of glucose, and the productivity was 0.28 g/L/h. The putrescine titer was much higher than that produced by most engineered strains obtained thus far.
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25
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Yang X, Bi Y, Ma X, Dong W, Wang X, Wang S. Transcriptomic analysis dissects the regulatory strategy of toxic cyanobacterium Microcystis aeruginosa under differential nitrogen forms. JOURNAL OF HAZARDOUS MATERIALS 2022; 428:128276. [PMID: 35051775 DOI: 10.1016/j.jhazmat.2022.128276] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/20/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
The critical role of nitrogen in the global proliferation of cyanobacterial blooms is arousing increasing attention. However, the mechanism underlying the algal responses to differential nitrogen forms remains unclarified. The physiological and transcriptomic changes of Microcystis aeruginosa supplied with different nitrogen forms (nitrate and ammonium) were highlighted in this study. The results indicated that ammonium behaves better in stimulating the initial growth in N-limited cells than nitrate. However, a concomitant side effect is that cellular growth and photosynthesis decreased due to photosystem II damage induced by excess absorbed light energy under 10 mg L-1 ammonium. By contrast, adequate nitrate supply favored more efficient photosynthesis, higher biomass yield and microcystin quotas than ammonium. Depending on the supplied nitrogen form, different transcriptomic patterns were observed in M. aeruginosa. Under nitrate, the upregulation of genes involved in Arg biosynthesis, ornithine-urea cycle and photosynthesis increased nitrogen storage and cellular growth, while genes involved in cyclic electron flow around photosystem I and CO2-concentrating mechanism were heightened to dissipate excess energy under high ammonium. These insights provided important clues for understanding the physiological and molecular effects of available nitrogen forms on the frequent outbreaks of cyanobacteria.
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Affiliation(s)
- Xiaolong Yang
- School of Life Sciences, Nantong University, Nantong 226019, China; Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yonghong Bi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaofei Ma
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Wei Dong
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Xun Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Shoubing Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.
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26
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Kato Y, Inabe K, Hidese R, Kondo A, Hasunuma T. Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review. BIORESOURCE TECHNOLOGY 2022; 344:126196. [PMID: 34710610 DOI: 10.1016/j.biortech.2021.126196] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.
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Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ryota Hidese
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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27
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Arora N, Philippidis GP. Unraveling metabolic alterations in Chlorella vulgaris cultivated on renewable sugars using time resolved multi-omics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149504. [PMID: 34426316 DOI: 10.1016/j.scitotenv.2021.149504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
The inherent metabolic versatility of Chlorella vulgaris that enables it to metabolize both inorganic and organic carbon under various trophic modes of cultivation makes it a promising candidate for industrial applications. To shed light on the metabolic flexibility of this microalga, time resolved proteomic and metabolomic studies were conducted in three distinct trophic modes (autotrophic, heterotrophic, mixotrophic) at two growth stages (end of linear growth at 6 days and during nutrient deprivation at 10 days). Sweet sorghum bagasse (SSB) hydrolysate was supplied to the cultivation medium as a renewable source of organic carbon mainly in the form of glucose. Integrated multi-omics data showed improved nitrogen assimilation, re-allocation, and recycling and increased levels of photosystem II (PS II) proteins indicating effective cellular quenching of excess electrons during mixotrophy. As external addition of organic carbon (glucose) to the cultivation medium decreases the cell's dependence on photosynthesis, an upregulation in the mitochondrial electron transport chain was recorded that led to increased cellular energy generation and hence higher growth rates under mixotrophy. Moreover, upregulation of the lipid-packaging proteins caleosin and 14_3_3 domain-containing protein resulted in maximum expression during mixotrophy suggesting a strong correlation between lipid synthesis, stabilization, and assembly. Overall, cells cultivated under mixotrophy showed better nutrient stress tolerance and redox balancing leading to higher biomass and lipid production. The study offers a panoramic view of the microalga's metabolic flexibility and contributes to a deeper understanding of the altered biochemical pathways that can be exploited to enhance algal productivity and commercial potential.
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Affiliation(s)
- Neha Arora
- Patel College of Global Sustainability, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA.
| | - George P Philippidis
- Patel College of Global Sustainability, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA.
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28
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Nitrogen Availability Affects the Metabolic Profile in Cyanobacteria. Metabolites 2021; 11:metabo11120867. [PMID: 34940625 PMCID: PMC8707274 DOI: 10.3390/metabo11120867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO3 or NH4Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH4Cl medium than in NaNO3 medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH4Cl medium than NaNO3 medium. 15N turnover rate analysis revealed that the nitrogen assimilation rate in NH4Cl medium was higher than in NaNO3 medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO3 and NH4Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen.
