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Fuchs B, Mert S, Kuhlmann C, Taha S, Birt A, Nickelsen J, Schenck TL, Giunta RE, Wiggenhauser PS, Moellhoff N. Biocompatibility of Synechococcus sp. PCC 7002 with Human Dermal Cells In Vitro. Int J Mol Sci 2024; 25:3922. [PMID: 38612734 PMCID: PMC11012068 DOI: 10.3390/ijms25073922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
Being the green gold of the future, cyanobacteria have recently attracted considerable interest worldwide. This study investigates the adaptability and biocompatibility of the cyanobacterial strain Synechococcus sp. PCC 7002 with human dermal cells, focusing on its potential application in biomedical contexts. First, we investigated the adaptability of Synechococcus PCC 7002 bacteria to human cell culture conditions. Next, we evaluated the biocompatibility of cyanobacteria with common dermal cells, like 3T3 fibroblasts and HaCaT keratinocytes. Therefore, cells were directly and indirectly cocultured with the corresponding cells, and we measured metabolic activity (AlamarBlue assay) and proliferation (cell count and PicoGreen assay). The lactate dehydrogenase (LDH) assay was performed to determine the cytotoxic effect of cyanobacteria and their nutrition medium on human dermal cells. The cyanobacteria exhibited exponential growth under conventional human cell culture conditions, with the temperature and medium composition not affecting their viability. In addition, the effect of illumination on the proliferation capacity was investigated, showing a significant impact of light exposure on bacterial growth. The measured oxygen production under hypoxic conditions demonstrated a sufficient oxygen supply for further tissue engineering approaches depending on the number of bacteria. There were no significant adverse effects on human cell viability and growth under coculture conditions, whereas the LDH assay assessed signs of cytotoxicity regarding 3T3 fibroblasts after 2 days of coculturing. These negative effects were dismissed after 4 days. The findings highlight the potential of Synechococcus sp. PCC 7002 for integration into biomedical approaches. We found no cytotoxicity of cyanobacteria on 3T3 fibroblasts and HaCaT keratinocytes, thus paving the way for further in vivo studies to assess long-term effects and systemic reactions.
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Affiliation(s)
- Benedikt Fuchs
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Sinan Mert
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Constanze Kuhlmann
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Sara Taha
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Alexandra Birt
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Jörg Nickelsen
- Molecular Plant Science, Department Biology I, LMU Munich, 80336 Munich, Germany;
| | - Thilo Ludwig Schenck
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Riccardo Enzo Giunta
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Paul Severin Wiggenhauser
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
| | - Nicholas Moellhoff
- Division of Hand, Plastic and Aesthetic Surgery, LMU University Hospital, LMU Munich, 80336 Munich, Germany; (S.M.); (C.K.); (S.T.); (A.B.); (T.L.S.); (R.E.G.); (P.S.W.); (N.M.)
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Kondo M, Aoki M, Hirai K, Ito R, Tsuzuki M, Sato N. Plastoquinone Lipids: Their Synthesis via a Bifunctional Gene and Physiological Function in a Euryhaline Cyanobacterium, Synechococcus sp. PCC 7002. Microorganisms 2023; 11:1177. [PMID: 37317151 DOI: 10.3390/microorganisms11051177] [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: 04/13/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Eukaryotic photosynthetic organisms synthesize triacylglycerols, which are crucial physiologically as major carbon and energy storage compounds and commercially as food oils and raw materials for carbon-neutral biofuel production. TLC analysis has revealed triacylglycerols are present in several cyanobacteria. However, mass spectrometric analysis has shown that freshwater cyanobacterium, Synechocystis sp. PCC 6803, contains plastoquinone-B and acyl plastoquinol with triacylglycerol-like TLC mobility, concomitantly with the absence of triacylglycerol. Synechocystis contains slr2103, which is responsible for the bifunctional synthesis of plastoquinone-B and acyl plastoquinol and also for NaCl-stress acclimatizing cell growth. However, information is limited on the taxonomical distribution of these plastoquinone lipids, and their synthesis genes and physiological roles in cyanobacteria. In this study, a euryhaline cyanobacterium, Synechococcus sp. PCC 7002, shows the same plastoquinone lipids as those in Synechocystis, although the levels are much lower than in Synechocystis, triacylglycerol being absent. Furthermore, through an analysis of a disruptant to the homolog of slr2103 in Synechococcus, it is found that the slr2103 homolog in Synechococcus, similar to slr2103 in Synechocystis, contributes bifunctionally to the synthesis of plastoquinone-B and acyl plastoquinol; however, the extent of the contribution of the homolog gene to NaCl acclimatization is smaller than that of slr2103 in Synechocystis. These observations suggest strain- or ecoregion-dependent development of the physiological roles of plastoquinone lipids in cyanobacteria and show the necessity to re-evaluate previously identified cyanobacterial triacylglycerol through TLC analysis with mass spectrometric techniques.
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Affiliation(s)
- Mimari Kondo
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Motohide Aoki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Kazuho Hirai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Ryo Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Mikio Tsuzuki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Norihiro Sato
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
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Wang Y, Ge H, Xiao Z, Huang C, Wang G, Duan X, Zheng L, Dong J, Huang X, Zhang Y, An H, Xu W, Wang Y. Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses. J Proteome Res 2023; 22:1255-1269. [PMID: 36930737 DOI: 10.1021/acs.jproteome.2c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Spatial proteome reorganization in response to a changing environment represents a different layer of adaptation mechanism in addition to differential expression of a subset of stress responsive genes in photosynthetic organisms. Profiling such reorganization events is critically important to extend our understanding how photosynthetic organisms adapt to adverse environments. Thus, we treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis), with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble fractions using a quantitative proteomics approach. A number of proteins showing such a redistribution in response to a single or multiple types of abiotic stresses were identified. These include 12 ribosomal proteins displaying unanimous cold-induced redistribution to the membrane and the protein FurA, a master regulator of iron acquisition, displaying iron deficiency- and nitrogen starvation-induced redistribution to the membrane. Such findings shed light on a novel regulatory mechanism underlying the corresponding stress responses, and establish the results in the present study as an important resource for future studies intended to understand how photosynthetic organisms cope with adverse environments.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Gaojie Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Jinghui Dong
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Hongyu An
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
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Santos-Merino M, Gargantilla-Becerra Á, de la Cruz F, Nogales J. Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling. Front Microbiol 2023; 14:1126030. [PMID: 36998399 PMCID: PMC10043229 DOI: 10.3389/fmicb.2023.1126030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 03/15/2023] Open
Abstract
Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and β-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.
