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Danial AW, Abdel-Basset R, Abdel-Kader HAA. Tuning photosynthetic oxygen for hydrogen evolution in synergistically integrated, sulfur deprived consortia of Coccomyxa chodatii and Rhodobium gokarnense at dim and high light. PHOTOSYNTHESIS RESEARCH 2023; 155:203-218. [PMID: 36418759 PMCID: PMC9879849 DOI: 10.1007/s11120-022-00961-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
In this work, tuning oxygen tension was targeted to improve hydrogen evolution. To achieve such target, various consortia of the chlorophyte Coccomyxa chodatii with a newly isolated photosynthetic purple non-sulfur bacterium (PNSB) strain Rhodobium gokarnense were set up, sulfur replete/deprived, malate/acetate fed, bicarbonate/sulfur added at dim/high light. C. chodatii and R. gokarnense are newly introduced to biohydrogen studies for the first time. Dim light was applied to avoid the inhibitory drawbacks of photosynthetic oxygen evolution, values of hydrogen are comparable with high light or even more and thus economically feasible to eliminate the costs of artificial illumination. Particularly, the consortium of 2n- (n = 1.9 × 105 cell/ml, sulfur deprived) demonstrated its perfection for the target, i.e., the highest possible cumulative hydrogen. This consortium exhibited negative photosynthesis, i.e., oxygen uptake in the light. Most hydrogen in consortia is from bacterial origin, although algae evolved much more hydrogen than bacteria on per cell basis, but for only one day (the second 24 h), as kinetics revealed. The higher hydrogen in unibacterial culture or consortia results from higher bacterial cell density (20 times). Consortia evolved more hydrogen than their respective separate cultures, further enhanced when bicarbonate and sulfur were supplemented at higher light. The share of algae relatively increased as bicarbonate or sulfur were added at higher light intensity, i.e., PSII activity partially recovered, resulting in a transient autotrophic hydrogen evolution. The addition of acetic acid in mixture with malic acid significantly enhanced the cumulative hydrogen levels, mostly decreased cellular ascorbic acid indicating less oxidative stress and relief of PSII, relative to malic acid alone. Starch, however, decreased, indicating the specificity of acetic acid. Exudates (reducing sugars, amino acids, and soluble proteins) were detected, indicating mutual utilization. Yet, hydrogen evolution is limited; tuning PSII activity remains a target for sustainable hydrogen production.
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Affiliation(s)
- Amal W Danial
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - R Abdel-Basset
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, Egypt.
| | - Huwida A A Abdel-Kader
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut, Egypt
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2
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Liu P, Ye DM, Chen M, Zhang J, Huang XH, Shen LL, Xia KK, Xu XJ, Xu YC, Guo YL, Wang YC, Huang F. Scaling-up and proteomic analysis reveals photosynthetic and metabolic insights toward prolonged H 2 photoproduction in Chlamydomonas hpm91 mutant lacking proton gradient regulation 5 (PGR5). PHOTOSYNTHESIS RESEARCH 2022; 154:397-411. [PMID: 35974136 PMCID: PMC9722884 DOI: 10.1007/s11120-022-00945-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Clean and sustainable H2 production is crucial to a carbon-neutral world. H2 generation by Chlamydomonas reinhardtii is an attractive approach for solar-H2 from H2O. However, it is currently not large-scalable because of lacking desirable strains with both optimal H2 productivity and sufficient knowledge of underlying molecular mechanism. We hereby carried out extensive and in-depth investigations of H2 photoproduction of hpm91 mutant lacking PGR5 (Proton Gradient Regulation 5) toward its up-scaling and fundamental mechanism issues. We show that hpm91 is at least 100-fold scalable (up to 10 L) with continuous H2 collection of 7287 ml H2/10L-HPBR in averagely 26 days under sulfur deprivation. Also, we show that hpm91 is robust and active during sustained H2 photoproduction, most likely due to decreased intracellular ROS relative to wild type. Moreover, we obtained quantitative proteomic profiles of wild type and hpm91 at four representing time points of H2 evolution, leading to 2229 and 1350 differentially expressed proteins, respectively. Compared to wild type, major proteome alterations of hpm91 include not only core subunits of photosystems and those related to anti-oxidative responses but also essential proteins in photosynthetic antenna, C/N metabolic balance, and sulfur assimilation toward both cysteine biosynthesis and sulfation of metabolites during sulfur-deprived H2 production. These results reveal not only new insights of cellular and molecular basis of enhanced H2 production in hpm91 but also provide additional candidate gene targets and modules for further genetic modifications and/or in artificial photosynthesis mimics toward basic and applied research aiming at advancing solar-H2 technology.