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29
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Huang D, Wang Y, Zhang J, Xu H, Bai J, Zhang H, Jiang X, Yuan J, Lu G, Jiang L, Liao X, Liu B, Liu H. Integrative Metabolomic and Transcriptomic Analyses Uncover Metabolic Alterations and Pigment Diversity in Monascus in Response to Different Nitrogen Sources. mSystems 2021; 6:e0080721. [PMID: 34491088 PMCID: PMC8547423 DOI: 10.1128/msystems.00807-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/15/2021] [Indexed: 02/07/2023] Open
Abstract
Nitrogen in different chemical forms is critical for metabolic alterations in Monascus strains and associated pigment diversity. In this study, we observed that ammonium-form nitrogen was superior in promoting the biosynthesis of Monascus pigments (MPs) when compared with nitrate and organic forms. Moreover, with any nitrogen source, the production of yellow and orange pigments was highly synchronized but distantly related to red pigments. However, transcriptional analyses of MP gene clusters suggested a low contribution to MP accumulation, suggesting that MP-limiting factors were located outside the gene cluster. Our metabolomic analyses demonstrated that red pigment biosynthesis was closely related to intracellular amino acids, whereas orange and yellow pigments were associated with nucleotides. In addition, weighted gene coexpression network analyses (WGCNA) based on transcriptomic data showed that multiple primary metabolic pathways were closely related to red pigment production, while several secondary pathways were related to orange pigments, and others were involved with yellow pigment regulation. These findings demonstrate that pigment diversity in Monascus is under combined regulation at metabolomic and transcriptomic levels. IMPORTANCE Natural MPs containing a mixture of red, orange, and yellow pigments are widely used as food coloring agents. MP diversity provides foods with versatile colors and health benefits but, in turn, complicate efforts to achieve maximum yield or desirable combination of pigments during the manufacturing process. Apart from the MP biosynthetic gene cluster, interactions between the main biosynthetic pathways and other intracellular genes/metabolites are critical to our understanding of MP differentiation. The integrative multiomics analytical strategy provides a technical platform and new perspectives for the identification of metabolic shunting mechanisms in MP biosynthesis. Equally, our research highlights the influence of intracellular metabolic alterations on MP differentiation, which will facilitate the rational engineering and optimization of MP production in the future.
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Affiliation(s)
- Di Huang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Yuhui Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Jing Zhang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Ministry of Education, Tianjin, China
| | - Huimin Xu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Ministry of Education, Tianjin, China
| | - Jing Bai
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Huijing Zhang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Xiaolong Jiang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Jian Yuan
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Gege Lu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Lingyan Jiang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Xiaoping Liao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Huanhuan Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Ministry of Education, Tianjin, China
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30
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Wang J, Ma S, Li W, Wang X, Huang D, Jiang L, Feng L. Salmonella enterica Serovar Typhi Induces Host Metabolic Reprogramming to Increase Glucose Availability for Intracellular Replication. Int J Mol Sci 2021; 22:ijms221810003. [PMID: 34576166 PMCID: PMC8467381 DOI: 10.3390/ijms221810003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is a human-limited intracellular pathogen and the cause of typhoid fever, a severe systemic disease. Pathogen–host interaction at the metabolic level affects the pathogenicity of intracellular pathogens, but it remains unclear how S. Typhi infection influences host metabolism for its own benefit. Herein, using metabolomics and transcriptomics analyses, combined with in vitro and in vivo infection assays, we investigated metabolic responses in human macrophages during S. Typhi infection, and the impact of these responses on S. Typhi intracellular replication and systemic pathogenicity. We observed increased glucose content, higher rates of glucose uptake and glycolysis, and decreased oxidative phosphorylation in S. Typhi-infected human primary macrophages. Replication in human macrophages and the bacterial burden in systemic organs of humanized mice were reduced by either the inhibition of host glucose uptake or a mutation of the bacterial glucose uptake system, indicating that S. Typhi utilizes host-derived glucose to enhance intracellular replication and virulence. Thus, S. Typhi promotes its pathogenicity by inducing metabolic changes in host macrophages and utilizing the glucose that subsequently accumulates as a nutrient for intracellular replication. Our findings provide the first metabolic signature of S. Typhi-infected host cells and identifies a new strategy utilized by S. Typhi for intracellular replication.
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Affiliation(s)
- Jingting Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Shuai Ma
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Wanwu Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xinyue Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Di Huang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Lingyan Jiang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Correspondence: (L.J.); (L.F.)
| | - Lu Feng
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (J.W.); (S.M.); (W.L.); (X.W.); (D.H.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Correspondence: (L.J.); (L.F.)