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Affiliation(s)
- María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, Santander, Cantabria, Spain
- *Correspondence: María Santos-Merino,
| | - Álvaro Gargantilla-Becerra
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, Santander, Cantabria, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Juan Nogales,
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Song Y, Hu Z, Xiong Z, Li S, Liu W, Tian T, Yang X. Comparative transcriptomic and lipidomic analyses indicate that cold stress enhanced the production of the long C18–C22 polyunsaturated fatty acids in Aurantiochytrium sp. Front Microbiol 2022; 13:915773. [PMID: 36204624 PMCID: PMC9530390 DOI: 10.3389/fmicb.2022.915773] [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: 04/08/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Aurantiochytrium sp. belonging to Thraustochytrids are known for their capacity to produce long-chain polyunsaturated fatty acids (PUFAs). However, effects of cold stress accompanied with staged-temperature control on the fatty acid metabolism in Aurantiochytrium sp. were rarely studied. In this study, cold stress (15°C, 5°C) was applied for Aurantiochytrium sp., with the physiological responses (morphology, growth, fatty acid profiling) and gene expression related FA synthesis, lipid metabolism, and regulatory processes was observed. Results showed that there is a significant change for the lipid types under 5°C (251 species) and 15°C (97 species) treatment. The 5°C treatment was benefit for the C18–C22 PUFAs with the yield of docosahexaenoic acid (DHA) increased to 1.25 times. After incubation at 15°C, the accumulation of eicosadienoic acid (EA) (20:2) was increased to 2.00-fold. Based on transcriptomic and qPCR analysis, an increase in genes involved in fatty acid synthase (FAS) and polyketide synthase (PKS) pathways was observed under low-temperature treatment. With upregulation of 3-ketoacyl-CoA synthase (2.44-fold), ketoreductase (2.50-fold), and dTDP-glucose 4,6-Dehydratase (rfbB) (2.31-fold) involved in PKS pathway, the accumulation of DHA was enhanced under 5°C. While, FAS and fatty elongase 3 (ELO) involved in the FAS pathway were upregulated (1.55-fold and 2.45-fold, respectively) to accumulate PUFAs at 15°C. Additionally, glycerol-3-phosphate acyltransferase (GPAT), lysophospholipid acyltransferase (LPAT), phosphatidic acid phosphatase (PAP), phosphatidylserine synthase (PSS), and phosphatidylserine decarboxylase (PSD) involved in glycerophospholipid biosynthesis were upregulated at 5°C increasing the accumulation of phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylinositol (PI). However, glycolysis and the TCA cycle were inhibited under 5°C. This study provides a contribution to the application of two-staged temperature control in the Aurantiochytrium sp. fermentation for producing cold stress-enhancing PUFAs, in order to better understand the function of the key genes for future genetic engineering.
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Affiliation(s)
- Yingjie Song
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zheng Xiong
- Shenzhen Institute of Modern Agricultural Equipment, Shenzhen, China
| | - Shuangfei Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Wei Liu
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tian Tian
- Shenzhen Institute of Modern Agricultural Equipment, Shenzhen, China
| | - Xuewei Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Xuewei Yang,
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Simkovsky R, Parnasa R, Wang J, Nagar E, Zecharia E, Suban S, Yegorov Y, Veltman B, Sendersky E, Schwarz R, Golden SS. Transcriptomic and Phenomic Investigations Reveal Elements in Biofilm Repression and Formation in the Cyanobacterium Synechococcus elongatus PCC 7942. Front Microbiol 2022; 13:899150. [PMID: 35814646 PMCID: PMC9260433 DOI: 10.3389/fmicb.2022.899150] [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: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Biofilm formation by photosynthetic organisms is a complex behavior that serves multiple functions in the environment. Biofilm formation in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is regulated in part by a set of small secreted proteins that promotes biofilm formation and a self-suppression mechanism that prevents their expression. Little is known about the regulatory and structural components of the biofilms in PCC 7942, or response to the suppressor signal(s). We performed transcriptomics (RNA-Seq) and phenomics (RB-TnSeq) screens that identified four genes involved in biofilm formation and regulation, more than 25 additional candidates that may impact biofilm formation, and revealed the transcriptomic adaptation to the biofilm state. In so doing, we compared the effectiveness of these two approaches for gene discovery.
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Affiliation(s)
- Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Rami Parnasa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jingtong Wang
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Zecharia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shiran Suban
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yevgeni Yegorov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Boris Veltman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Susan S Golden
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
- Center for Circadian Biology, University of California, San Diego, San Diego, CA, United States
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Chen Z, Wang Y, Huang R, Zhang Z, Huang J, Yu F, Lin Y, Guo Y, Liang K, Zhou Y, Chen F. Integration of transcriptomic and proteomic analyses reveals several levels of metabolic regulation in the excess starch and early senescent leaf mutant lses1 in rice. BMC PLANT BIOLOGY 2022; 22:137. [PMID: 35321646 PMCID: PMC8941791 DOI: 10.1186/s12870-022-03510-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The normal metabolism of transitory starch in leaves plays an important role in ensuring photosynthesis, delaying senescence and maintaining high yield in crops. OsCKI1 (casein kinase I1) plays crucial regulatory roles in multiple important physiological processes, including root development, hormonal signaling and low temperature-treatment adaptive growth in rice; however, its potential role in regulating temporary starch metabolism or premature leaf senescence remains unclear. To reveal the molecular regulatory mechanism of OsCKI1 in rice leaves, physiological, transcriptomic and proteomic analyses of leaves of osckI1 allele mutant lses1 (leaf starch excess and senescence 1) and its wild-type varieties (WT) were performed. RESULTS Phenotypic identification and physiological measurements showed that the lses1 mutant exhibited starch excess in the leaves and an obvious leaf tip withering phenotype as well as high ROS and MDA contents, low chlorophyll content and protective enzyme activities compared to WT. The correlation analyses between protein and mRNA abundance are weak or limited. However, the changes of several important genes related to carbohydrate metabolism and apoptosis at the mRNA and protein levels were consistent. The protein-protein interaction (PPI) network might play accessory roles in promoting premature senescence of lses1 leaves. Comprehensive transcriptomic and proteomic analysis indicated that multiple key genes/proteins related to starch and sugar metabolism, apoptosis and ABA signaling exhibited significant differential expression. Abnormal increase in temporary starch was highly correlated with the expression of starch biosynthesis-related genes, which might be the main factor that causes premature leaf senescence and changes in multiple metabolic levels in leaves of lses1. In addition, four proteins associated with ABA accumulation and signaling, and three CKI potential target proteins related to starch biosynthesis were up-regulated in the lses1 mutant, suggesting that LSES1 may affect temporary starch accumulation and premature leaf senescence through phosphorylation crosstalk ABA signaling and starch anabolic pathways. CONCLUSION The current study established the high correlation between the changes in physiological characteristics and mRNA and protein expression profiles in lses1 leaves, and emphasized the positive effect of excessive starch on accelerating premature leaf senescence. The expression patterns of genes/proteins related to starch biosynthesis and ABA signaling were analyzed via transcriptomes and proteomes, which provided a novel direction and research basis for the subsequent exploration of the regulation mechanism of temporary starch and apoptosis via LSES1/OsCKI1 in rice.
