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Wei N, Hu C, Dittmann E, Song L, Gan N. The biological functions of microcystins. WATER RESEARCH 2024; 262:122119. [PMID: 39059200 DOI: 10.1016/j.watres.2024.122119] [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: 05/21/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
Microcystins are potent hepatotoxins predominantly produced by bloom-forming freshwater cyanobacteria (e.g., Microcystis, Planktothrix, Dolichospermum). Microcystin biosynthesis involves large multienzyme complexes and tailoring enzymes encoded by the mcy gene cluster. Mutation, recombination, and deletion events have shaped the mcy gene cluster in the course of evolution, resulting in a large diversity of microcystin congeners and the natural coexistence of toxic and non-toxic strains. The biological functions of microcystins and their association with algal bloom formation have been extensively investigated over the past decades. This review synthesizes recent advances in decoding the biological role of microcystins in carbon/nitrogen metabolism, antioxidation, colony formation, and cell-to-cell communication. Microcystins appear to adopt multifunctional roles in cyanobacteria that reflect the adaptive plasticity of toxic cyanobacteria to changing environments.
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Affiliation(s)
- Nian Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Chenlin Hu
- College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Elke Dittmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Lirong Song
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Nanqin Gan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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2
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Lucius S, Hagemann M. The primary carbon metabolism in cyanobacteria and its regulation. FRONTIERS IN PLANT SCIENCE 2024; 15:1417680. [PMID: 39036361 PMCID: PMC11257934 DOI: 10.3389/fpls.2024.1417680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024]
Abstract
Cyanobacteria are the only prokaryotes capable of performing oxygenic photosynthesis. Many cyanobacterial strains can live in different trophic modes, ranging from photoautotrophic and heterotrophic to mixotrophic growth. However, the regulatory mechanisms allowing a flexible switch between these lifestyles are poorly understood. As anabolic fixation of CO2 in the Calvin-Benson-Bassham (CBB) cycle and catabolic sugar-degradation pathways share intermediates and enzymatic capacity, a tight regulatory network is required to enable simultaneous opposed metabolic fluxes. The Entner-Doudoroff (ED) pathway was recently predicted as one glycolytic route, which cooperates with other pathways in glycogen breakdown. Despite low carbon flux through the ED pathway, metabolite analyses of mutants deficient in the ED pathway revealed a distinct phenotype pointing at a strong regulatory impact of this route. The small Cp12 protein downregulates the CBB cycle in darkness by inhibiting phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase. New results of metabolomic and redox level analyses on strains with Cp12 variants extend the known role of Cp12 regulation towards the acclimation to external glucose supply under diurnal conditions as well as to fluctuations in CO2 levels in the light. Moreover, carbon and nitrogen metabolism are closely linked to maintain an essential C/N homeostasis. The small protein PirC was shown to be an important regulator of phosphoglycerate mutase, which identified this enzyme as central branching point for carbon allocation from CBB cycle towards lower glycolysis. Altered metabolite levels in the mutant ΔpirC during nitrogen starvation experiments confirm this regulatory mechanism. The elucidation of novel mechanisms regulating carbon allocation at crucial metabolic branching points could identify ways for targeted redirection of carbon flow towards desired compounds, and thus help to further establish cyanobacteria as green cell factories for biotechnological applications with concurrent utilization of sunlight and CO2.
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Affiliation(s)
| | - Martin Hagemann
- Department Plant Physiology, University of Rostock, Rostock, Germany
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3
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Kang W, Mu L, Hu X. Marine Colloids Boost Nitrogen Fixation in Trichodesmium erythraeum by Photoelectrophy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9236-9249. [PMID: 38748855 DOI: 10.1021/acs.est.4c01849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Nitrogen fixation by the diazotrophic cyanobacterium Trichodesmium contributes up to 50% of the bioavailable nitrogen in the ocean. N2 fixation by Trichodesmium is limited by the availability of nutrients, such as iron (Fe) and phosphorus (P). Although colloids are ubiquitous in the ocean, the effects of Fe limitation on nitrogen fixation by marine colloids (MC) and the related mechanisms are largely unexplored. In this study, we found that MC exhibit photoelectrochemical properties that boost nitrogen fixation by photoelectrophy in Trichodesmium erythraeum. MC efficiently promote photosynthesis in T. erythraeum, thus enhancing its growth. Photoexcited electrons from MC are directly transferred to the photosynthetic electron transport chain and contribute to nitrogen fixation and ammonia assimilation. Transcriptomic analysis revealed that MC significantly upregulates genes related to the electron transport chain, photosystem, and photosynthesis, which is consistent with elevated photosynthetic capacities (e.g., Fv/Fm and carboxysomes). As a result, MC increase the N2 fixation rate by 67.5-89.3%. Our findings highlight a proof-of-concept electron transfer pathway by which MC boost nitrogen fixation, broadening our knowledge on the role of ubiquitous colloids in marine nitrogen biogeochemistry.
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Affiliation(s)
- Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-Environment and Product Safety, Key Laboratory for Environmental Factors Controlling Agro-Product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-Environmental Protection, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Carbon Neutrality Interdisciplinary Science Centre, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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4
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Salinas P, Bibak S, Cantos R, Tremiño L, Jerez C, Mata-Balaguer T, Contreras A. Studies on the PII-PipX-NtcA Regulatory Axis of Cyanobacteria Provide Novel Insights into the Advantages and Limitations of Two-Hybrid Systems for Protein Interactions. Int J Mol Sci 2024; 25:5429. [PMID: 38791467 PMCID: PMC11121479 DOI: 10.3390/ijms25105429] [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: 04/05/2024] [Revised: 05/11/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Yeast two-hybrid approaches, which are based on fusion proteins that must co-localise to the nucleus to reconstitute the transcriptional activity of GAL4, have greatly contributed to our understanding of the nitrogen interaction network of cyanobacteria, the main hubs of which are the trimeric PII and the monomeric PipX regulators. The bacterial two-hybrid system, based on the reconstitution in the E. coli cytoplasm of the adenylate cyclase of Bordetella pertussis, should provide a relatively faster and presumably more physiological assay for cyanobacterial proteins than the yeast system. Here, we used the bacterial two-hybrid system to gain additional insights into the cyanobacterial PipX interaction network while simultaneously assessing the advantages and limitations of the two most popular two-hybrid systems. A comprehensive mutational analysis of PipX and bacterial two-hybrid assays were performed to compare the outcomes between yeast and bacterial systems. We detected interactions that were previously recorded in the yeast two-hybrid system as negative, as well as a "false positive", the self-interaction of PipX, which is rather an indirect interaction that is dependent on PII homologues from the E. coli host, a result confirmed by Western blot analysis with relevant PipX variants. This is, to our knowledge, the first report of the molecular basis of a false positive in the bacterial two-hybrid system.
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Affiliation(s)
| | | | | | | | | | | | - Asunción Contreras
- Departamento. de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (P.S.); (S.B.); (R.C.); (L.T.); (C.J.); (T.M.-B.)
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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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Li B, Wang XQ, Li QY, Xu D, Li J, Hou WT, Chen Y, Jiang YL, Zhou CZ. Allosteric regulation of nitrate transporter NRT via the signaling protein PII. Proc Natl Acad Sci U S A 2024; 121:e2318320121. [PMID: 38457518 PMCID: PMC10945777 DOI: 10.1073/pnas.2318320121] [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: 10/21/2023] [Accepted: 01/10/2024] [Indexed: 03/10/2024] Open
Abstract
Coordinated carbon and nitrogen metabolism is crucial for bacteria living in the fluctuating environments. Intracellular carbon and nitrogen homeostasis is maintained by a sophisticated network, in which the widespread signaling protein PII acts as a major regulatory hub. In cyanobacteria, PII was proposed to regulate the nitrate uptake by an ABC (ATP-binding cassette)-type nitrate transporter NrtABCD, in which the nucleotide-binding domain of NrtC is fused with a C-terminal regulatory domain (CRD). Here, we solved three cryoelectron microscopy structures of NrtBCD, bound to nitrate, ATP, and PII, respectively. Structural and biochemical analyses enable us to identify the key residues that form a hydrophobic and a hydrophilic cavity along the substrate translocation channel. The core structure of PII, but not the canonical T-loop, binds to NrtC and stabilizes the CRD, making it visible in the complex structure, narrows the substrate translocation channel in NrtB, and ultimately locks NrtBCD at an inhibited inward-facing conformation. Based on these results and previous reports, we propose a putative transport cycle driven by NrtABCD, which is allosterically inhibited by PII in response to the cellular level of 2-oxoglutarate. Our findings provide a distinct regulatory mechanism of ABC transporter via asymmetrically binding to a signaling protein.
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Affiliation(s)
- Bo Li
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Xiao-Qian Wang
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Qin-Yao Li
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Da Xu
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Jing Li
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Wen-Tao Hou
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Yuxing Chen
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Yong-Liang Jiang
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
| | - Cong-Zhao Zhou
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei230027, China
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7
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Schiksnis C, Xu M, Saito MA, McIlvin M, Moran D, Bian X, John SG, Zheng Q, Yang N, Fu F, Hutchins DA. Proteomics analysis reveals differential acclimation of coastal and oceanic Synechococcus to climate warming and iron limitation. Front Microbiol 2024; 15:1323499. [PMID: 38444803 PMCID: PMC10912551 DOI: 10.3389/fmicb.2024.1323499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
In many oceanic regions, anthropogenic warming will coincide with iron (Fe) limitation. Interactive effects between warming and Fe limitation on phytoplankton physiology and biochemical function are likely, as temperature and Fe availability affect many of the same essential cellular pathways. However, we lack a clear understanding of how globally significant phytoplankton such as the picocyanobacteria Synechococcus will respond to these co-occurring stressors, and what underlying molecular mechanisms will drive this response. Moreover, ecotype-specific adaptations can lead to nuanced differences in responses between strains. In this study, Synechococcus isolates YX04-1 (oceanic) and XM-24 (coastal) from the South China Sea were acclimated to Fe limitation at two temperatures, and their physiological and proteomic responses were compared. Both strains exhibited reduced growth due to warming and Fe limitation. However, coastal XM-24 maintained relatively higher growth rates in response to warming under replete Fe, while its growth was notably more compromised under Fe limitation at both temperatures compared with YX04-1. In response to concurrent heat and Fe stress, oceanic YX04-1 was better able to adjust its photosynthetic proteins and minimize the generation of reactive oxygen species while reducing proteome Fe demand. Its intricate proteomic response likely enabled oceanic YX04-1 to mitigate some of the negative impact of warming on its growth during Fe limitation. Our study highlights how ecologically-shaped adaptations in Synechococcus strains even from proximate oceanic regions can lead to differing physiological and proteomic responses to these climate stressors.