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Zhang ZC, Wang K, Hao FH, Shang JL, Tang HR, Qiu BS. New types of ATP-grasp ligase are associated with the novel pathway for complicated mycosporine-like amino acid production in desiccation-tolerant cyanobacteria. Environ Microbiol 2021; 23:6420-6432. [PMID: 34459073 DOI: 10.1111/1462-2920.15732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Mycosporine-like amino acids (MAAs) were widespread in diverse organisms to attenuate UV radiation. We recently characterized the large, complicated MAA mycosporine-2-(4-deoxygadusolyl-ornithine) in desert cyanobacterium Nostoc flagelliforme. Synthesis of this MAA requires the five-gene cluster mysABDC2C3. Here, bioinformatic analysis indicated that mysC duplication within five-gene mys clusters is strictly limited to drought-tolerant cyanobacteria. Phylogenic analysis distinguished these duplicated MysCs into two clades that separated from canonical MysCs. Heterologous expression of N. flagelliforme mys genes in Escherichia coli showed that MysAB produces 4-deoxygadusol. The ATP-grasp ligase of MysC3 catalyses the linkage of the δ- or ε-amino group of ornithine/lysine to 4-deoxygadusol, yielding mycosporine-ornithine or mycosporine-lysine respectively. The ATP-grasp ligase of MysC2 strictly condenses the α-amino group of mycosporine-ornithine to another 4-deoxygadusol. MysD (D-Ala-D-Ala ligase) functions following MysC2 to catalyse the formation of mycosporine-2-(4-deoxygadusolyl-ornithine). High arginine content likely provides a greater pool of ornithine over other amino acids during rehydration of desiccated N. flagelliforme. Duplication of ATP-grasp ligases is specific for the use of substrates that have two amino groups (such as ornithine) for the production of complicated MAAs with multiple chromophores. This five-enzyme biosynthesis pathway for complicated MAAs is a novel adaptation of cyanobacteria for UV tolerance in drought environments.
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Affiliation(s)
- Zhong-Chun Zhang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Kai Wang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Fu-Hua Hao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Hui-Ru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Contemporary Anthropology, Metabonomics and Systems Biology Laboratory, Fudan University, Shanghai, 200438, China
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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32
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A guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteria. Nat Commun 2021; 12:5150. [PMID: 34446715 PMCID: PMC8390497 DOI: 10.1038/s41467-021-25369-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
Recent studies have revealed the prevalence and biological significance of guanidine metabolism in nature. However, the metabolic pathways used by microbes to degrade guanidine or mitigate its toxicity have not been widely studied. Here, via comparative proteomics and subsequent experimental validation, we demonstrate that Sll1077, previously annotated as an agmatinase enzyme in the model cyanobacterium Synechocystis sp. PCC 6803, is more likely a guanidinase as it can break down guanidine rather than agmatine into urea and ammonium. The model cyanobacterium Synechococcus elongatus PCC 7942 strain engineered to express the bacterial ethylene-forming enzyme (EFE) exhibits unstable ethylene production due to toxicity and genomic instability induced by accumulation of the EFE-byproduct guanidine. Co-expression of EFE and Sll1077 significantly enhances genomic stability and enables the resulting strain to achieve sustained high-level ethylene production. These findings expand our knowledge of natural guanidine degradation pathways and demonstrate their biotechnological application to support ethylene bioproduction. The metabolic pathways used by microbes to degrade guanidine or mitigate its toxicity remain unclear. Here, the authors report a guanidine degrading enzyme that controls genomic stability of ethylene producing cyanobacterial strains.