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Affiliation(s)
- Zhiming Chen
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongsheng Wang
- Postdoctoral Station of Biology, School of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Rongyu Huang
- School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Zesen Zhang
- School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Jinpeng Huang
- School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Feng Yu
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yaohai Lin
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuchun Guo
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Kangjing Liang
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuanchang Zhou
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Fangyu Chen
- Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Simkovsky R, Parnasa R, Wang J, Nagar E, Zecharia E, Suban S, Yegorov Y, Veltman B, Sendersky E, Schwarz R, Golden SS. Transcriptomic and Phenomic Investigations Reveal Elements in Biofilm Repression and Formation in the Cyanobacterium Synechococcus elongatus PCC 7942. Front Microbiol 2022; 13:899150. [PMID: 35814646 DOI: 10.1101/2022.01.27.477154] [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: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 05/20/2023] Open
Abstract
Biofilm formation by photosynthetic organisms is a complex behavior that serves multiple functions in the environment. Biofilm formation in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is regulated in part by a set of small secreted proteins that promotes biofilm formation and a self-suppression mechanism that prevents their expression. Little is known about the regulatory and structural components of the biofilms in PCC 7942, or response to the suppressor signal(s). We performed transcriptomics (RNA-Seq) and phenomics (RB-TnSeq) screens that identified four genes involved in biofilm formation and regulation, more than 25 additional candidates that may impact biofilm formation, and revealed the transcriptomic adaptation to the biofilm state. In so doing, we compared the effectiveness of these two approaches for gene discovery.
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Affiliation(s)
- Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Rami Parnasa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jingtong Wang
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Zecharia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shiran Suban
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yevgeni Yegorov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Boris Veltman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Susan S Golden
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
- Center for Circadian Biology, University of California, San Diego, San Diego, CA, United States
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9
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Zhou P, Wang L, Liu H, Li C, Li Z, Wang J, Tan X. CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. Nucleic Acids Res 2021; 50:D758-D764. [PMID: 34614159 PMCID: PMC8728175 DOI: 10.1093/nar/gkab891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/14/2022] Open
Abstract
With their photosynthetic ability and established genetic modification systems, cyanobacteria are essential for fundamental and biotechnological research. Till now, hundreds of cyanobacterial genomes have been sequenced, and transcriptomic analysis has been frequently applied in the functional genomics of cyanobacteria. However, the massive omics data have not been extensively mined and integrated. Here, we describe CyanoOmicsDB (http://www.cyanoomics.cn/), a database aiming to provide comprehensive functional information for each cyanobacterial gene. CyanoOmicsDB consists of 8 335 261 entries of cyanobacterial genes from 928 genomes. It provides multiple gene identifiers, visualized genomic location, and DNA sequences for each gene entry. For protein-encoding genes, CyanoOmicsDB can provide predicted gene function, amino acid sequences, homologs, protein-domain super-families, and accession numbers for various public protein function databases. CyanoOmicsDB integrates both transcriptional and translational profiles of Synechocystis sp. PCC 6803 under various environmental culture coditions and genetic backgrounds. Moreover, CyanoOmicsDB includes 23 689 gene transcriptional start sites, 94 644 identified peptides, and 16 778 post-translation modification sites obtained from transcriptomes or proteomes of several model cyanobacteria. Compared with other existing cyanobacterial databases, CyanoOmicsDB comprises more datasets and more comprehensive functional information. CyanoOmicsDB will provide researchers in this field with a convenient way to retrieve functional information on cyanobacterial genes.