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Affiliation(s)
- Cara Schiksnis
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Min Xu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Mak A. Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Matthew McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Dawn Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Xiaopeng Bian
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Seth G. John
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nina Yang
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Feixue Fu
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - David A. Hutchins
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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Hidese R, Ohbayashi R, Kato Y, Matsuda M, Tanaka K, Imamura S, Ashida H, Kondo A, Hasunuma T. ppGpp accumulation reduces the expression of the global nitrogen homeostasis-modulating NtcA regulon by affecting 2-oxoglutarate levels. Commun Biol 2023; 6:1285. [PMID: 38145988 PMCID: PMC10749895 DOI: 10.1038/s42003-023-05632-1] [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: 03/06/2023] [Accepted: 11/23/2023] [Indexed: 12/27/2023] Open
Abstract
The cyanobacterium Synechococcus elongatus PCC 7942 accumulates alarmone guanosine tetraphosphate (ppGpp) under stress conditions, such as darkness. A previous study observed that artificial ppGpp accumulation under photosynthetic conditions led to the downregulation of genes involved in the nitrogen assimilation system, which is activated by the global nitrogen regulator NtcA, suggesting that ppGpp regulates NtcA activity. However, the details of this mechanism have not been elucidated. Here, we investigate the metabolic responses associated with ppGpp accumulation by heterologous expression of the ppGpp synthetase RelQ. The pool size of 2-oxoglutarate (2-OG), which activates NtcA, is significantly decreased upon ppGpp accumulation. De novo 13C-labeled CO2 assimilation into the Calvin-Benson-Bassham cycle and glycolytic intermediates continues irrespective of ppGpp accumulation, whereas the labeling of 2-OG is significantly decreased under ppGpp accumulation. The low 2-OG levels in the RelQ overexpression cells could be because of the inhibition of metabolic enzymes, including aconitase, which are responsible for 2-OG biosynthesis. We propose a metabolic rearrangement by ppGpp accumulation, which negatively regulates 2-OG levels to maintain carbon and nitrogen balance.
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Affiliation(s)
- Ryota Hidese
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Ryudo Ohbayashi
- Laboratory for Chemistry and Life Science Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Mami Matsuda
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
- NTT Space Environment and Enegy Laboratories, Nippon Telegraph and Telephone Corporation, 3-9-11 Midori-cho, Musashino-shi, Tokyo, 180-8585, Japan
| | - Hiroki Ashida
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-Ku, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Research Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Research Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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9
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Wu S, Zheng H, Wang Y, Wang L, Chen W. Cyanobacterial bioreporter of nitrate bioavailability in aquatic ecosystems. WATER RESEARCH 2023; 247:120749. [PMID: 37918203 DOI: 10.1016/j.watres.2023.120749] [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: 03/27/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The water eutrophication, resulting from the discharge of industrial and agricultural wastewater, leads to ecological degradation. However, to date, how to assess and manage the risks of water pollution, especially nitrogen pollution, remains a particularly noteworthy issue. Nitrate, the most important nitrogen compound, has become a bottleneck restricting total nitrogen management. The development of bioreporters monitoring nitrate pollution contributes to the estimation of water quality, especially the availability of nutrients. In this study, we obtained 9 bioreporters from 40 cyanobacterial derivatives which were constructed based on different hosts, copy numbers, and sensing elements and evaluated the performance of bioreporters. The results showed that single-celled Synechocystis was more sensitive to nitrate than filamentous Anabaena, that the reporter gene luxABCDE responded faster than sfgfp in most bioreporters, and that relatively medium-copy plasmid improved the performance of sensing elements. Nine bioreporters performed well in bioavailable nitrate detection, of which AD-AS-X and AR-NI-X, activated by nitrate repletion, had the shortest response time (2 h) and the widest response range (20-800 μM), respectively. Moreover, SR-GLN-SG, activated by nitrate deficiency, exhibited the best linear response (R2 = 0.998). After parameter optimization, exponential growth phase bioreporters, culture temperature of 30 °C, sample volume of 200 μL were determined as optimal monitoring conditions. We found that common water contaminants (copper, cadmium, and phosphorus) had no impact on the performance of bioreporters, indicating the stability of bioreporters. Six out of 9 bioreporters, especially the SR-NB-X, were highly effective in detecting the bioavailable nitrate in wastewater sample. This study provides valuable references for developing more cyanobacterial bioreporters and their practical application in nitrate detection.
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Affiliation(s)
- Shanyu Wu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hongyan Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuwei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Li Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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10
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Maltsev Y, Kulikovskiy M, Maltseva S. Nitrogen and phosphorus stress as a tool to induce lipid production in microalgae. Microb Cell Fact 2023; 22:239. [PMID: 37981666 PMCID: PMC10658923 DOI: 10.1186/s12934-023-02244-6] [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: 09/11/2023] [Accepted: 11/04/2023] [Indexed: 11/21/2023] Open
Abstract
Microalgae, capable of accumulating large amounts of lipids, are of great value for biodiesel production. The high cost of such production stimulates the search for cultivation conditions that ensure their highest productivity. Reducing the content of nitrogen and phosphorus in the culture medium is widely used to change the content and productivity of lipids in microalgae. Achieving the right balance between maximum growth and maximum lipid content and productivity is the primary goal of many experimental works to ensure cost-effective biodiesel production from microalgae. The content of nitrogen and phosphorus in nutrient media for algal cultivation after converted to nitrogen (-N) and phosphorus (-P) lies in an extensive range: from 0.007 g L- 1 to 0.417 g L- 1 and from 0.0003 g L- 1 to 0.227 g L- 1 and N:P ratio from 0.12:1 to 823.33:1. When studying nutritional stress in microalgae, no single approach is used to determine the experimental concentrations of nitrogen and phosphorus. This precludes the possibility of correct interpretation of the data and may lead to erroneous conclusions. This work results from the systematisation of information on using nitrogen and phosphorus restriction to increase the lipid productivity of microalgae of different taxonomic and ecological groups to identify future research directions. The results of 301 experiments were included in the analysis using the principal components method. The investigation considered various divisions and classes: Cyanobacteria, Rhodophyta, Dinophyta, Haptophyta, Cryptophyta, Heterokontophyta/Ochrophyta (Bacillariophyceae, Eustigmatophyceae, Xanthophyceae), Chlorophyta, and also the ratio N:P, the time of the experiment, the light intensity during cultivation. Based on the concentrations of nitrogen and phosphorus existing in various nutrient media, a general scheme for designating the supply of nutrient media for nitrogen (as NO3- or NH4+, N g L- 1) and phosphorus (as РO4-, P g L- 1) has been proposed: replete -N (˃0.4 g L- 1), moderate -N (0.4-0.2), moderate N-limitation (0.19-0.1), strong N-limitation (˂0.1), without nitrogen (0), replete -Р (˃0.2), moderate -P (0.2-0.02), moderate P-limitation (0.019-0.01), strong P-limitation (˂0.01), without phosphorus (0).
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Affiliation(s)
- Yevhen Maltsev
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia.
| | - Maxim Kulikovskiy
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Svetlana Maltseva
- К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
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11
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Eungrasamee K, Lindblad P, Jantaro S. Improved lipid production and component of mycosporine-like amino acids by co-overexpression of amt1 and aroB genes in Synechocystis sp. PCC6803. Sci Rep 2023; 13:19439. [PMID: 37945676 PMCID: PMC10636201 DOI: 10.1038/s41598-023-46290-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: 07/09/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Implementing homologous overexpression of the amt1 (A) and aroB (B) genes involved in ammonium transporter and the synthesis of mycosporine-like amino acids (MAAs) and aromatic amino acids, respectively, we created three engineered Synechocystis sp. PCC6803 strains, including Ox-A, Ox-B, and Ox-AB, to study the utilization of carbon and nitrogen in cyanobacteria for the production of valuable products. With respect to amt1 overexpression, the Ox-A and Ox-AB strains had a greater growth rate under (NH4)2SO4 supplemented condition. Both the higher level of intracellular accumulation of lipids in Ox-A and Ox-AB as well as the increased secretion of free fatty acids from the Ox-A strain were impacted by the late-log phase of cell growth. It is noteworthy that among all strains, the Ox-B strain undoubtedly spotted a substantial accumulation of glycogen as a consequence of aroB overexpression. Additionally, the ammonium condition drove the potent antioxidant activity in Ox strains with a late-log phase, particularly in the Ox-B and Ox-AB strains. This was probably related to the altered MAA component inside the cells. The higher proportion of P4-fraction was induced by the ammonium condition in both Ox-B and Ox-AB, while the noted increase of the P1 component was found in the Ox-A strain.