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33
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Xu HF, Raanan H, Dai GZ, Oren N, Berkowicz S, Murik O, Kaplan A, Qiu BS. Reading and surviving the harsh conditions in desert biological soil crust: The cyanobacterial viewpoint. FEMS Microbiol Rev 2021; 45:6308820. [PMID: 34165541 DOI: 10.1093/femsre/fuab036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
Biological soil crusts (BSCs) are found in drylands, cover ∼12% of the Earth's surface in arid and semi-arid lands and their destruction is considered an important promoter of desertification. These crusts are formed by the adhesion of soil particles to polysaccharides excreted mostly by filamentous cyanobacteria, which are the pioneers and main primary producers in BSCs. Desert BSCs survive in one of the harshest environments on Earth, and are exposed to daily fluctuations of extreme conditions. The cyanobacteria inhabiting these habitats must precisely read the changing conditions and predict, for example, the forthcoming desiccation. Moreover, they evolved a comprehensive regulation of multiple adaptation strategies to enhance their stress tolerance. Here we focus on what distinguishes cyanobacteria able to revive after dehydration from those that cannot. While important progress has been made in our understanding of physiological, biochemical and omics aspects, clarification of the sensing, signal transduction and responses enabling desiccation tolerance are just emerging. We plot the trajectory of current research and open questions ranging from general strategies and regulatory adaptations in the hydration/desiccation cycle, to recent advances in our understanding of photosynthetic adaptation. The acquired knowledge provides new insights to mitigate desertification and improve plant productivity under drought conditions.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
| | - Hagai Raanan
- Department of Plant Pathology and Weed Research, Gilat Research Center, Agricultural Research Organization, Mobile Post Negev 2, 8531100 Israel
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
| | - Nadav Oren
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Simon Berkowicz
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel.,Interuniversity Institute for Marine Sciences in Eilat, P.O.B 469, Eilat, 8810302 Israel
| | - Omer Murik
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079 China
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34
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Hernández VM, Arteaga A, Dunn MF. Diversity, properties and functions of bacterial arginases. FEMS Microbiol Rev 2021; 45:6308370. [PMID: 34160574 DOI: 10.1093/femsre/fuab034] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
The metalloenzyme arginase hydrolyzes L-arginine to produce L-ornithine and urea. In bacteria, arginase has important functions in basic nitrogen metabolism and redistribution, production of the key metabolic precursor L-ornithine, stress resistance and pathogenesis. We describe the regulation and specific functions of the arginase pathway as well as summarize key characteristics of related arginine catabolic pathways. The use of arginase-derived ornithine as a precursor molecule is reviewed. We discuss the biochemical and transcriptional regulation of arginine metabolism, including arginase, with the latter topic focusing on the RocR and AhrC transcriptional regulators in the model organism Bacillus subtilis. Finally, we consider similarities and contrasts in the structure and catalytic mechanism of the arginases from Bacillus caldovelox and Helicobacter pylori. The overall aim of this review is to provide a panorama of the diversity of physiological functions, regulation, and biochemical features of arginases in a variety of bacterial species.
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Affiliation(s)
- Victor M Hernández
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Alejandra Arteaga
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
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Studies on the Regulation of Arginine Metabolism in Cyanobacteria Should Include Mixotrophic Conditions. mBio 2021; 12:e0143321. [PMID: 34154397 PMCID: PMC8262935 DOI: 10.1128/mbio.01433-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Huang B, Wang H, Zhong D, Meng J, Li M, Yang B, Ran J. Expression of Urea Transporter B in Normal and Injured Brain. Front Neuroanat 2021; 15:591726. [PMID: 34122018 PMCID: PMC8194276 DOI: 10.3389/fnana.2021.591726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
Urea transporter B (UT-B) is a membrane channel protein widely distributed in mammals, and plays a significant physiological role by regulating urea and water transportation in different tissues. More and more studies have found that UT-B is related to neurological diseases, including myelinopathy and depression. When urea accumulates in the brains of UT-B knockout mice, the synaptic plasticity of neurons is reduced, and the morphology and function of glial cells are also changed. However, the distribution and expression change of UT-B remain unclear. The purpose of this study is to determine the expression characteristics of UT-B in the brain. Through single-cell RNA sequencing, UT-B was found to express universally and substantially throughout the various cells in the central nervous system except for endothelial and smooth muscle cells. UT-B was detected in the third cerebral ventricular wall, granule cell layer of the dentate gyrus, and other parts of the hippocampal, cerebral cortex, substantia nigra, habenular, and lateral hypothalamic nucleus by immunohistochemistry. Compared with the membrane expression of UT-B in glial cells, the subcellular localization of UT-B is in the Golgi apparatus of neurons. Further, the expression of UT-B was regulated by osmotic pressure in vitro. In the experimental traumatic brain injury model (TBI), the number of UT-B positive neurons near the ipsilateral cerebral cortex increased first and then decreased over time, peaking at the 24 h. We inferred that change in UT-B expression after the TBI was an adaptation to changed urea levels. The experimental data suggest that the UT-B may be a potential target for the treatment of TBI and white matter edema.
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Affiliation(s)
- Boyue Huang
- Department of Anatomy, Laboratory of Neuroscience and Tissue Engineering, Basic Medical College, Chongqing Medical University, Chongqing, China.,Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Hongkai Wang
- Department of Anatomy, Laboratory of Neuroscience and Tissue Engineering, Basic Medical College, Chongqing Medical University, Chongqing, China.,Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Dandan Zhong
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Jia Meng
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Min Li
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Baoxue Yang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Jianhua Ran
- Department of Anatomy, Laboratory of Neuroscience and Tissue Engineering, Basic Medical College, Chongqing Medical University, Chongqing, China
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Liu C, Hashimoto J, Kudo K, Shin-Ya K, Kakeya H. An Atypical Arginine Dihydrolase Involved in the Biosynthesis of Cyclic Hexapeptide Longicatenamides. Chem Asian J 2021; 16:1382-1387. [PMID: 33886165 DOI: 10.1002/asia.202100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/02/2021] [Indexed: 11/07/2022]
Abstract
The incorporation of non-proteinogenic amino acids (NPAAs) enriches the structural diversity of nonribosomal peptides. Recently, four NPAA-containing cyclic hexapeptides, longicatenamides A-D, were isolated using a combined-culture strategy. Based on in silico analysis, we discovered their putative biosynthetic gene cluster (lon) and proposed a possible biosynthetic mechanism. Surprisingly, the lon22 gene encodes an atypical arginine dihydrolase, which can also catalyze the hydrolysis of citrulline to ornithine. Phylogenetic analysis showed that Lon22-like proteins form a novel clade that is separated from other guanidine-modifying enzymes. After rational design, the catalytic efficiencies of a Lon22 Y80F mutant for arginine and citrulline substrates were 2.31- and 4.70-fold that of the wild-type (WT), respectively. In addition, characterization of the Lon20-A4 adenylation domain suggested that it can incorporate both ornithine and lysine into the final products.