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Affiliation(s)
- Peng Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan430062, China
| | - Li Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan430062, China
| | - Hai Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan430062, China
| | - Chunyan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan430062, China
| | - Zhimin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan430062, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang330045, China
| | - Jinxiang Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan430062, China
| | - Xiaoming Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan430062, China
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10
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Chávez MN, Fuchs B, Moellhoff N, Hofmann D, Zhang L, Selão TT, Giunta RE, Egaña JT, Nickelsen J, Schenck TL. Use of photosynthetic transgenic cyanobacteria to promote lymphangiogenesis in scaffolds for dermal regeneration. Acta Biomater 2021; 126:132-143. [PMID: 33753313 DOI: 10.1016/j.actbio.2021.03.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/28/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023]
Abstract
Impaired wound healing represents an unsolved medical need with a high impact on patients´ quality of life and global health care. Even though its causes are diverse, ischemic-hypoxic conditions and exacerbated inflammation are shared pathological features responsible for obstructing tissue restoration. In line with this, it has been suggested that promoting a normoxic pro-regenerative environment and accelerating inflammation resolution, by reinstating the lymphatic fluid transport, could allow the wound healing process to be resumed. Our group was first to demonstrate the functional use of scaffolds seeded with photosynthetic microorganisms to supply tissues with oxygen. Moreover, we previously proposed a photosynthetic gene therapy strategy to create scaffolds that deliver other therapeutic molecules, such as recombinant human growth factors into the wound area. In the present work, we introduce the use of transgenic Synechococcus sp. PCC 7002 cyanobacteria (SynHA), which can produce oxygen and lymphangiogenic hyaluronic acid, in photosynthetic biomaterials. We show that the co-culture of lymphatic endothelial cells with SynHA promotes their survival and proliferation under hypoxic conditions. Also, hyaluronic acid secreted by the cyanobacteria enhanced their lymphangiogenic potential as shown by changes to their gene expression profile, the presence of lymphangiogenic protein markers and their capacity to build lymph vessel tubes. Finally, by seeding SynHA into collagen-based dermal regeneration materials, we developed a viable photosynthetic scaffold that promotes lymphangiogenesis in vitro under hypoxic conditions. The results obtained in this study lay the groundwork for future tissue engineering applications using transgenic cyanobacteria that could become a therapeutic alternative for chronic wound treatment. STATEMENT OF SIGNIFICANCE: In this study, we introduce the use of transgenic Synechococcus sp. PCC 7002 (SynHA) cyanobacteria, which were genetically engineered to produce hyaluronic acid, to create lymphangiogenic photosynthetic scaffolds for dermal regeneration. Our results confirmed that SynHA cyanobacteria maintain their photosynthetic capacity under standard human cell culture conditions and efficiently proliferate when seeded inside fibrin-collagen scaffolds. Moreover, we show that SynHA supported the viability of co-cultured lymphatic endothelial cells (LECs) under hypoxic conditions by providing them with photosynthetic-derived oxygen, while cyanobacteria-derived hyaluronic acid stimulated the lymphangiogenic capacity of LECs. Since tissue hypoxia and impaired lymphatic drainage are two key factors that directly affect wound healing, our results suggest that lymphangiogenic photosynthetic biomaterials could become a treatment option for chronic wound management.
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Affiliation(s)
- Myra N Chávez
- Molecular Plant Science, Department Biology I, LMU Munich, Munich, Germany
| | - Benedikt Fuchs
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Munich, Germany
| | - Nicholas Moellhoff
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Munich, Germany
| | - Daniel Hofmann
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Munich, Germany
| | - Lifang Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Tiago Toscano Selão
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Riccardo E Giunta
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Munich, Germany
| | - José Tomás Egaña
- Institute for Biological and Medical Engineering, Schools of Engineering, Biological Sciences and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jörg Nickelsen
- Molecular Plant Science, Department Biology I, LMU Munich, Munich, Germany; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Thilo L Schenck
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Munich, Germany; Frauenklinik Dr. Geisenhofer, Munich, Germany.
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11
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Zhang H, Ge H, Zhang Y, Wang Y, Zhang P. Slr0320 Is Crucial for Optimal Function of Photosystem II during High Light Acclimation in Synechocystis sp. PCC 6803. Life (Basel) 2021; 11:life11040279. [PMID: 33810453 PMCID: PMC8065906 DOI: 10.3390/life11040279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
Upon exposure of photosynthetic organisms to high light (HL), several HL acclimation responses are triggered. Herein, we identified a novel gene, slr0320, critical for HL acclimation in Synechocystis sp. PCC 6803. The growth rate of the Δslr0320 mutant was similar to wild type (WT) under normal light (NL) but severely declined under HL. Net photosynthesis of the mutant was lower under HL, but maximum photosystem II (PSII) activity was higher under NL and HL. Immunodetection revealed the accumulation and assembly of PSII were similar between WT and the mutant. Chlorophyll fluorescence traces showed the stable fluorescence of the mutant under light was much higher. Kinetics of single flash-induced chlorophyll fluorescence increase and decay revealed the slower electron transfer from QA to QB in the mutant. These data indicate that, in the Δslr0320 mutant, the number of functional PSIIs was comparable to WT even under HL but the electron transfer between QA and QB was inefficient. Quantitative proteomics and real-time PCR revealed that expression profiles of psbL, psbH and psbI were significantly altered in the Δslr0320 mutant. Thus, Slr0320 protein plays critical roles in optimizing PSII activity during HL acclimation and is essential for PSII electron transfer from QA to QB.
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Affiliation(s)
- Hao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (Y.Z.)
| | - Haitao Ge
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.G.); (Y.W.)
| | - Ye Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (Y.Z.)
| | - Yingchun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.G.); (Y.W.)
| | - Pengpeng Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (Y.Z.)
- Correspondence:
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12
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Jiang Y, Liu Y, Zhang J. Mechanisms for the stimulatory effects of a five-component mixture of antibiotics in Microcystis aeruginosa at transcriptomic and proteomic levels. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124722. [PMID: 33296757 DOI: 10.1016/j.jhazmat.2020.124722] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/16/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Antibiotic contaminants could promote the formation of harmful cyanobacterial blooms through hormetic stimulation, but the mechanisms underlying these stimulatory effects remain unclear. This study investigated the biochemical, transcriptomic, and proteomic responses of a dominant bloom-forming cyanobacterium, Microcystis aeruginosa, to a five-component mixture of frequently detected antibiotics at current contamination levels. The growth rate of M. aeruginosa presented a U-shaped dose-response to 50-500 ng L-1 of mixed antibiotics. Alterations in the transcriptome of M. aeruginosa suggested the excitation of both photosynthesis and carbon metabolism, increasing energy generation in response to oxidative stress induced by low-dose antibiotics, and thus contributing to the significant (p < 0.05) increase in growth rate, Fv/Fm, and cell density. Comparison between transcriptomic and proteomic responses further confirmed the action mode of the mixed antibiotics. Proteins and their corresponding genes related to ROS scavenging, photosynthesis, carbon fixation, electron transport, oxidative phosphorylation, and biosynthesis, showed consistent expression tendencies in response to 200 ng L-1 of mixed antibiotics, which were credible action targets of mixed antibiotics in M. aeruginosa. Mixed antibiotics stimulated microcystin synthesis by upregulating a microcystin synthetase and its encoding gene (mcyC), which could increase the hazard of M. aeruginosa in aquatic environments.