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Affiliation(s)
- Kamonchanock Eungrasamee
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Box 523, 75120, Uppsala, Sweden
| | - Saowarath Jantaro
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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12
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Llop A, Tremiño L, Cantos R, Contreras A. The Signal Transduction Protein PII Controls the Levels of the Cyanobacterial Protein PipX. Microorganisms 2023; 11:2379. [PMID: 37894037 PMCID: PMC10609283 DOI: 10.3390/microorganisms11102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Cyanobacteria, microorganisms performing oxygenic photosynthesis, must adapt their metabolic processes to environmental challenges such as day and night changes. PipX, a unique regulatory protein from cyanobacteria, provides a mechanistic link between the signalling protein PII, a widely conserved (in bacteria and plants) transducer of carbon/nitrogen/energy richness, and the transcriptional regulator NtcA, which controls a large regulon involved in nitrogen assimilation. PipX is also involved in translational regulation through interaction with the ribosome-assembly GTPase EngA. However, increases in the PipX/PII ratio are toxic, presumably due to the abnormally increased binding of PipX to other partner(s). Here, we present mutational and structural analyses of reported PipX-PII and PipX-NtcA complexes, leading to the identification of single amino acid changes that decrease or abolish PipX toxicity. Notably, 4 out of 11 mutations decreasing toxicity did not decrease PipX levels, suggesting that the targeted residues (F12, D23, L36, and R54) provide toxicity determinants. In addition, one of those four mutations (D23A) argued against the over-activation of NtcA as the cause of PipX toxicity. Most mutations at residues contacting PII decreased PipX levels, indicating that PipX stability would depend on its ability to bind to PII, a conclusion supported by the light-induced decrease of PipX levels in Synechococcus elongatus PCC7942 (hereafter S. elongatus).
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Affiliation(s)
| | | | | | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain; (A.L.); (L.T.); (R.C.)
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13
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Huang C, Duan X, Ge H, Xiao Z, Zheng L, Wang G, Dong J, Wang Y, Zhang Y, Huang X, An H, Xu W, Wang Y. Parallel Proteomic Comparison of Mutants With Altered Carbon Metabolism Reveals Hik8 Regulation of P II Phosphorylation and Glycogen Accumulation in a Cyanobacterium. Mol Cell Proteomics 2023; 22:100582. [PMID: 37225018 PMCID: PMC10315926 DOI: 10.1016/j.mcpro.2023.100582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023] Open
Abstract
Carbon metabolism is central to photosynthetic organisms and involves the coordinated operation and regulation of numerous proteins. In cyanobacteria, proteins involved in carbon metabolism are regulated by multiple regulators including the RNA polymerase sigma factor SigE, the histidine kinases Hik8, Hik31 and its plasmid-borne paralog Slr6041, and the response regulator Rre37. To understand the specificity and the cross-talk of such regulations, we simultaneously and quantitatively compared the proteomes of the gene knockout mutants for the regulators. A number of proteins showing differential expression in one or more mutants were identified, including four proteins that are unanimously upregulated or downregulated in all five mutants. These represent the important nodes of the intricate and elegant regulatory network for carbon metabolism. Moreover, serine phosphorylation of PII, a key signaling protein sensing and regulating in vivo carbon/nitrogen (C/N) homeostasis through reversible phosphorylation, is massively increased with a concomitant significant decrease in glycogen content only in the hik8-knockout mutant, which also displays impaired dark viability. An unphosphorylatable PII S49A substitution restored the glycogen content and rescued the dark viability of the mutant. Together, our study not only establishes the quantitative relationship between the targets and the corresponding regulators and elucidated their specificity and cross-talk but also unveils that Hik8 regulates glycogen accumulation through negative regulation of PII phosphorylation, providing the first line of evidence that links the two-component system with PII-mediated signal transduction and implicates them in the regulation of carbon metabolism.
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Affiliation(s)
- Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Gaojie Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jinghui Dong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongyu An
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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14
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Guo Y, Zhao X, Yao Z, Qian Z, Wang Y, Xian Q. The effects of exogenous amino acids on production of microcystin variants in Microcystis aeruginosa. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 259:106525. [PMID: 37087861 DOI: 10.1016/j.aquatox.2023.106525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/25/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Dissolved free amino acids are a significant component of dissolved organic nitrogen (DON) in natural waterbodies. The effects of four amino acids (glutamic acid, phenylalanine, leucine, and arginine) on the growth and microcystins (MCs) production of Microcystis aeruginosa were studied in batch culture. The profiles of five MCs variants and the expression levels of target genes involved in MCs biosynthesis and nitrogen metabolism were measured. When amino acids were used as the sole nitrogen source instead of nitrate at different levels (0.5, 2.0 and 8.0 mg/L based on N) in BG-11 medium, algal cell growth and intracellular MCs quotas were inhibited slightly by the treatments with glutamic acid and arginine. The treatments with phenylalanine and leucine, on the other hand, had a strong inhibitory effect on algal cell growth and MCs production. Moreover, the concentrations of Chlorophyll a, phycocyanin and allophycocyanin in cells cultured in glutamic acid, leucine and phenylalanine were lower than those in the control group with nitrate as nitrogen source. The existence of leucine or phenylalanine can lead to a significant increase in the relative abundance of MCs variants structured with the corresponding amino acids. The expression of microcystin-producing gene mcyD was downregulated while the gene pipX associated with nitrogen metabolism was upregulated during the cultivation of M. aeruginosa with amino acids as sole nitrogen source. M. aeruginosa undergoes significant alterations due to exogenous amino acids and exhibits advanced strategies for MCs production.
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Affiliation(s)
- Yaxin Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiating Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Zongcheng Yao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Zongyao Qian
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Yuting Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qiming Xian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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15
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Llop A, Labella JI, Borisova M, Forchhammer K, Selim KA, Contreras A. Pleiotropic effects of PipX, PipY, or RelQ overexpression on growth, cell size, photosynthesis, and polyphosphate accumulation in the cyanobacterium Synechococcus elongatus PCC7942. Front Microbiol 2023; 14:1141775. [PMID: 37007489 PMCID: PMC10060972 DOI: 10.3389/fmicb.2023.1141775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
The cyanobacterial protein PipY belongs to the Pyridoxal-phosphate (PLP)-binding proteins (PLPBP/COG0325) family of pyridoxal-phosphate-binding proteins, which are represented in all three domains of life. These proteins share a high degree of sequence conservation, appear to have purely regulatory functions, and are involved in the homeostasis of vitamin B6 vitamers and amino/keto acids. Intriguingly, the genomic context of the pipY gene in cyanobacteria connects PipY with PipX, a protein involved in signaling the intracellular energy status and carbon-to-nitrogen balance. PipX regulates its cellular targets via protein–protein interactions. These targets include the PII signaling protein, the ribosome assembly GTPase EngA, and the transcriptional regulators NtcA and PlmA. PipX is thus involved in the transmission of multiple signals that are relevant for metabolic homeostasis and stress responses in cyanobacteria, but the exact function of PipY is still elusive. Preliminary data indicated that PipY might also be involved in signaling pathways related to the stringent stress response, a pathway that can be induced in the unicellular cyanobacterium Synechococcus elongatus PCC7942 by overexpression of the (p)ppGpp synthase, RelQ. To get insights into the cellular functions of PipY, we performed a comparative study of PipX, PipY, or RelQ overexpression in S. elongatus PCC7942. Overexpression of PipY or RelQ caused similar phenotypic responses, such as growth arrest, loss of photosynthetic activity and viability, increased cell size, and accumulation of large polyphosphate granules. In contrast, PipX overexpression decreased cell length, indicating that PipX and PipY play antagonistic roles on cell elongation or cell division. Since ppGpp levels were not induced by overexpression of PipY or PipX, it is apparent that the production of polyphosphate in cyanobacteria does not require induction of the stringent response.
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Affiliation(s)
- Antonio Llop
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Jose I. Labella
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Marina Borisova
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Khaled A. Selim
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
- *Correspondence: Asunción Contreras,
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16
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Du C, Sang W, Xu C, Jiang Z, Wang J, Fang Y, Zhu C, Wizi J, Akram MA, Ni L, Li S. Integrated transcriptomic and metabolomic analysis of Microcystis aeruginosa exposed to artemisinin sustained-release microspheres. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130114. [PMID: 36368067 DOI: 10.1016/j.jhazmat.2022.130114] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Artemisinin sustained-release microspheres (ASMs) have been shown to inhibit Microcystis aeruginosa (M. aeruginosa) blooms. Previous studies have focused on inhibitory mechanism of ASMs on the physiological level of M. aeruginosa, but the algal inhibitory mechanism of ASMs has not been comprehensively and profoundly revealed. The study proposed to reveal the toxicity mechanism of ASMs on M. aeruginosa based on transcriptomics and metabolomics. After exposure to 0.2 g·L-1 ASMs for 7 days, M. aeruginosa biomass was significantly inhibited, with an inhibition rate (IR) of 47 % on day 7. Transcriptomic and metabolomic results showed that: (1) 478 differentially expressed genes (DEGs) and 251 differential metabolites (DMs) were obtained; (2) ASMs inhibited photosynthesis by blocking photosynthetic pigment synthesis, destroying photoreaction centers and photosynthetic carbon reactions; (3) ASMs reduced L-glutamic acid content and blocked glutathione (GSH) synthesis, leading to an imbalance in the antioxidant system; (4) ASM disrupted nitrogen metabolism and the hindered synthesis of various amino acids; (5) ASMs inhibited glyoxylate cycle and TCA cycle. This study provides an important prerequisite for the practical application of ASMs and a new perspective for the management of harmful algal blooms (HABs).
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Affiliation(s)
- Cunhao Du
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Wenlu Sang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Chu Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Zhiyun Jiang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Jiajia Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Yuanyi Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Chengjie Zhu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Jakpa Wizi
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Muhammad Asif Akram
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China
| | - Lixiao Ni
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 210098 Nanjing, China.
| | - Shiyin Li
- School of Environment, Nanjing Normal University, 210023 Nanjing, China.
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17
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Díez J, López-Lozano A, Domínguez-Martín MA, Gómez-Baena G, Muñoz-Marín MC, Melero-Rubio Y, García-Fernández JM. Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria. FEMS Microbiol Rev 2023; 47:6794272. [PMID: 36323406 DOI: 10.1093/femsre/fuac043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.