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Affiliation(s)
- Chao Liu
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
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Dong W, Nie X, Zhu H, Liu Q, Shi K, You L, Zhang Y, Fan H, Yan B, Niu C, Lyu LD, Zhao GP, Yang C. Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence. Proc Natl Acad Sci U S A 2021; 118:e2019305118. [PMID: 33853942 PMCID: PMC8072231 DOI: 10.1073/pnas.2019305118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Host-derived fatty acids are an important carbon source for pathogenic mycobacteria during infection. How mycobacterial cells regulate the catabolism of fatty acids to serve the pathogenicity, however, remains unknown. Here, we identified a TetR-family transcriptional factor, FdmR, as the key regulator of fatty acid catabolism in the pathogen Mycobacterium marinum by combining use of transcriptomics, chromatin immunoprecipitation followed by sequencing, dynamic 13C-based flux analysis, metabolomics, and lipidomics. An M. marinum mutant deficient in FdmR was severely attenuated in zebrafish larvae and adult zebrafish. The mutant showed defective growth but high substrate consumption on fatty acids. FdmR was identified as a long-chain acyl-coenzyme A (acyl-CoA)-responsive repressor of genes involved in fatty acid degradation and modification. We demonstrated that FdmR functions as a valve to direct the flux of exogenously derived fatty acids away from β-oxidation toward lipid biosynthesis, thereby avoiding the overactive catabolism and accumulation of biologically toxic intermediates. Moreover, we found that FdmR suppresses degradation of long-chain acyl-CoAs endogenously synthesized through the type I fatty acid synthase. By modulating the supply of long-chain acyl-CoAs for lipogenesis, FdmR controls the abundance and chain length of virulence-associated lipids and mycolates and plays an important role in the impermeability of the cell envelope. These results reveal that despite the fact that host-derived fatty acids are used as an important carbon source, overactive catabolism of fatty acids is detrimental to mycobacterial cell growth and pathogenicity. This study thus presents FdmR as a potentially attractive target for chemotherapy.
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Affiliation(s)
- Wenyue Dong
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqun Nie
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hong Zhu
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Kunxiong Shi
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Linlin You
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
| | - Hongyan Fan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Bo Yan
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
| | - Chen Niu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China;
| | - Guo-Ping Zhao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences (MOE/NHC/CAMS), School of Basic Medical Sciences, Department of Microbiology, School of Life Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200000, China
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chen Yang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, China;
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Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803. Biosci Rep 2021; 40:222317. [PMID: 32149336 PMCID: PMC7133116 DOI: 10.1042/bsr20193325] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.