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Affiliation(s)
- Yunhan Jiang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, PR China
| | - Ying Liu
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, PR China.
| | - Jian Zhang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, PR China
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13
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The Two TpsB-Like Proteins in Anabaena sp. Strain PCC 7120 Are Involved in Secretion of Selected Substrates. J Bacteriol 2021; 203:JB.00568-20. [PMID: 33257527 DOI: 10.1128/jb.00568-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/23/2020] [Indexed: 11/20/2022] Open
Abstract
The outer membrane of Gram-negative bacteria acts as an initial diffusion barrier that shields the cell from the environment. It contains many membrane-embedded proteins required for functionality of this system. These proteins serve as solute and lipid transporters or as machines for membrane insertion or secretion of proteins. The genome of Anabaena sp. strain PCC 7120 codes for two outer membrane transporters termed TpsB1 and TpsB2. They belong to the family of the two-partner secretion system proteins which are characteristic of pathogenic bacteria. Because pathogenicity of Anabaena sp. strain PCC 7120 has not been reported, the function of these two cyanobacterial TpsB proteins was analyzed. TpsB1 is encoded by alr1659, while TpsB2 is encoded by all5116 The latter is part of a genomic region containing 11 genes encoding TpsA-like proteins. However, tpsB2 is transcribed independently of a tpsA gene cluster. Bioinformatics analysis revealed the presence of at least 22 genes in Anabaena sp. strain PCC 7120 putatively coding for substrates of the TpsB system, suggesting a rather global function of the two TpsB proteins. Insertion of a plasmid into each of the two genes resulted in altered outer membrane integrity and antibiotic resistance. In addition, the expression of genes coding for the Clp and Deg proteases is dysregulated in these mutants. Moreover, for two of the putative substrates, a dependence of the secretion on functional TpsB proteins could be confirmed. We confirm the existence of a two-partner secretion system in Anabaena sp. strain PCC 7120 and predict a large pool of putative substrates.IMPORTANCE Cyanobacteria are important organisms for the ecosystem, considering their contribution to carbon fixation and oxygen production, while at the same time some species produce compounds that are toxic to their environment. As a consequence, cyanobacterial overpopulation might negatively impact the diversity of natural communities. Thus, a detailed understanding of cyanobacterial interaction with the environment, including other organisms, is required to define their impact on ecosystems. While two-partner secretion systems in pathogenic bacteria are well known, we provide a first description of the cyanobacterial two-partner secretion system.
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14
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Vijayakumar S, Rahman PK, Angione C. A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria. iScience 2020; 23:101818. [PMID: 33354660 PMCID: PMC7744713 DOI: 10.1016/j.isci.2020.101818] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 01/20/2023] Open
Abstract
Machine learning has recently emerged as a promising tool for inferring multi-omic relationships in biological systems. At the same time, genome-scale metabolic models (GSMMs) can be integrated with such multi-omic data to refine phenotypic predictions. In this work, we use a multi-omic machine learning pipeline to analyze a GSMM of Synechococcus sp. PCC 7002, a cyanobacterium with large potential to produce renewable biofuels. We use regularized flux balance analysis to observe flux response between conditions across photosynthesis and energy metabolism. We then incorporate principal-component analysis, k-means clustering, and LASSO regularization to reduce dimensionality and extract key cross-omic features. Our results suggest that combining metabolic modeling with machine learning elucidates mechanisms used by cyanobacteria to cope with fluctuations in light intensity and salinity that cannot be detected using transcriptomics alone. Furthermore, GSMMs introduce critical mechanistic details that improve the performance of omic-based machine learning methods.
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Affiliation(s)
- Supreeta Vijayakumar
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
| | - Pattanathu K.S.M. Rahman
- Centre for Enzyme Innovation, Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2UP, UK
- Tara Biologics, Woking, Surrey GU21 6BP, UK
| | - Claudio Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
- Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK
- Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK
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15
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Hu F, Clevenger AL, Zheng P, Huang Q, Wang Z. Low-temperature effects on docosahexaenoic acid biosynthesis in Schizochytrium sp. TIO01 and its proposed underlying mechanism. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:172. [PMID: 33088342 PMCID: PMC7565746 DOI: 10.1186/s13068-020-01811-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/06/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Schizochytrium species are known for their abundant production of docosahexaenoic acid (DHA). Low temperatures can promote the biosynthesis of polyunsaturated fatty acids (PUFAs) in many species. This study investigates low-temperature effects on DHA biosynthesis in Schizochytrium sp. TIO01 and its underlying mechanism. RESULTS The Schizochytrium fatty acid biosynthesis pathway was evaluated based on de novo genome assembly (contig N50 = 2.86 Mb) and iTRAQ-based protein identification. Our findings revealed that desaturases, involved in DHA synthesis via the fatty acid synthase (FAS) pathway, were completely absent. The polyketide synthase (PKS) pathway and the FAS pathway are, respectively, responsible for DHA and saturated fatty acid synthesis in Schizochytrium. Analysis of fatty acid composition profiles indicates that low temperature has a significant impact on the production of DHA in Schizochytrium, increasing the DHA content from 43 to 65% of total fatty acids. However, the expression levels of PKS pathway genes were not significantly regulated as the DHA content increased. Further, gene expression analysis showed that pathways related to the production of substrates (acetyl-CoA and NADPH) for fatty acid synthesis (the branched-chain amino acid degradation pathway and the pentose phosphate pathway) and genes related to saturated fatty acid biosynthesis (the FAS pathway genes and malic enzyme) were, respectively, upregulated and downregulated. These results indicate that low temperatures increase the DHA content by likely promoting the entry of relatively large amounts of substrates into the PKS pathway. CONCLUSIONS In this study, we provide genomic, proteomic, and transcriptomic evidence for the fatty acid synthesis pathway in Schizochytrium and propose a mechanism by which low temperatures promote the accumulation of DHA in Schizochytrium. The high-quality and nearly complete genome sequence of Schizochytrium provides a valuable reference for investigating the regulation of polyunsaturated fatty acid biosynthesis and the evolutionary characteristics of Thraustochytriidae species.