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Affiliation(s)
- J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - Y Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
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18
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Wang Z, Zeng Y, Cheng K, Cai Z, Zhou J. The quorum sensing system of Novosphingobium sp. ERN07 regulates aggregate formation that promotes cyanobacterial growth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158354. [PMID: 36041622 DOI: 10.1016/j.scitotenv.2022.158354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/03/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Microbial aggregates play key roles in cyanobacterial blooms. Being a bacterial communication mechanism, quorum sensing (QS) synchronizes gene expression in a density-dependent manner and regulates bacterial physiological behavior. However, the regulatory role of QS in the formation of cyanobacteria-associated bacterial aggregates remains poorly understood. Here, we present insight into the role of QS in regulating bacterial aggregate formation in a representative bacterial strain, Novosphingobium sp. ERN07, which was isolated from Microcystis blooms in Lake Taihu. A biosensor assay showed that ERN07 exhibits significant AHL-producing capacity. Biochemical and microscopic analysis revealed that this strain possesses the ability to form aggregated communities. Gene knockout experiments indicated that the AHL-mediated QS system positively regulates bacterial aggregation. The aggregated communities possess the ability to enhance the production of extracellular polymeric substances (EPS), alter EPS composition ratios, and affect biofilm formation. The addition of aggregated substances also has a significant growth-promoting effect on M. aeruginosa. Transcriptomic analysis revealed that the aggregated substances positively regulate photosynthetic efficiency and energy metabolism of M. aeruginosa. These findings show that QS can mediate the aggregation phenotype and associated substrate spectrum composition, contributing to a better understanding of microalgal-bacterial interactions and mechanisms of Microcystis bloom maintenance in the natural environment.
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Affiliation(s)
- Zhaoyi Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Yanhua Zeng
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou 570228, Hainan Province, PR China
| | - Keke Cheng
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Jin Zhou
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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19
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Shi N, Yan X, Adeleye AS, Zhang X, Zhou D, Zhao L. Effects of WS 2 Nanosheets on N 2-fixing Cyanobacteria: ROS overproduction, cell membrane damage, and cell metabolic reprogramming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157706. [PMID: 35908696 DOI: 10.1016/j.scitotenv.2022.157706] [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: 05/29/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The ecotoxicity of tungsten disulfide (WS2) nanomaterials remains unclear so far. Here, the toxicity of WS2 nanosheets on N2-fixing cyanobacteria (Nostoc sphaeroides) was evaluated. Specifically, Nostoc were cultivated in media spiked with different concentrations of WS2 nanosheets (0, 0.05, 0.1 and 0.5 mg/L) for 96 h. Relative to unexposed cells, WS2 nanosheets at 0.5 mg/L significantly decreased cell density, content of total sugar and protein by 10.9 %, 0.43 %, and 6.1 %, respectively. Gas chromatography-mass spectrometry (GC-MS)-based metabolomics revealed that WS2 nanosheets exposure altered the metabolite profile of Nostoc in a dose-dependent manner. Energy metabolism related pathways, including the Calvin-Benson-Bassham (CBB) cycle and tricarboxylic acid (TCA) cycle, were significantly inhibited. In addition, WS2 nanosheets exposure resulted in downregulation (20-40 %) of S-containing amino acids (cystine, methionine, and cysteine) and sulfuric acid. Additionally, fatty acids and antioxidant-related compounds (formononetin, catechin, epigallocatechin, dehydroascorbic acid, and alpha-tocopherol) in Nostoc were drastically decreased by 4-50 % upon exposure to WS2 nanosheets, which implies oxidative stress induced by the nanomaterials. Biochemical assays for reactive oxygen species (ROS) and malondialdehyde (MDA) confirmed that WS2 nanosheets triggered ROS overproduction and induced lipid peroxidation. Taken together, WS2 exposure perturbed carbon (C), nitrogen (N), and sulfate (S) metabolism of Nostoc, which may influence C, N, and S cycling, given the important roles of cyanobacteria in these processes. These results highlight the need for caution in the application and environmental release of WS2 nanomaterials to prevent unintended environmental impacts due to their potential ecotoxicity.
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Affiliation(s)
- Nibin Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Xin Yan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Adeyemi S Adeleye
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697-2175, USA
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Dongmei Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Lijuan Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
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20
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Rajpurohit H, Eiteman MA. Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals. Microorganisms 2022; 10:2226. [PMID: 36363817 PMCID: PMC9695796 DOI: 10.3390/microorganisms10112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 08/24/2023] Open
Abstract
Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.
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Affiliation(s)
| | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
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21
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Cobos M, Condori RC, Grandez MA, Estela SL, Del Aguila MT, Castro CG, Rodríguez HN, Vargas JA, Tresierra AB, Barriga LA, Marapara JL, Adrianzén PM, Ruiz R, Castro JC. Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region. Front Genet 2022; 13:973324. [DOI: 10.3389/fgene.2022.973324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications.
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22
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Sawant KR, Sarnaik AP, Savvashe P, Hajinajaf N, Poole P, Varman AM, Lali A, Pandit R. One cell-two wells bio-refinery: Demonstrating cyanobacterial chassis for co-production of heterologous and natural hydrocarbons. BIORESOURCE TECHNOLOGY 2022; 363:127921. [PMID: 36089131 DOI: 10.1016/j.biortech.2022.127921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
In order to improve the potential of cyanobacterial cell factories, Synechococcus sp. PCC7002 was engineered as 'one cell-two wells bio-refinery', for ethylene ('heterologous' hydrocarbon) and carotenoids ('natural' metabolites) production, and demonstrating its outdoor performance. Although the cultures showed better production outdoor, they experienced multiple collapses during scale-up. Hence, flux balance analysis was performed which predicted higher ethylene production with increase in carbon input under outdoor light conditions. Furthermore, FBA predicted that ethylene production will not increase beyond a threshold carbon input flux, owing to limitations on ribulose-1,5-bisphosphate regeneration. Hence, a bicarbonate-supplementation strategy was devised. Cultures grown outdoor at optimal bicarbonate concentration (20 g/L) resulted in improved growth (0.141/h) and ethylene productivity (1.88 mL/L.h) for > 10 days, with enhanced carotenoid titres (40.4 mg/L). In a 100 L air-lift photo-bioreactor; cultures exhibited efficient ethylene (2.464 mL/L.h) and biomass (0.3 g/L.d) productivities, and carotenoids titres (64.4 mg/L), establishing a significant step towards commercialization.
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Affiliation(s)
- Kaustubh R Sawant
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Aditya P Sarnaik
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India; Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Prashant Savvashe
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India; Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Nima Hajinajaf
- Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Parker Poole
- Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Arul M Varman
- Chemical Engineering Department, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Lali
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Reena Pandit
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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Huang X, Luo Y, Luo L, Xie D, Li Z. The nitrite reductase encoded by nirBDs in Pseudomonas putida Y-9 influences ammonium transformation. Front Microbiol 2022; 13:982674. [PMID: 36312953 PMCID: PMC9597696 DOI: 10.3389/fmicb.2022.982674] [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: 06/30/2022] [Accepted: 09/21/2022] [Indexed: 09/13/2023] Open
Abstract
It is unknown whether nirBDs, which conventionally encode an NADH nitrite reductase, play other novel roles in nitrogen cycling. In this study, we explored the role of nirBDs in the nitrogen cycling of Pseudomonas putida Y-9. nirBDs had no effect on organic nitrogen transformation by strain Y-9. The △nirBD strain exhibited higher ammonium removal efficiency (90.7%) than the wild-type strain (76.1%; P < 0.05) and lower end gaseous nitrogen (N2O) production. Moreover, the expression of glnA (control of the ammonium assimilation) in the △nirBD strain was higher than that in the wild-type strain (P < 0.05) after being cultured in ammonium-containing medium. Furthermore, nitrite noticeably inhibited the ammonium elimination of the wild-type strain, with a corresponding removal rate decreasing to 44.8%. However, no similar impact on ammonium transformation was observed for the △nirBD strain, with removal efficiency reaching 97.5%. In conclusion, nirBDs in strain Y-9 decreased the ammonium assimilation and increased the ammonium oxidation to nitrous oxide.
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Affiliation(s)
- Xuejiao Huang
- Key Laboratory of (Guangxi) Agricultural Environment and Products Safety, College of Agronomy, Guangxi University, Nanning, China
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing, China
- Guangxi Bossco Environmental Protection Technology Co., Ltd., Nanning, China
| | - Yuwen Luo
- Key Laboratory of (Guangxi) Agricultural Environment and Products Safety, College of Agronomy, Guangxi University, Nanning, China
| | - Luo Luo
- Key Laboratory of (Guangxi) Agricultural Environment and Products Safety, College of Agronomy, Guangxi University, Nanning, China
| | - Deti Xie
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing, China
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing, China
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24
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Chen Q, Lian M, Guo J, Zhang B, Yang S, Huang K, Peng F, Xiao Y. Comparative Transcriptome Analysis of Two Peach Rootstocks Uncovers the Effect of Gene Differential Expression on Nitrogen Use Efficiency. Int J Mol Sci 2022; 23:ijms231911144. [PMID: 36232452 PMCID: PMC9570093 DOI: 10.3390/ijms231911144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2022] Open
Abstract
Nitrogen is an important nutrient element that limits plant growth and yield formation, but excessive nitrogen has negative effects on plants and the environment. It is important to reveal the molecular mechanism of high NUE (nitrogen use efficiency) for breeding peach rootstock and variety with high NUE. In this study, two peach rootstocks, Shannong–1 (S) and Maotao (M), with different NUE were used as materials and treated with 0.1 mM KNO3 for transcriptome sequencing together with the control group. From the results of comparison between groups, we found that the two rootstocks had different responses to KNO3, and 2151 (KCL_S vs. KCL_M), 327 (KNO3_S vs. KCL_S), 2200 (KNO3_S vs. KNO3_M) and 146 (KNO3_M vs. KCL_M) differentially expressed genes (DEGs) were identified, respectively, which included multiple transcription factor families. These DEGs were enriched in many biological processes and signal transduction pathways, including nitrogen metabolism and plant hormone signal transduction. The function of PpNRT2.1, which showed up-regulated expression under KNO3 treatment, was verified by heterologous expression in Arabidopsis. The plant height, SPAD (soil and plant analyzer development) of leaf and primary root length of the transgenic plants were increased compared with those of WT, indicating the roles of PpNRT2.1 in nitrogen metabolism. The study uncovered for the first time the different molecular regulatory pathways involved in nitrogen metabolism between two peach rootstocks and provided gene reserve for studying the molecular mechanism of nitrogen metabolism and theoretical basis for screening peach rootstock or variety with high NUE.