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40
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Bolay P, Rozbeh R, Muro-Pastor MI, Timm S, Hagemann M, Florencio FJ, Forchhammer K, Klähn S. The Novel P II-Interacting Protein PirA Controls Flux into the Cyanobacterial Ornithine-Ammonia Cycle. mBio 2021; 12:e00229-21. [PMID: 33758091 PMCID: PMC8092223 DOI: 10.1128/mbio.00229-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Among prokaryotes, cyanobacteria have an exclusive position as they perform oxygenic photosynthesis. Cyanobacteria substantially differ from other bacteria in further aspects, e.g., they evolved a plethora of unique regulatory mechanisms to control primary metabolism. This is exemplified by the regulation of glutamine synthetase (GS) via small proteins termed inactivating factors (IFs). Here, we reveal another small protein, encoded by the ssr0692 gene in the model strain Synechocystis sp. PCC 6803, that regulates flux into the ornithine-ammonia cycle (OAC), the key hub of cyanobacterial nitrogen stockpiling and remobilization. This regulation is achieved by the interaction with the central carbon/nitrogen control protein PII, which commonly controls entry into the OAC by activating the key enzyme of arginine synthesis, N-acetyl-l-glutamate kinase (NAGK). In particular, the Ssr0692 protein competes with NAGK for PII binding and thereby prevents NAGK activation, which in turn lowers arginine synthesis. Accordingly, we termed it PII-interacting regulator of arginine synthesis (PirA). Similar to the GS IFs, PirA accumulates in response to ammonium upshift due to relief from repression by the global nitrogen control transcription factor NtcA. Consistent with this, the deletion of pirA affects the balance of metabolite pools of the OAC in response to ammonium shocks. Moreover, the PirA-PII interaction requires ADP and is prevented by PII mutations affecting the T-loop conformation, the major protein interaction surface of this signal processing protein. Thus, we propose that PirA is an integrator determining flux into N storage compounds not only depending on the N availability but also the energy state of the cell.IMPORTANCE Cyanobacteria contribute a significant portion to the annual oxygen yield and play important roles in biogeochemical cycles, e.g., as major primary producers. Due to their photosynthetic lifestyle, cyanobacteria also arouse interest as hosts for the sustainable production of fuel components and high-value chemicals. However, their broad application as microbial cell factories is hampered by limited knowledge about the regulation of metabolic fluxes in these organisms. Our research identified a novel regulatory protein that controls nitrogen flux, in particular arginine synthesis. Besides its role as a proteinogenic amino acid, arginine is a precursor for the cyanobacterial storage compound cyanophycin, which is of potential interest to biotechnology. Therefore, the obtained results will not only enhance our understanding of flux control in these organisms but also help to provide a scientific basis for targeted metabolic engineering and, hence, the design of photosynthesis-driven biotechnological applications.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
| | - Rokhsareh Rozbeh
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Stefan Timm
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
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Polerecky L, Masuda T, Eichner M, Rabouille S, Vancová M, Kienhuis MVM, Bernát G, Bonomi-Barufi J, Campbell DA, Claquin P, Červený J, Giordano M, Kotabová E, Kromkamp J, Lombardi AT, Lukeš M, Prášil O, Stephan S, Suggett D, Zavřel T, Halsey KH. Temporal Patterns and Intra- and Inter-Cellular Variability in Carbon and Nitrogen Assimilation by the Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. Front Microbiol 2021; 12:620915. [PMID: 33613489 PMCID: PMC7890256 DOI: 10.3389/fmicb.2021.620915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/11/2021] [Indexed: 12/05/2022] Open
Abstract
Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the relative amounts of N assimilated into cyanophycin from sources external and internal to the cells. Whether growing on N2 or NO3, cells prioritized cyanophycin synthesis when N assimilation rates were highest. N assimilation in cells growing on NO3 switched from cyanophycin synthesis to protein synthesis, suggesting that once a cyanophycin quota is met, it is bypassed in favor of protein synthesis. Growth on NO3 also revealed that at night, there is a very low level of CO2 assimilation into polysaccharides simultaneous with their catabolism for protein synthesis. This study revealed multiple, detailed mechanisms underlying C and N management in Cyanothece that facilitate its success in dynamic aquatic environments.
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Affiliation(s)
- Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Takako Masuda
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Meri Eichner
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sophie Rabouille
- Sorbonne Université, CNRS, Laboratoire d’Océanographie de Villefranche, Villefranche-sur-mer, France
- Sorbonne Université, CNRS, Laboratoire d’Océanographie Microbienne, Banyuls-sur-mer, France
| | - Marie Vancová
- Institute of Parasitology, Czech Academy of Sciences, Biology Centre, České Budějovice, Czechia
| | | | - Gabor Bernát
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- Centre for Ecological Research, Balaton Limnological Institute, Tihany, Hungary
| | - Jose Bonomi-Barufi
- Botany Department, Federal University of Santa Catarina, Campus de Trindade, Florianópolis, Brazil
| | | | - Pascal Claquin
- Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques, FRE 2030, Muséum National d’Histoire Naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Normandie Université, Esplanade de la Paix, France
| | - Jan Červený
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Mario Giordano
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, College of Sciences, Shantou University, Shantou, China
| | - Eva Kotabová
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Jacco Kromkamp
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Netherlands
| | | | - Martin Lukeš
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Ondrej Prášil
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Třeboň, Czechia
| | - Susanne Stephan
- Department Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Department of Ecology, Berlin Institute of Technology, Berlin, Germany
| | - David Suggett