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Affiliation(s)
- Fan Hu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - April L. Clevenger
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK USA
| | - Peng Zheng
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065 China
| | - Qiongye Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Zhaokai Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
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16
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Luimstra VM, Schuurmans JM, Hellingwerf KJ, Matthijs HCP, Huisman J. Blue light induces major changes in the gene expression profile of the cyanobacterium Synechocystis sp. PCC 6803. PHYSIOLOGIA PLANTARUM 2020; 170:10-26. [PMID: 32141606 PMCID: PMC7496141 DOI: 10.1111/ppl.13086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 05/18/2023]
Abstract
Although cyanobacteria absorb blue light, they use it less efficiently for photosynthesis than other colors absorbed by their photosynthetic pigments. A plausible explanation for this enigmatic phenomenon is that blue light is not absorbed by phycobilisomes and, hence, causes an excitation shortage at photosystem II (PSII). This hypothesis is supported by recent physiological studies, but a comprehensive understanding of the underlying changes in gene expression is still lacking. In this study, we investigate how a switch from artificial white light to blue, orange or red light affects the transcriptome of the cyanobacterium Synechocystis sp. PCC 6803. In total, 145 genes were significantly regulated in response to blue light, whereas only a few genes responded to orange and red light. In particular, genes encoding the D1 and D2 proteins of PSII, the PSII chlorophyll-binding protein CP47 and genes involved in PSII repair were upregulated in blue light, whereas none of the photosystem I (PSI) genes responded to blue light. These changes were accompanied by a decreasing PSI:PSII ratio. Furthermore, many genes involved in gene transcription and translation and several ATP synthase genes were transiently downregulated, concurrent with a temporarily decreased growth rate in blue light. After 6-7 days, when cell densities had strongly declined, the growth rate recovered and the expression of these growth-related genes returned to initial levels. Hence, blue light induces major changes in the transcriptome of cyanobacteria, in an attempt to increase the photosynthetic activity of PSII and cope with the adverse growth conditions imposed by blue light.
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Affiliation(s)
- Veerle M. Luimstra
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Wetsus – Center of Excellence for Sustainable Water TechnologyLeeuwardenThe Netherlands
| | - J. Merijn Schuurmans
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Klaas J. Hellingwerf
- Swammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamThe Netherlands
| | - Hans C. P. Matthijs
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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17
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Babele PK, Kumar J, Chaturvedi V. Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses. Front Microbiol 2019; 10:1315. [PMID: 31263458 PMCID: PMC6584798 DOI: 10.3389/fmicb.2019.01315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs, exhibiting a cosmopolitan distribution in almost all possible environments and are significantly responsible for half of the global net primary productivity. They are well adapted to the diverse environments including harsh conditions by evolving a range of fascinating repertoires of unique biomolecules and secondary metabolites to support their growth and survival. These phototrophs are proved as excellent models for unraveling the mysteries of basic biochemical and physiological processes taking place in higher plants. Several known species of cyanobacteria have tremendous biotechnological applications in diverse fields such as biofuels, biopolymers, secondary metabolites and much more. Due to their potential biotechnological and commercial applications in various fields, there is an imperative need to engineer robust cyanobacteria in such a way that they can tolerate and acclimatize to ever-changing environmental conditions. Adaptations to stress are mainly governed by a precise gene regulation pathways resulting in the expression of novel protein/enzymes and metabolites. Despite the demand, till date few proteins/enzymes have been identified which play a potential role in improving tolerance against abiotic stresses. Therefore, it is utmost important to study environmental stress responses related to post-genomic investigations, including proteomic changes employing advanced proteomics, synthetic and structural biology workflows. In this respect, the study of stress proteomics offers exclusive advantages to scientists working on these aspects. Advancements on these fields could be helpful in dissecting, characterization and manipulation of physiological and metabolic systems of cyanobacteria to understand the stress induced proteomic responses. Till date, it remains ambiguous how cyanobacteria perceive changes in the ambient environment that lead to the stress-induced proteins thus metabolic deregulation. This review briefly describes the current major findings in the fields of proteome research on the cyanobacteria under various abiotic stresses. These findings may improve and advance the information on the role of different class of proteins associated with the mechanism(s) of stress mitigation in cyanobacteria under harsh environmental conditions.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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18
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Battchikova N, Muth-Pawlak D, Aro EM. Proteomics of cyanobacteria: current horizons. Curr Opin Biotechnol 2018; 54:65-71. [DOI: 10.1016/j.copbio.2018.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 12/01/2022]
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19
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Rangsrikitphoti P, Durnford DG. Transcriptome Profiling of Bigelowiella natans in Response to Light Stress. J Eukaryot Microbiol 2018; 66:316-333. [PMID: 30055063 DOI: 10.1111/jeu.12672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/17/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
Abstract
Bigelowiella natans is a marine chlorarachniophyte whose plastid was acquired secondarily via endosymbiosis with a green alga. During plastid evolution, the photosynthetic endosymbiont would have integrated with the host metabolic pathways. This would require the evolution and coordination of strategies to cope with changes in light intensity that includes changes in the expression of both endosymbiont and host-derived genes. To investigate the transcriptional response to light intensity in chlorarachniophytes, we conducted an RNA-seq experiment to identify differentially expressed genes following a 4-h shift to high or very-low light. A shift to high light altered the expression of over 2,000 genes, many involved with photosynthesis, PSII assembly, primary metabolism, and reactive-oxygen scavenging. These changes are an attempt to optimize photosynthesis and increase energy sinks for excess reductant, while minimizing photooxidative stress. A transfer to very-low light resulted in a lower photosynthetic performance and metabolic alteration, reflecting an energy-limited state. Genes located on the nucleomorph, the vestigial nucleus in the plastid, had few changes in expression in either light treatment, indicating this organelle has relinquished most transcriptional control to the nucleus. Overall, during plastid origin, both host and transferred endosymbiont genes evolved a harmonized transcriptional network to respond to a classic photosynthetic stress.