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25
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Giordano M, Goodman CA, Huang F, Raven JA, Ruan Z. A mechanistic study of the influence of nitrogen and energy availability on the NH4+ sensitivity of nitrogen assimilation in Synechococcus. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5596-5611. [PMID: 35595516 PMCID: PMC9467657 DOI: 10.1093/jxb/erac219] [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: 02/16/2022] [Accepted: 05/19/2022] [Indexed: 05/23/2023]
Abstract
In most algae, NO3- assimilation is tightly controlled and is often inhibited by the presence of NH4+. In the marine, non-colonial, non-diazotrophic cyanobacterium Synechococcus UTEX 2380, NO3- assimilation is sensitive to NH4+ only when N does not limit growth. We sequenced the genome of Synechococcus UTEX 2380, studied the genetic organization of the nitrate assimilation related (NAR) genes, and investigated expression and kinetics of the main NAR enzymes, under N or light limitation. We found that Synechococcus UTEX 2380 is a β-cyanobacterium with a full complement of N uptake and assimilation genes and NAR regulatory elements. The nitrate reductase of our strain showed biphasic kinetics, previously observed only in freshwater or soil diazotrophic Synechococcus strains. Nitrite reductase and glutamine synthetase showed little response to our growth treatments, and their activity was usually much higher than that of nitrate reductase. NH4+ insensitivity of NAR genes may be associated with the stimulation of the binding of the regulator NtcA to NAR gene promoters by the high 2-oxoglutarate concentrations produced under N limitation. NH4+ sensitivity in energy-limited cells fits with the fact that, under these conditions, the use of NH4+ rather than NO3- decreases N-assimilation cost, whereas it would exacerbate N shortage under N limitation.
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Affiliation(s)
- Mario Giordano
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona 60131, Italy
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA
- Institute of Microbiology ASCR, Algatech, Trebon, Czech Republic
- National Research Council, Institute of Marine Science, Venezia, Italy
| | - Charles A Goodman
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA
| | - Fengying Huang
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5 DA, UK
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo NSW 2007, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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26
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Kramer BJ, Jankowiak JG, Nanjappa D, Harke MJ, Gobler CJ. Nitrogen and phosphorus significantly alter growth, nitrogen fixation, anatoxin-a content, and the transcriptome of the bloom-forming cyanobacterium, Dolichospermum. Front Microbiol 2022; 13:955032. [PMID: 36160233 PMCID: PMC9490380 DOI: 10.3389/fmicb.2022.955032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/19/2022] [Indexed: 11/27/2022] Open
Abstract
While freshwater cyanobacteria are traditionally thought to be limited by the availability of phosphorus (P), fixed nitrogen (N) supply can promote the growth and/or toxin production of some genera. This study characterizes how growth on N2 (control), nitrate (NO3 -), ammonium (NH4 +), and urea as well as P limitation altered the growth, toxin production, N2 fixation, and gene expression of an anatoxin-a (ATX-A) - producing strain of Dolichospermum sp. 54. The transcriptomes of fixed N and P-limited cultures differed significantly from those of fixed N-deplete, P-replete (control) cultures, while the transcriptomes of P-replete cultures amended with either NH4 + or NO3 - were not significantly different relative to those of the control. Growth rates of Dolichospermum (sp. 54) were significantly higher when grown on fixed N relative to without fixed N; growth on NH4 + was also significantly greater than growth on NO3 -. NH4 + and urea significantly lowered N2 fixation and nifD gene transcript abundance relative to the control while cultures amended with NO3 - exhibited N2 fixation and nifD gene transcript abundance that was not different from the control. Cultures grown on NH4 + exhibited the lowest ATX-A content per cell and lower transcript abundance of genes associated ATX-A synthesis (ana), while the abundance of transcripts of several ana genes were highest under fixed N and P - limited conditions. The significant negative correlation between growth rate and cellular anatoxin quota as well as the significantly higher number of transcripts of ana genes in cultures deprived of fixed N and P relative to P-replete cultures amended with NH4 + suggests ATX-A was being actively synthesized under P limitation. Collectively, these findings indicate that management strategies that do not regulate fixed N loading will leave eutrophic water bodies vulnerable to more intense and toxic (due to increased biomass) blooms of Dolichospermum.
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Affiliation(s)
- Benjamin J. Kramer
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | | | - Deepak Nanjappa
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | - Matthew J. Harke
- Gloucester Marine Genomics Institute, Gloucester, MA, United States
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
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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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Domínguez-Martín MA, López-Lozano A, Melero-Rubio Y, Gómez-Baena G, Jiménez-Estrada JA, Kukil K, Diez J, García-Fernández JM. Marine Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate. Microbiol Spectr 2022; 10:e0018722. [PMID: 35852322 PMCID: PMC9430850 DOI: 10.1128/spectrum.00187-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022] Open
Abstract
Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment. IMPORTANCE Marine Synechococcus are a very abundant group of photosynthetic organisms on our planet. Previous studies have shown blooms of these organisms when nanomolar concentrations of nitrate become available. We have assessed the effect of nanomolar nitrate concentrations by studying the transcriptome and proteome of Synechococcus sp. WH7803, together with some physiological parameters. We found evidence that Synechococcus sp. strain WH7803 does sense and react to nanomolar concentrations of nitrate, suggesting the occurrence of specific adaptive mechanisms to allow their utilization. Thus, very low concentrations of nitrate in the ocean seem to be a significant nitrogen source for marine picocyanobacteria.
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Grants
- Ministerio de Ciencia e Innovacion, Government of Spain (cofunded by the FEDER program, European Union)
- Consejeria de Conocimiento, Investigacion y Universidad, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
- Universidad de Cordoba (Spain), Programa Propio de Investigacion
- Junta de Andalucia (Spain), Programa Operativo de Empleo Juvenil, cofunded by the FEDER programme (European Union)
- Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
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Affiliation(s)
- María Agustina Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Yesica Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Juan Andrés Jiménez-Estrada
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Kateryna Kukil
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Diez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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29
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Zhao Y, Shang M, Xu X, Sun J, Zang X. Analysis of morphological change mechanism of linear Arthrospira platensis based on transcriptome results. Gene X 2022; 834:146573. [PMID: 35609795 DOI: 10.1016/j.gene.2022.146573] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 11/27/2022] Open
Abstract
Arthrospira platensis is a kind of filament cyanobacteria, which is mainly helical with a few linear. The shape of the filaments, such as the length and the pitch, may change with the changes in the environment. Natural Arthrospira platensis FACHB793 is linear, although it has become helical due to a mutation introduced in the process of cultivation. To study the molecular mechanism responsible for the morphological changes of the filaments, two samples were isolated from a natural mutant of Arthrospira platensis FACHB793, which were helical shaped (named A793_H) and linear shaped (named A793_L). Transcriptome sequencing, GO and KEGG enrichment analysis showed that the expression of genes related to or involved in peptidoglycan biosynthesis, beta lactam resistance, photosynthetic antenna protein expression, bacterial secretion, and ABC transporter activity changed between the two samples. The expression of murE and murG in the peptidoglycan biosynthesis pathway and that of oppD in beta lactam resistance were all down-regulated in the helical filaments, which may be related to the longer cell wall and higher peptidoglycan synthesis in linear filaments than helical filaments. In helical filaments, the up-regulation of tatC gene expression in bacterial secretion may be related to the secretion of peptidoglycan degrading enzymes, which may help to change the shape from linear to helical. Moreover, apcA and cpcA in photosynthetic antenna protein expression and nrt and nirA in nitrogen metabolism were all down regulated in the helical filaments, which may be due to the deformed shape of A. platensis FACHB793, resulting in decreased photosynthetic activity in helical filaments. This research provides a foundation for elucidating the possible morphogenetic mechanism of Arthrospira platensis.
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Affiliation(s)
- Yue Zhao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, Shandong, China
| | - Menghui Shang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, Shandong, China
| | - Xiaoting Xu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, Shandong, China
| | - Jianfei Sun
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, Shandong, China
| | - Xiaonan Zang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, Shandong, China.
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30
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Reinl KL, Harris TD, Elfferich I, Coker A, Zhan Q, De Senerpont Domis LN, Morales-Williams AM, Bhattacharya R, Grossart HP, North RL, Sweetman JN. The role of organic nutrients in structuring freshwater phytoplankton communities in a rapidly changing world. WATER RESEARCH 2022; 219:118573. [PMID: 35643062 DOI: 10.1016/j.watres.2022.118573] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/27/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Carbon, nitrogen, and phosphorus are critical macroelements in freshwater systems. Historically, researchers and managers have focused on inorganic forms, based on the premise that the organic pool was not available for direct uptake by phytoplankton. We now know that phytoplankton can tap the organic nutrient pool through a number of mechanisms including direct uptake, enzymatic hydrolysis, mixotrophy, and through symbiotic relationships with microbial communities. In this review, we explore these mechanisms considering current and projected future anthropogenically-driven changes to freshwater systems. In particular, we focus on how naturally- and anthropogenically- derived organic nutrients can influence phytoplankton community structure. We also synthesize knowledge gaps regarding phytoplankton physiology and the potential challenges of nutrient management in an organically dynamic and anthropogenically modified world. Our review provides a basis for exploring these topics and suggests several avenues for future work on the relation between organic nutrients and eutrophication and their ecological implications in freshwater systems.