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tomas Zavřel
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Kimberly H. Halsey
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvation. J Bacteriol 2021; 204:JB0015821. [PMID: 34228497 PMCID: PMC8765419 DOI: 10.1128/jb.00158-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small proteins are critically involved in the acclimation response of photosynthetic cyanobacteria to nitrogen starvation. NblD is the 66-amino-acid effector of nitrogen-limitation-induced phycobilisome breakdown, which is believed to replenish the cellular amino acid pools. To address the physiological functions of NblD, the concentrations of amino acids, intermediates of the arginine catabolism pathway and several organic acids were measured during the response to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 wild type and in an nblD deletion strain. A characteristic signature of metabolite pool composition was identified, which shows that NblD-mediated phycobilisome degradation is required to maintain the cellular amino acid and organic acid pools during nitrogen starvation. Specific deviations from the wild type suggest wider-reaching effects that also affect such processes as redox homeostasis via glutathione and tetrapyrrole biosynthesis, both of which are linked to the strongly decreased glutamate pool, and transcriptional reprogramming via an enhanced concentration of 2-oxoglutarate, the metabolite co-regulator of the NtcA transcription factor. The essential role played by NblD in metabolic homeostasis is consistent with the widespread occurrence of NblD throughout the cyanobacterial radiation and the previously observed strong positive selection for the nblD gene under fluctuating nitrogen supply. Importance Cyanobacteria play important roles in the global carbon and nitrogen cycles. In their natural environment, these organisms are exposed to fluctuating nutrient conditions. Nitrogen starvation induces a coordinated nitrogen-saving program that includes the breakdown of nitrogen-rich photosynthetic pigments, particularly phycobiliproteins. The small protein NblD was recently identified as an effector of phycobilisome breakdown in cyanobacteria. In this study, we demonstrate that the NblD-mediated degradation of phycobiliproteins is needed to sustain cellular pools of soluble amino acids and other crucial metabolites. The essential role played by NblD in metabolic homeostasis explains why genes encoding this small protein are conserved in almost all members of cyanobacterial radiation.
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43
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Revisiting nitrogen utilization in algae: A review on the process of regulation and assimilation. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100584] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Steiner PA, Geijo J, Fadeev E, Obiol A, Sintes E, Rattei T, Herndl GJ. Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea. Front Microbiol 2020; 11:584222. [PMID: 33304331 PMCID: PMC7701263 DOI: 10.3389/fmicb.2020.584222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/23/2020] [Indexed: 01/04/2023] Open
Abstract
Marine snow is an important habitat for microbes, characterized by chemical and physical properties contrasting those of the ambient water. The higher nutrient concentrations in marine snow lead to compositional differences between the ambient water and the marine snow-associated prokaryotic community. Whether these compositional differences vary due to seasonal environmental changes, however, remains unclear. Thus, we investigated the seasonal patterns of the free-living and marine snow-associated microbial community composition and their functional potential in the northern Adriatic Sea. Our data revealed seasonal patterns in both, the free-living and marine snow-associated prokaryotes. The two assemblages were more similar to each other in spring and fall than in winter and summer. The taxonomic distinctness resulted in a contrasting functional potential. Motility and adaptations to low temperature in winter and partly anaerobic metabolism in summer characterized the marine snow-associated prokaryotes. Free-living prokaryotes were enriched in genes indicative for functions related to phosphorus limitation in winter and in genes tentatively supplementing heterotrophic growth with proteorhodopsins and CO-oxidation in summer. Taken together, the results suggest a strong influence of environmental parameters on both free-living and marine snow-associated prokaryotic communities in spring and fall leading to higher similarity between the communities, while the marine snow habitat in winter and summer leads to a specific prokaryotic community in marine snow in these two seasons.
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Affiliation(s)
- Paul A. Steiner
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Javier Geijo
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Aleix Obiol
- Institut de Ciències del Mar, Institut de Ci ncies del Mar – Consejo Superior de Investigaciones Cient ficas (ICM-CSIC), Barcelona, Spain
| | - Eva Sintes
- Instituto Español de Oceanografia, Centre Oceanogràfic de les Balears, Palma, Spain
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Utrecht, Netherlands
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45
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Horák A, Allen AE, Oborník M. Common origin of ornithine-urea cycle in opisthokonts and stramenopiles. Sci Rep 2020; 10:16687. [PMID: 33028894 PMCID: PMC7542463 DOI: 10.1038/s41598-020-73715-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/22/2020] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic complex phototrophs exhibit a colorful evolutionary history. At least three independent endosymbiotic events accompanied by the gene transfer from the endosymbiont to host assembled a complex genomic mosaic. Resulting patchwork may give rise to unique metabolic capabilities; on the other hand, it can also blur the reconstruction of phylogenetic relationships. The ornithine–urea cycle (OUC) belongs to the cornerstone of the metabolism of metazoans and, as found recently, also photosynthetic stramenopiles. We have analyzed the distribution and phylogenetic positions of genes encoding enzymes of the urea synthesis pathway in eukaryotes. We show here that metazoan and stramenopile OUC enzymes share common origins and that enzymes of the OUC found in primary algae (including plants) display different origins. The impact of this fact on the evolution of stramenopiles is discussed here.