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Affiliation(s)
| | - Dion G Durnford
- Department of Biology, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
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Sun T, Li S, Song X, Diao J, Chen L, Zhang W. Toolboxes for cyanobacteria: Recent advances and future direction. Biotechnol Adv 2018; 36:1293-1307. [DOI: 10.1016/j.biotechadv.2018.04.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/09/2018] [Accepted: 04/26/2018] [Indexed: 12/20/2022]
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Peng Z, He S, Gong W, Xu F, Pan Z, Jia Y, Geng X, Du X. Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton. BMC PLANT BIOLOGY 2018; 18:128. [PMID: 29925319 PMCID: PMC6011603 DOI: 10.1186/s12870-018-1350-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/12/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes. RESULTS In the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels. However, we observed no significant change in mRNA corresponding to most of the strongly differentially abundant proteins. This finding may have resulted from global changes in alternative splicing events and miRNA levels under salt stress conditions. Evidence was provided indicating that several salt stress-responsive proteins can alter miRNAs and modulate alternative splicing events in upland cotton. The results of the stringent screening of the mRNA-seq and proteomic data between the salt-tolerant and salt-sensitive genotypes identified 63 and 85 candidate genes/proteins related to salt tolerance after 4 and 24 h of salt stress, respectively, between the tolerant and sensitive genotype. Finally, we predicted an interaction network comprising 158 genes/proteins and then discovered that two main clusters in the network were composed of ATP synthase (CotAD_74681) and cytochrome oxidase (CotAD_46197) in mitochondria. The results revealed that mitochondria, as important organelles involved in energy metabolism, play an essential role in the synthesis of resistance proteins during the process of salt exposure. CONCLUSION We provided a plausible schematic for the systematic salt tolerance model; this schematic reveals multiple levels of gene regulation in response to salt stress in cotton and provides a list of salt tolerance-related genes/proteins. The information here will facilitate candidate gene discovery and molecular marker development for salt tolerance breeding in cotton.
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Affiliation(s)
- Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Feifei Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Clark RL, McGinley LL, Purdy HM, Korosh TC, Reed JL, Root TW, Pfleger BF. Light-optimized growth of cyanobacterial cultures: Growth phases and productivity of biomass and secreted molecules in light-limited batch growth. Metab Eng 2018; 47:230-242. [PMID: 29601856 PMCID: PMC5984190 DOI: 10.1016/j.ymben.2018.03.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/23/2018] [Accepted: 03/25/2018] [Indexed: 11/22/2022]
Abstract
Cyanobacteria are photosynthetic microorganisms whose metabolism can be modified through genetic engineering for production of a wide variety of molecules directly from CO2, light, and nutrients. Diverse molecules have been produced in small quantities by engineered cyanobacteria to demonstrate the feasibility of photosynthetic biorefineries. Consequently, there is interest in engineering these microorganisms to increase titer and productivity to meet industrial metrics. Unfortunately, differing experimental conditions and cultivation techniques confound comparisons of strains and metabolic engineering strategies. In this work, we discuss the factors governing photoautotrophic growth and demonstrate nutritionally replete conditions in which a model cyanobacterium can be grown to stationary phase with light as the sole limiting substrate. We introduce a mathematical framework for understanding the dynamics of growth and product secretion in light-limited cyanobacterial cultures. Using this framework, we demonstrate how cyanobacterial growth in differing experimental systems can be easily scaled by the volumetric photon delivery rate using the model organisms Synechococcus sp. strain PCC7002 and Synechococcus elongatus strain UTEX2973. We use this framework to predict scaled up growth and product secretion in 1L photobioreactors of two strains of Synechococcus PCC7002 engineered for production of l-lactate or L-lysine. The analytical framework developed in this work serves as a guide for future metabolic engineering studies of cyanobacteria to allow better comparison of experiments performed in different experimental systems and to further investigate the dynamics of growth and product secretion.
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Affiliation(s)
- Ryan L Clark
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Laura L McGinley
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Hugh M Purdy
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Travis C Korosh
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States; Department of Environmental Chemistry and Technology, University of Wisconsin - Madison, 660 N Park St., Madison, WI 53706, United States.
| | - Jennifer L Reed
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Thatcher W Root
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
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Screening of miRNA profiles and construction of regulation networks in early and late lactation of dairy goat mammary glands. Sci Rep 2017; 7:11933. [PMID: 28931951 PMCID: PMC5607250 DOI: 10.1038/s41598-017-12297-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/06/2017] [Indexed: 01/12/2023] Open
Abstract
In recent years, studies related to the expression profiles of miRNAs in the dairy goat mammary gland were performed, but regulatory mechanisms in the physiological environment and the dynamic homeostasis of mammary gland development and lactation are not clear. In the present study, sequencing data analysis of early and late lactation uncovered a total of 1,487 unique miRNAs, including 45 novel miRNA candidates and 1,442 known and conserved miRNAs, of which 758 miRNAs were co-expressed and 378 differentially expressed with P < 0.05. Moreover, 76 non-redundant target genes were annotated in 347 GO consortiums, with 3,143 candidate target genes grouped into 33 pathways. Additionally, 18 predicted target genes of 214 miRNAs were directly annotated in mammary gland development and used to construct regulatory networks based on GO annotation and the KEGG pathway. The expression levels of seven known miRNAs and three novel miRNAs were examined using quantitative real-time PCR. The results showed that miRNAs might play important roles in early and late lactation during dairy goat mammary gland development, which will be helpful to obtain a better understanding of the genetic control of mammary gland lactation and development.
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Wu Y, Lou QY, Ge F, Xiong Q. Quantitative Proteomics Analysis Reveals Novel Targets of miR-21 in Zebrafish Embryos. Sci Rep 2017. [PMID: 28642470 PMCID: PMC5481331 DOI: 10.1038/s41598-017-04166-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are noncoding RNAs which control gene expression by the suppression of translation or the degradation of mRNAs. Dre-miR-21 (miR-21) has been reported to impact cardiac valvulogenesis in zebrafish embryos. However, the target genes of miR-21 are still largely unknown. Here a tandem isobaric mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-21-regulated proteins. A total of 251 proteins were dysregulated after miR-21 knockdown, suggesting that they may be regulated by miR-21. Bioinformatics analysis indicated that these differentially expressed proteins (DEPs) participate in various biological processes, suggesting that miR-21 may be involved in diverse cellular pathways. Sixteen DEPs were also predicted to be miR-21 targets by at least two algorithms, and several candidate target genes were selected for further luciferase reporter analysis. The results showed that genes encoding tropomyosin 1 (tpm1) and poly(rC) binding protein 2 (pcbp2) are direct miR-21 targets. Taken together, our results not only reveal a large number of novel miR-21 regulated proteins that possess pleiotropic functions, but also provide novel insights into the molecular mechanisms of miR-21 regulation of zebrafish cardiac valvulogenesis and embryonic development.