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Affiliation(s)
- Kaitlin L Reinl
- Lake Superior National Estuarine Research Reserve, University of Wisconsin-Madison Division of Extension, 14 Marina Drive, Superior, Wisconsin 54880, US; University of Wisconsin-Madison, Center for Limnology, 608 N. Park St., Madison, WI, US; University of Minnesota-Duluth, Large Lakes Observatory, 2205 E. 5th St., Duluth, MN, US.
| | - Ted D Harris
- Kansas Biological Survey and Center for Ecological Research, 2101 Constant Ave., Lawrence, KS, US
| | - Inge Elfferich
- Cardiff University, Earth and Environmental Sciences, Main Building, Park Place CF10 3AT, Cardiff, UK
| | - Ayooluwateso Coker
- University of Minnesota-Duluth, Large Lakes Observatory, 2205 E. 5th St., Duluth, MN, US
| | - Qing Zhan
- Netherlands Institute of Ecology, Dept. of Aquatic Ecology, Droevendaalsesteeg 10, Wageningen, NL
| | | | - Ana M Morales-Williams
- University of Vermont, Rubenstein School of Environment and Natural Resources, 81 Carrigan Drive, Burlington, VT, US
| | - Ruchi Bhattacharya
- University of Waterloo, Department of Earth and Environmental Sciences, 200 University Ave., N2L 1V6, Waterloo, ON, CA
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Dept. Plankton and Microbial Ecology, Zur alten Fischerhuette 2, D-16775 Stechlin, DE; Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam
| | - Rebecca L North
- University of Missouri-Columbia, School of Natural Resources, 303L Anheuser Busch Natural Resource Building, Columbia, MO, US
| | - Jon N Sweetman
- Pennsylvania State University, Ecological Science and Management, 457 Agriculture Sciences and Industries Building, State College, PA, US
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Du R, Gao D, Wang Y, Liu L, Cheng J, Liu J, Zhang XH, Yu M. Heterotrophic Sulfur Oxidation of Halomonas titanicae SOB56 and Its Habitat Adaptation to the Hydrothermal Environment. Front Microbiol 2022; 13:888833. [PMID: 35774465 PMCID: PMC9237845 DOI: 10.3389/fmicb.2022.888833] [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: 03/03/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Halomonas bacteria are ubiquitous in global marine environments, however, their sulfur-oxidizing abilities and survival adaptations in hydrothermal environments are not well understood. In this study, we characterized the sulfur oxidation ability and metabolic mechanisms of Halomonas titanicae SOB56, which was isolated from the sediment of the Tangyin hydrothermal field in the Southern Okinawa Trough. Physiological characterizations showed that it is a heterotrophic sulfur-oxidizing bacterium that can oxidize thiosulfate to tetrathionate, with the Na2S2O3 degradation reaching 94.86%. Two potential thiosulfate dehydrogenase-related genes, tsdA and tsdB, were identified as encoding key catalytic enzymes, and their expression levels in strain SOB56 were significantly upregulated. Nine of fifteen examined Halomonas genomes possess TsdA- and TsdB-homologous proteins, whose amino acid sequences have two typical Cys-X2-Cys-His heme-binding regions. Moreover, the thiosulfate oxidation process in H. titanicae SOB56 might be regulated by quorum sensing, and autoinducer-2 synthesis protein LuxS was identified in its genome. Regarding the mechanisms underlying adaptation to hydrothermal environment, strain SOB56 was capable of forming biofilms and producing EPS. In addition, genes related to complete flagellum assembly system, various signal transduction histidine kinases, heavy metal transporters, anaerobic respiration, and variable osmotic stress regulation were also identified. Our results shed light on the potential functions of heterotrophic Halomonas bacteria in hydrothermal sulfur cycle and revealed possible adaptations for living at deep-sea hydrothermal fields by H. titanicae SOB56.
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Affiliation(s)
- Rui Du
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Di Gao
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yiting Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Lijun Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jingguang Cheng
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Min Yu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- *Correspondence: Min Yu,
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Van Camp C, Fraikin C, Claverie E, Onderwater R, Wattiez R. Capsular polysaccharides and exopolysaccharides from Gloeothece verrucosa under various nitrogen regimes and their potential plant defence stimulation activity. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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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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Tang J, Shah MR, Yao D, Jiang Y, Du L, Zhao K, Li L, Li M, Waleron MM, Waleron M, Waleron K, Daroch M. Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae. Front Microbiol 2022; 13:765105. [PMID: 35418964 PMCID: PMC8997340 DOI: 10.3389/fmicb.2022.765105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/31/2022] [Indexed: 01/07/2023] Open
Abstract
Thermal environments are an important reservoir of thermophiles with significant ecological and biotechnological potentials. However, thermophilic isolates remain largely unrecovered from their habitats and are rarely systematically identified. In this study, we characterized using polyphasic approaches a thermophilic strain, PKUAC-SCTAE412 (E412 hereafter), recovered from Lotus Lake hot spring based in Ganzi prefecture, China. The results of 16S rRNA/16S-23S ITS phylogenies, secondary structure, and morphology comparison strongly supported that strain E412 represent a novel genus within Leptolyngbyaceae. This delineation was further confirmed by genome-based analyses [phylogenomic inference, average nucleotide/amino-acid identity, and the percentages of conserved proteins (POCP)]. Based on the botanical code, the isolate is herein delineated as Leptothermofonsia sichuanensis gen. sp. nov, a genus adjacent to recently delineated Kovacikia and Stenomitos. In addition, we successfully obtained the first complete genome of this new genus. Genomic analysis revealed its adaptations to the adverse hot spring environment and extensive molecular components related to mobile genetic elements, photosynthesis, and nitrogen metabolism. Moreover, the strain was capable of modifying the composition of its light-harvesting apparatus depending on the wavelength and photoperiod, showing chromatic adaptation capacity characteristic for T1 and T2 pigmentation types. Other physiological studies showed the strain’s ability to utilize sodium bicarbonate and various sulfur compounds. The strain was also shown to be diazotrophic. Interestingly, 24.6% of annotated protein-coding genes in the E412 genome were identified as putatively acquired, hypothesizing that a large number of genes acquired through HGT might contribute to the genome expansion and habitat adaptation of those thermophilic strains. Most the HGT candidates (69.4%) were categorized as metabolic functions as suggested by the KEGG analysis. Overall, the complete genome of strain E412 provides the first insight into the genomic feature of the genus Leptothermofonsia and lays the foundation for future global ecogenomic and geogenomic studies.
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Affiliation(s)
- Jie Tang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Mahfuzur R Shah
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Dan Yao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Ying Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Lianming Du
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Liheng Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Meijin Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Michal M Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy Medical University of Gdańsk, Gdańsk, Poland
| | - Malgorzata Waleron
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy Medical University of Gdańsk, Gdańsk, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
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Yang B, Qin Y, He X, Li H, Ma J. The removal of ammonia nitrogen via heterotrophic assimilation by a novel Paracoccus sp. FDN-02 under anoxic condition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152236. [PMID: 34896137 DOI: 10.1016/j.scitotenv.2021.152236] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
A novel strain FDN-02 was isolated from a sequencing batch biofilm reactor. FDN-02 was identified as Paracoccus sp., and the Genbank Sequence_ID was MW652628. Comparing with the removal efficiency of ammonia nitrogen (NH4+-N) by bacterium FDN-02 under different growth conditions, the optimal initial pH, carbon source, and C/N ratio were 7.0, sucrose, and 16, respectively. The maximum removal efficiency and rate of NH4+-N were respectively 96.2% and 10.06 mg-N/L/h within 8 h under anoxic condition when the concentration of NH4+-N was 44.87 mg/L. Specifically, 71.9% of NH4+-N was utilized by strain FDN-02 through heterotrophic assimilation to synthetize organic nitrogen, and approximately 24.1% of NH4+-N was lost in the form of gaseous nitrogen without the emission of nitrous oxide. Bacterium FDN-02 was also found to be a denitrifying organism, and nitrate nitrogen and nitrite nitrogen of lower concentrations were removed by denitrification after the enlargement of biomass. Further investigation showed that the biomass after the removal of NH4+-N by strain FDN-02 had resource utilization potential, and the contents of proteins and amino acids were 635 and 192.97 mg/g, respectively, especially for the usage as an alternative nutrient source for livestock and organic fertilizers. This study provided a promising environmentally friendly biological treatment method for the removal of NH4+-N in the wastewater.
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Affiliation(s)
- Biqi Yang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yuyang Qin
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Xianglong He
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Hongjing Li
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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36
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Lorenzi AS, Bonatelli ML, Varani AM, Quecine MC, Bittencourt-Oliveira MDC. Draft genome sequence of the cyanobacterium Sphaerospermopsis aphanizomenoides BCCUSP55 from the Brazilian semiarid region reveals potential for anti-cancer applications. Arch Microbiol 2021; 204:4. [DOI: 10.1007/s00203-021-02602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 11/29/2022]
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37
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Hou P, Sun X, Fang Z, Feng Y, Guo Y, Wang Q, Chen C. Simultaneous removal of phosphorous and nitrogen by ammonium assimilation and aerobic denitrification of novel phosphate-accumulating organism Pseudomonas chloritidismutans K14. BIORESOURCE TECHNOLOGY 2021; 340:125621. [PMID: 34325396 DOI: 10.1016/j.biortech.2021.125621] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Pseudomonas chloritidismutans K14, a novel phosphate-accumulating organism with the capacity to perform ammonium assimilation, aerobic denitrification, and phosphorus removal, was isolated from aquaculture sediments. It produced no hemolysin, and showed susceptibility to most antibiotics. Optimum conditions were achieved with sodium pyruvate as a carbon source, a C/N ratio of 10, pH of 7.5, temperature of 27 °C, P/N ratio of 0.26, and shaking at 140 rpm. Under optimum conditions, the highest removal efficiencies of ammonium, nitrite, and nitrate were 99.82%, 99.11%, and 99.78%, respectively; the corresponding removal rates were 6.27, 4.51, and 4.99 mg/L/h. The strain removed over 98% of phosphorus, and over 87% of chemical oxygen demand. The highest biomass nitrogen during ammonium assimilation was 99.18 mg/L; no gaseous nitrogen was produced. The genes involved in nitrogen and phosphorus removal were amplified by PCR. This study demonstrated the potential application prospects of strain K14 for nitrogen and phosphorus removal.