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Affiliation(s)
- Aleš Horák
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Branišovská 31, 37005, České Budějovice, Czech Republic.,Department of Molecular Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Andrew E Allen
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, 92121, USA.,Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Miroslav Oborník
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Branišovská 31, 37005, České Budějovice, Czech Republic. .,Department of Molecular Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 37005, České Budějovice, Czech Republic.
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46
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Del Castello F, Nejamkin A, Foresi N, Lamattina L, Correa-Aragunde N. Chimera of Globin/Nitric Oxide Synthase: Toward Improving Nitric Oxide Homeostasis and Nitrogen Recycling and Availability. FRONTIERS IN PLANT SCIENCE 2020; 11:575651. [PMID: 33101345 PMCID: PMC7554344 DOI: 10.3389/fpls.2020.575651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
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47
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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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48
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Biological insights into non-model microbial hosts through stable-isotope metabolic flux analysis. Curr Opin Biotechnol 2020; 64:32-38. [DOI: 10.1016/j.copbio.2019.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/16/2022]
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49
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Qu D, Hou Z, Li J, Luo L, Su S, Ye Z, Bai Y, Zhang X, Chen G, Li Z, Wang Y, Xue X, Luo X, Li M. A new coumarin compound DCH combats methicillin-resistant Staphylococcus aureus biofilm by targeting arginine repressor. SCIENCE ADVANCES 2020; 6:eaay9597. [PMID: 32832655 PMCID: PMC7439407 DOI: 10.1126/sciadv.aay9597] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 06/05/2020] [Indexed: 05/26/2023]
Abstract
Staphylococcus aureus infection is difficult to eradicate because of biofilm formation and antibiotic resistance. The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) infection necessitates the development of a new agent against bacterial biofilms. We report a new coumarin compound, termed DCH, that effectively combats MRSA in vitro and in vivo and exhibits potent antibiofilm activity without detectable resistance. Cellular proteome analysis suggests that the molecular mechanism of action of DCH involves the arginine catabolic pathway. Using molecular docking and binding affinity assays of DCH, and comparison of the properties of wild-type and ArgR-deficient MRSA strains, we demonstrate that the arginine repressor ArgR, an essential regulator of the arginine catabolic pathway, is the target of DCH. These findings indicate that DCH is a promising lead compound and validate bacterial ArgR as a potential target in the development of new drugs against MRSA biofilms.
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Affiliation(s)
- Di Qu
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Zheng Hou
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Jing Li
- Key Laboratory for Surface Engineering and Remanufacturing in Shaanxi province, School of Chemical Engineering, Xi’an University, Xi’an 710065, China
| | - Liyang Luo
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Shan Su
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Zichen Ye
- Department of Pharmacogenomics, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Yinlan Bai
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi’an 710032, China
| | - Xinlei Zhang
- Department of Medical Chemistry, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Guanghui Chen
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Zhoupeng Li
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Yikun Wang
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Xiaoyan Xue
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Xiaoxing Luo
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
| | - Mingkai Li
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi’an 710032, China
- Precision Pharmacy and Drug Development Center, The Fourth Military Medical University, Xi’an 710032, China
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50
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Krausfeldt LE, Farmer AT, Castro HF, Boyer GL, Campagna SR, Wilhelm SW. Nitrogen flux into metabolites and microcystins changes in response to different nitrogen sources in Microcystis aeruginosa NIES-843. Environ Microbiol 2020; 22:2419-2431. [PMID: 32338427 DOI: 10.1111/1462-2920.15032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/13/2020] [Accepted: 04/18/2020] [Indexed: 01/17/2023]
Abstract
The over-enrichment of nitrogen (N) in the environment has contributed to severe and recurring harmful cyanobacterial blooms, especially by the non-N2 -fixing Microcystis spp. N chemical speciation influences cyanobacterial growth, persistence and the production of the hepatotoxin microcystin, but the physiological mechanisms to explain these observations remain unresolved. Stable-labelled isotopes and metabolomics were employed to address the influence of nitrate, ammonium, and urea on cellular physiology and production of microcystins in Microcystis aeruginosa NIES-843. Global metabolic changes were driven by both N speciation and diel cycling. Tracing 15 N-labelled nitrate, ammonium, and urea through the metabolome revealed N uptake, regardless of species, was linked to C assimilation. The production of amino acids, like arginine, and other N-rich compounds corresponded with greater turnover of microcystins in cells grown on urea compared to nitrate and ammonium. However, 15 N was incorporated into microcystins from all N sources. The differences in N flux were attributed to the energetic efficiency of growth on each N source. While N in general plays an important role in sustaining biomass, these data show that N-speciation induces physiological changes that culminate in differences in global metabolism, cellular microcystin quotas and congener composition.
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Affiliation(s)
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Hector F Castro
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Gregory L Boyer
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
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