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Affiliation(s)
- Ying Wu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi-Yong Lou
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Zhao JY, Zhao XT, Sun JT, Zou LF, Yang SX, Han X, Zhu WC, Yin Q, Hong XY. Transcriptome and proteome analyses reveal complex mechanisms of reproductive diapause in the two-spotted spider mite, Tetranychus urticae. INSECT MOLECULAR BIOLOGY 2017; 26:215-232. [PMID: 28001328 DOI: 10.1111/imb.12286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Although a variety of factors underlying diapause have been identified in arthropods and other organisms, the molecular mechanisms regulating diapause are still largely unknown. Here, to better understand this process, we examined diapause-associated genes in the two-spotted spider mite, Tetranychus urticae, by comparing the transcriptomes and proteomes of early diapausing and reproductive adult females. Amongst genes underlying diapause revealed by the transcriptomic and proteomic data sets, we described the noticeable change in Ca2+ -associated genes, including 65 Ca2+ -binding protein genes and 23 Ca2+ transporter genes, indicating that Ca2+ signalling has a substantial role in diapause regulation. Other interesting changes in diapause included up-regulation of (1) glutamate receptors that may be involved in synaptic plasticity changes, (2) genes involved in cytoskeletal reorganization including genes encoding each of the components of thick and thin filaments, tubulin and members of integrin signalling and (3) genes involved in anaerobic energy metabolism, which reflects a shift to anaerobic energy metabolism in early diapausing mites.
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Affiliation(s)
- J-Y Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - X-T Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - J-T Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - L-F Zou
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - S-X Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - X Han
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - W-C Zhu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Q Yin
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - X-Y Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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Fesenko I, Seredina A, Arapidi G, Ptushenko V, Urban A, Butenko I, Kovalchuk S, Babalyan K, Knyazev A, Khazigaleeva R, Pushkova E, Anikanov N, Ivanov V, Govorun VM. The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation. FRONTIERS IN PLANT SCIENCE 2016; 7:1661. [PMID: 27867392 PMCID: PMC5095126 DOI: 10.3389/fpls.2016.01661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/21/2016] [Indexed: 05/29/2023]
Abstract
Plant protoplasts are widely used for genetic manipulation and functional studies in transient expression systems. However, little is known about the molecular pathways involved in a cell response to the combined stress factors resulted from protoplast generation. Plants often face more than one type of stress at a time, and how plants respond to combined stress factors is therefore of great interest. Here, we used protoplasts of the moss Physcomitrella patens as a model to study the effects of short-term stress on the chloroplast proteome. Using label-free comparative quantitative proteomic analysis (SWATH-MS), we quantified 479 chloroplast proteins, 219 of which showed a more than 1.4-fold change in abundance in protoplasts. We additionally quantified 1451 chloroplast proteins using emPAI. We observed degradation of a significant portion of the chloroplast proteome following the first hour of stress imposed by the protoplast isolation process. Electron-transport chain (ETC) components underwent the heaviest degradation, resulting in the decline of photosynthetic activity. We also compared the proteome changes to those in the transcriptional level of nuclear-encoded chloroplast genes. Globally, the levels of the quantified proteins and their corresponding mRNAs showed limited correlation. Genes involved in the biosynthesis of chlorophyll and components of the outer chloroplast membrane showed decreases in both transcript and protein abundance. However, proteins like dehydroascorbate reductase 1 and 2-cys peroxiredoxin B responsible for ROS detoxification increased in abundance. Further, genes such as thylakoid ascorbate peroxidase were induced at the transcriptional level but down-regulated at the proteomic level. Together, our results demonstrate that the initial chloroplast reaction to stress is due changes at the proteomic level.
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Affiliation(s)
- Igor Fesenko
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Anna Seredina
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Georgij Arapidi
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Vasily Ptushenko
- Department of Bioenergetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
- Department of Biocatalysis, Emanuel Institute of Biochemical Physics, Russian Academy of SciencesMoscow, Russia
| | - Anatoly Urban
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Ivan Butenko
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical MedicineMoscow, Russia
| | - Sergey Kovalchuk
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Konstantin Babalyan
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Andrey Knyazev
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Regina Khazigaleeva
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Elena Pushkova
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Nikolai Anikanov
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Vadim Ivanov
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Vadim M. Govorun
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical MedicineMoscow, Russia
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27
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Xiong Q, Chen Z, Ge F. Proteomic analysis of post translational modifications in cyanobacteria. J Proteomics 2016; 134:57-64. [DOI: 10.1016/j.jprot.2015.07.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/28/2015] [Accepted: 07/30/2015] [Indexed: 01/16/2023]
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28
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Zhou D, Yang Y, Zhang J, Jiang F, Craft E, Thannhauser TW, Kochian LV, Liu J. Quantitative iTRAQ Proteomics Revealed Possible Roles for Antioxidant Proteins in Sorghum Aluminum Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:2043. [PMID: 28119720 PMCID: PMC5220100 DOI: 10.3389/fpls.2016.02043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/21/2016] [Indexed: 05/19/2023]
Abstract
Aluminum (Al) toxicity inhibits root growth and limits crop yields on acid soils worldwide. However, quantitative information is scarce on protein expression profiles under Al stress in crops. In this study, we report on the identification of potential Al responsive proteins from root tips of Al sensitive BR007 and Al tolerant SC566 sorghum lines using a strategy employing iTRAQ and 2D-liquid chromatography (LC) coupled to MS/MS (2D-LC-MS/MS). A total of 771 and 329 unique proteins with abundance changes of >1.5 or <0.67-fold were identified in BR007 and SC566, respectively. Protein interaction and pathway analyses indicated that proteins involved in the antioxidant system were more abundant in the tolerant line than in the sensitive one after Al treatment, while opposite trends were observed for proteins involved in lignin biosynthesis. Higher levels of ROS accumulation in root tips of the sensitive line due to decreased activity of antioxidant enzymes could lead to higher lignin production and hyper-accumulation of toxic Al in cell walls. These results indicated that activities of peroxidases and the balance between production and consumption of ROS could be important for Al tolerance and lignin biosynthesis in sorghum.
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Affiliation(s)
- Dangwei Zhou
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
- Center of Plateau Ecology, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
| | - Jinbiao Zhang
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
- College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Fei Jiang
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
- Agricultural Biotechnology Center, Chengdu Institute of Biology, Chinese Academy of SciencesChengdu, China
| | - Eric Craft
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
| | - Theodore W. Thannhauser
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
| | - Leon V. Kochian
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
| | - Jiping Liu
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Cornell UniversityIthaca, NY, USA
- *Correspondence: Jiping Liu
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