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Affiliation(s)
- Pengfei Hou
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Xueliang Sun
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China; College of Environmental Science and Engineering, Tianjin University, Tianjin 300073, China
| | - Zhanming Fang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Yongyi Feng
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Yingying Guo
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Qingkui Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Chengxun Chen
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China.
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38
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Hu X, Zhang T, Ji K, Luo K, Wang L, Chen W. Transcriptome and metabolome analyses of response of Synechocystis sp. PCC 6803 to methyl viologen. Appl Microbiol Biotechnol 2021; 105:8377-8392. [PMID: 34668984 DOI: 10.1007/s00253-021-11628-w] [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: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
The toxicity of methyl viologen (MV) to organisms is mainly due to the oxidative stress caused by reactive oxygen species produced from cell response. This study mainly investigated the response of Synechocystis sp. PCC 6803 to MV by combining transcriptomic and metabolomic analyses. Through transcriptome sequencing, we found many genes responding to MV stress, and analyzed them by weighted gene co-expression network analysis (WGCNA). Meanwhile, many metabolites were also found by metabolomic analysis to be regulated post MV treatment. Based on the analysis results of Kyoto encyclopedia of genes and genomes (KEGG) of the differentially expressed genes (DEGs) in the transcriptome and the differential metabolites in the metabolome, the dynamic changes of genes and metabolites involved in ten metabolic pathways in response to MV were analyzed. The results indicated that although the oxidative stress caused by MV was the strongest at 6 h, the proportion of the upregulated genes and metabolites involved in these ten metabolic pathways was the highest. Photosynthesis positively regulated the response to MV-induced oxidative stress, and the regulation of environmental information processing was inhibited by MV. Other metabolic pathways played different roles at different times and interacted with each other to respond to MV. This study comprehensively analyzed the response of Synechocystis sp. PCC 6803 to oxidative stress caused by MV from a multi-omics perspective, with providing key data and important information for in-depth analysis of the response of organisms to MV, especially photosynthetic organisms. KEY POINTS: • Methyl viologen (MV) treatment caused regulatory changes in genes and metabolites. • Proportion of upregulated genes and metabolites was the highest at 6-h MV treatment. • Photosynthesis and environmental information processing involved in MV response.
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Affiliation(s)
- Xinyu Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Tianyuan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Kai Ji
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ke Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Li Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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39
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Shabestary K, Hernández HP, Miao R, Ljungqvist E, Hallman O, Sporre E, Branco Dos Santos F, Hudson EP. Cycling between growth and production phases increases cyanobacteria bioproduction of lactate. Metab Eng 2021; 68:131-141. [PMID: 34601120 DOI: 10.1016/j.ymben.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/03/2021] [Accepted: 09/25/2021] [Indexed: 01/23/2023]
Abstract
Decoupling growth from product synthesis is a promising strategy to increase carbon partitioning and maximize productivity in cell factories. However, reduction in both substrate uptake rate and metabolic activity in the production phase are an underlying problem for upscaling. Here, we used CRISPR interference to repress growth in lactate-producing Synechocystis sp. PCC 6803. Carbon partitioning to lactate in the production phase exceeded 90%, but CO2 uptake was severely reduced compared to uptake during the growth phase. We characterized strains during the onset of growth arrest using transcriptomics and proteomics. Multiple genes involved in ATP homeostasis were regulated once growth was inhibited, which suggests an alteration of energy charge that may lead to reduced substrate uptake. In order to overcome the reduced metabolic activity and take advantage of increased carbon partitioning, we tested a novel production strategy that involved alternating growth arrest and recovery by periodic addition of an inducer molecule to activate CRISPRi. Using this strategy, we maintained lactate biosynthesis in Synechocystis for 30 days in a constant light turbidostat cultivation. Cumulative lactate titers were also increased by 100% compared to a constant growth-arrest regime, and reached 1 g/L. Further, the cultivation produced lactate for 30 days, compared to 20 days for the non-growth arrest cultivation. Periodic growth arrest could be applicable for other products, and in cyanobacteria, could be linked to internal circadian rhythms that persist in constant light.
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Affiliation(s)
- Kiyan Shabestary
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Hugo Pineda Hernández
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Rui Miao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emil Ljungqvist
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Olivia Hallman
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emil Sporre
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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40
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Wei N, Song L, Gan N. Quantitative Proteomic and Microcystin Production Response of Microcystis aeruginosa to Phosphorus Depletion. Microorganisms 2021; 9:microorganisms9061183. [PMID: 34072711 PMCID: PMC8227402 DOI: 10.3390/microorganisms9061183] [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: 04/21/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/20/2022] Open
Abstract
Microcystis blooms are the most widely distributed and frequently occurring cyanobacterial blooms in freshwater. Reducing phosphorus is suggested to be effective in mitigating cyanobacterial blooms, while the underlying molecular mechanisms are yet to be elucidated. In the present study, isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics was employed to study the effects of phosphorus depletion on Microcystis aeruginosa FACHB-905. The production of microcystins (MCs), a severe hazard of Microcystis blooms, was also analyzed. In total, 230 proteins were found to be differentially abundant, with 136 downregulated proteins. The results revealed that, upon phosphorus limitation stress, Microcystis aeruginosa FACHB-905 raised the availability of phosphorus primarily by upregulating the expression of orthophosphate transport system proteins, with no alkaline phosphatase producing ability. Phosphorus depletion remarkably inhibited cell growth and the primary metabolic processes of Microcystis, including transcription, translation and photosynthesis, with structures of photosystems remaining intact. Moreover, expression of nitrogen assimilation proteins was downregulated, while proteins involved in carbon catabolism were significantly upregulated, which was considered beneficial for the intracellular balance among carbon, nitrogen and phosphorus. The expression of MC synthetase was not significantly different upon phosphorus depletion, while MC content was significantly suppressed. It is assumed that phosphorus depletion indirectly regulates the production of MC by the inhibition of metabolic processes and energy production. These results contribute to further understanding of the influence mechanisms of phosphorus depletion on both biological processes and MC production in Microcystis cells.
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Affiliation(s)
- Nian Wei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430072, China
| | - Lirong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
- Correspondence: (L.S.); (N.G.)
| | - Nanqin Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
- Correspondence: (L.S.); (N.G.)
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41
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Wang Q, Han Y, Lan S, Hu C. Metagenomic Insight Into Patterns and Mechanism of Nitrogen Cycle During Biocrust Succession. Front Microbiol 2021; 12:633428. [PMID: 33815315 PMCID: PMC8009985 DOI: 10.3389/fmicb.2021.633428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
The successional ecology of nitrogen cycling in biocrusts and the linkages to ecosystem processes remains unclear. To explore this, four successional stages of natural biocrust with five batches of repeated sampling and three developmental stages of simulated biocrust were studied using relative and absolute quantified multi-omics methods. A consistent pattern across all biocrust was found where ammonium assimilation, mineralization, dissimilatory nitrite to ammonium (DNiRA), and assimilatory nitrate to ammonium were abundant, while denitrification medium, N-fixation, and ammonia oxidation were low. Mathematic analysis showed that the nitrogen cycle in natural biocrust was driven by dissolved organic N and NO3–. pH and SO42– were the strongest variables affecting denitrification, while C:(N:P) was the strongest variable affecting N-fixation, DNiRA, nitrite oxidation, and dissimilatory nitrate to nitrite. Furthermore, N-fixation and DNiRA were closely related to elemental stoichiometry and redox balance, while assimilatory nitrite to ammonium (ANiRA) and mineralization were related to hydrological cycles. Together with the absolute quantification and network models, our results suggest that responsive ANiRA and mineralization decreased during biocrust succession; whereas central respiratory DNiRA, the final step of denitrification, and the complexity and interaction of the whole nitrogen cycle network increased. Therefore, our study stresses the changing environmental functions in the biocrust N-cycle, which are succession-dependent.
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Affiliation(s)
- Qiong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingchun Han
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shubin Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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42
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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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Du W, Li G, Ho N, Jenkins L, Hockaday D, Tan J, Cao H. CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms. Brief Bioinform 2020; 22:6035272. [PMID: 33320930 DOI: 10.1093/bib/bbaa375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 11/14/2022] Open
Abstract
CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) driving CyanoHABs, customized pathway maps, classification of blooming type based on databases and the genomes of cyanobacteria. A total of 19 pathways are reconstructed, which are involved in the utilization of macronutrients (e.g. carbon, nitrogen, phosphorus and sulfur), micronutrients (e.g. zinc, magnesium, iron, etc.) and other resources (e.g. light and vitamins) and in stress resistance (e.g. lead and copper). These pathways, comprised of both transport and biochemical reactions, are reconstructed with proteins from NCBI and reactions from KEGG and visualized with self-created transport/reaction maps. The pathways are hierarchical and consist of subpathways, protein/enzyme complexes and constituent proteins. New cyanobacterial genomes can be annotated and visualized for these pathways and compared with existing species. This set of genomic functional repertoire is useful in analyzing aquatic metagenomes and metatranscriptomes in CyanoHAB research. Most importantly, it establishes a link between genome and ecology. All these reference proteins, pathways and maps and genomes are free to download at http://www.csbg-jlu.info/CyanoPATH.
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Affiliation(s)
| | | | - Nicholas Ho
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
| | - Landon Jenkins
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
| | - Drew Hockaday
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
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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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Brandenburg F, Klähn S. Small but Smart: On the Diverse Role of Small Proteins in the Regulation of Cyanobacterial Metabolism. Life (Basel) 2020; 10:E322. [PMID: 33271798 PMCID: PMC7760959 DOI: 10.3390/life10120322] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past few decades, bioengineered cyanobacteria have become a major focus of research for the production of energy carriers and high value chemical compounds. Besides improvements in cultivation routines and reactor technology, the integral understanding of the regulation of metabolic fluxes is the key to designing production strains that are able to compete with established industrial processes. In cyanobacteria, many enzymes and metabolic pathways are regulated differently compared to other bacteria. For instance, while glutamine synthetase in proteobacteria is mainly regulated by covalent enzyme modifications, the same enzyme in cyanobacteria is controlled by the interaction with unique small proteins. Other prominent examples, such as the small protein CP12 which controls the Calvin-Benson cycle, indicate that the regulation of enzymes and/or pathways via the attachment of small proteins might be a widespread mechanism in cyanobacteria. Accordingly, this review highlights the diverse role of small proteins in the control of cyanobacterial metabolism, focusing on well-studied examples as well as those most recently described. Moreover, it will discuss their potential to implement metabolic engineering strategies in order to make cyanobacteria more definable for biotechnological applications.
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Affiliation(s)
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany;
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Rachedi R, Foglino M, Latifi A. Stress Signaling in Cyanobacteria: A Mechanistic Overview. Life (Basel) 2020; 10:life10120312. [PMID: 33256109 PMCID: PMC7760821 DOI: 10.3390/life10120312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Cyanobacteria are highly diverse, widely distributed photosynthetic bacteria inhabiting various environments ranging from deserts to the cryosphere. Throughout this range of niches, they have to cope with various stresses and kinds of deprivation which threaten their growth and viability. In order to adapt to these stresses and survive, they have developed several global adaptive responses which modulate the patterns of gene expression and the cellular functions at work. Sigma factors, two-component systems, transcriptional regulators and small regulatory RNAs acting either separately or collectively, for example, induce appropriate cyanobacterial stress responses. The aim of this review is to summarize our current knowledge about the diversity of the sensors and regulators involved in the perception and transduction of light, oxidative and thermal stresses, and nutrient starvation responses. The studies discussed here point to the fact that various stresses affecting the photosynthetic capacity are transduced by common mechanisms.
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Understanding the Differences in the Growth and Toxin Production of Anatoxin-Producing Cuspidothrix issatschenkoi Cultured with Inorganic and Organic N Sources from a New Perspective: Carbon/Nitrogen Metabolic Balance. Toxins (Basel) 2020; 12:toxins12110724. [PMID: 33228063 PMCID: PMC7699347 DOI: 10.3390/toxins12110724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022] Open
Abstract
Cyanotoxins are the underlying cause of the threat that globally pervasive Cyanobacteria Harmful algal blooms (CyanoHABs) pose to humans. Major attention has been focused on the cyanobacterial hepatotoxin microcystins (MCs); however, there is a dearth of studies on cyanobacterial neurotoxin anatoxins. In this study, we explored how an anatoxin-producing Cuspidothrix issatschenkoi strain responded to culture with inorganic and organic nitrogen sources in terms of growth and anatoxins production. The results of our study revealed that ʟ- alanine could greatly boost cell growth, and was associated with the highest cell productivity, while urea significantly stimulated anatoxin production with the maximum anatoxin yield reaching 25.86 μg/mg dry weight, which was 1.56-fold higher than that in the control group (BG11). To further understand whether the carbon/nitrogen balance in C. issatschenkoi would affect anatoxin production, we explored growth and toxin production in response to different carbon/nitrogen ratios (C/N). Anatoxin production was mildly promoted when the C/N ratio was within low range, and significantly inhibited when the C/N ratio was within high range, showing approximately a three-fold difference. Furthermore, the transcriptional profile revealed that anaC gene expression was significantly up-regulated over 2–24 h when the C/N ratio was increased, and was significantly down-regulated after 96 h. Overall, our results further enriched the evidence that urea can stimulate cyanotoxin production, and ʟ-alanine could boost C. issatschenkoi proliferation, thus providing information for better management of aquatic systems. Moreover, by focusing on the intracellular C/N metabolic balance, this study explained the anatoxin production dynamics in C. issatschenkoi in response to different N sources.
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Campbell MA, Grice K, Visscher PT, Morris T, Wong HL, White RA, Burns BP, Coolen MJL. Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses. Front Microbiol 2020; 11:560336. [PMID: 33312167 PMCID: PMC7702295 DOI: 10.3389/fmicb.2020.560336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/09/2020] [Indexed: 11/25/2022] Open
Abstract
Microbial mat communities possess extensive taxonomic and functional diversity, which drive high metabolic rates and rapid cycling of major elements. Modern microbial mats occurring in hypersaline environments are considered as analogs to extinct geobiological formations dating back to ∼ 3.5 Gyr ago. Despite efforts to understand the diversity and metabolic potential of hypersaline microbial mats in Shark Bay, Western Australia, there has yet to be molecular analyses at the transcriptional level in these microbial communities. In this study, we generated metatranscriptomes for the first time from actively growing mats comparing the type of mat, as well as the influence of diel and seasonal cycles. We observed that the overall gene transcription is strongly influenced by microbial community structure and seasonality. The most transcribed genes were associated with tackling the low nutrient conditions by the uptake of fatty acids, phosphorus, iron, and nickel from the environment as well as with protective mechanisms against elevated salinity conditions and to prevent build-up of ammonium produced by nitrate reducing microorganisms. A range of pathways involved in carbon, nitrogen, and sulfur cycles were identified in mat metatranscriptomes, with anoxygenic photosynthesis and chemoautotrophy using the Arnon–Buchanan cycle inferred as major pathways involved in the carbon cycle. Furthermore, enrichment of active anaerobic pathways (e.g., sulfate reduction, methanogenesis, Wood–Ljungdahl) in smooth mats corroborates previous metagenomic studies and further advocates the potential of these communities as modern analogs of ancient microbialites.
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Affiliation(s)
- Matthew A Campbell
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Kliti Grice
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
| | - Pieter T Visscher
- Departments of Marine Sciences and Geoscience, University of Connecticut, Storrs, CT, United States.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Therese Morris
- Applied Geology, Curtin University, Perth, WA, Australia
| | - Hon Lun Wong
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Richard Allen White
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,Plant Pathology, Washington State University, Pullman, WA, United States.,RAW Molecular Systems (RMS) LLC, Spokane, WA, United States
| | - Brendan P Burns
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Marco J L Coolen
- WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, WA, Australia
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Li H, Barber M, Lu J, Goel R. Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake. WATER RESEARCH 2020; 185:116292. [PMID: 33086464 PMCID: PMC7737503 DOI: 10.1016/j.watres.2020.116292] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 05/06/2023]
Abstract
The current study reports the community succession of different toxin and non-toxin producing cyanobacteria at different stages of cyanobacterial harmful algal blooms (CyanoHABs) and their connectivity with nitrogen and phosphorus cycles in a freshwater lake using an ecogenomics framework. Comprehensive high throughput DNA sequencing, water quality parameter measurements, and functional gene expressions over temporal and spatial scales were employed. Among the cyanobacterial community, the lake was initially dominated by Cyanobium during the months of May, June, and early July, and later primarily by Aphanizomenon and Dolichospermum depicting functional redundancy. Finally, Planktothrix appeared in late August and then the dominance switched to Planktothrix in September. Microcystis aeruginosa and Microcystis panniformis; two species responsible for cyanotoxin production, were also present in August and September, but in significantly smaller relative abundance. MC-LR (0.06-1.32 µg/L) and MC-RR (0.01-0.26 µg/L) were two major types of cyanotoxins detected. The presence of MC-LR and MC-RR were significantly correlated with the Microcystis-related genes (16SMic/mcyA/mcyG) and their expressions (r = 0.33 to 0.8, p < 0.05). The metabolic analyses further linked the presence of different cyanobacterial groups with distinct functions. The nitrogen metabolisms detected a relatively higher abundance of nitrite/nitrate reductase in early summer, indicating significant denitrification activity and the activation of N-fixation in the blooms dominated by Aphanizomenon/Dolichospermum (community richness) during nutrient-limited conditions. The phosphorus and carbohydrate metabolisms detected a trend to initiate a nutrient starvation alert and store nutrients from early summer, while utilizing the stored polyphosphate and carbohydrate (PPX and F6PPK) during the extreme ortho-P scarcity period, mostly in August or September. Specifically, the abundance of Aphanizomenon and Dolichospermum was positively correlated with the nitrogen-fixing nif gene and (p < 0.001) and the PPX enzyme for the stored polyphosphate utilization (r = 0.77, p < 0.001). Interestingly, the lake experienced a longer N-fixing period (2-3 months) before non-fixing cyanobacteria (Planktothrix) dominated the entire lake in late summer. The Provo Bay site, which is known to be nutrient-rich historically, had early episodes of filamentous cyanobacteria blooms compared to the rest of the lake.
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Affiliation(s)
- Hanyan Li
- Civil & Environmental Engineering, University of Utah, 110 S. Central Campus Drive, 2000 MCE, Salt Lake City, UT 84121, USA
| | - Mike Barber
- Civil & Environmental Engineering, University of Utah, 110 S. Central Campus Drive, 2000 MCE, Salt Lake City, UT 84121, USA
| | - Jingrang Lu
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Ramesh Goel
- Civil & Environmental Engineering, University of Utah, 110 S. Central Campus Drive, 2000 MCE, Salt Lake City, UT 84121, USA.
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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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