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Affiliation(s)
- Peng Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Min Ye
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia-He Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li-Li Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke-Ke Xia
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiao-Jing Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ying-Chun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fang Huang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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3
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Sustainable Microalgae and Cyanobacteria Biotechnology. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Marine organisms are a valuable source of new compounds, many of which have remarkable biotechnological properties, such as microalgae and cyanobacteria, which have attracted special attention to develop new industrial production routes. These organisms are a source of many biologically active molecules in nature, including antioxidants, immunostimulants, antivirals, antibiotics, hemagglutinates, polyunsaturated fatty acids, peptides, proteins, biofuels, and pigments. The use of several technologies to improve biomass production, in the first step, industrial processes schemes have been addressed with different accomplishments. It is critical to consider all steps involved in producing a bioactive valuable compound, such as species and strain selection, nutrient supply required to support productivity, type of photobioreactor, downstream processes, namely extraction, recovery, and purification. In general, two product production schemes can be mentioned; one for large amounts of product, such as biodiesel or any other biofuel and the biomass for feeding purposes; the other for when the product will be used in the human health domain, such as antivirals, antibiotics, antioxidants, etc. Several applications for microalgae have been documented. In general, the usefulness of an application for each species of microalgae is determined by growth and product production. Furthermore, the use of OMICS technologies enabled the development of a new design for human therapeutic recombinant proteins, including strain selection based on previous proteomic profiles, gene cloning, and the development of expression networks. Microalgal expression systems have an advantage over traditional microbial, plant, and mammalian expression systems for new and sustainable microalga applications, for responsible production and consumption.
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4
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Carnovale G, Lama C, Torres S, Rosa F, Mantecón L, Horn SJ, Skjånes K, Infante C. Metabolic pathways for biosynthesis and degradation of starch in Tetraselmis chui during nitrogen deprivation and recovery. BIORESOURCE TECHNOLOGY 2022; 354:127222. [PMID: 35477101 DOI: 10.1016/j.biortech.2022.127222] [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: 02/24/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Tetraselmis chui is known to accumulate starch when subjected to stress. This phenomenon is widely studied for the purpose of industrial production and process development. Yet, knowledge about the metabolic pathways involved is still immature. Hence, in this study, transcription of 27 starch-related genes was monitored under nitrogen deprivation and resupply in 25 L tubular photobioreactors. T. chui proved to be an efficient starch producer under nitrogen deprivation, accumulating starch up to 56% of relative biomass content. The prolonged absence of nitrogen led to an overall down-regulation of the tested genes, in most instances maintained even after nitrogen replenishment when starch was actively degraded. These gene expression patterns suggest post-transcriptional regulatory mechanisms play a key role in T. chui under nutrient stress. Finally, the high productivity combined with an efficient recovery after nitrogen restitution makes this species a suitable candidate for industrial production of high-starch biomass.
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Affiliation(s)
- Giorgia Carnovale
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, PO 115, NO-1431 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Chemistry, Biotechnology and Food Science, P.O. Box 5003, NO-1432 Ås, Norway
| | - Carmen Lama
- Fitoplancton Marino, S.L., Dársena comercial s/n (Muelle pesquero), 11500 El Puerto de Santa María, Cádiz, Spain
| | - Sonia Torres
- Fitoplancton Marino, S.L., Dársena comercial s/n (Muelle pesquero), 11500 El Puerto de Santa María, Cádiz, Spain
| | - Filipa Rosa
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, PO 115, NO-1431 Ås, Norway
| | - Lalia Mantecón
- Fitoplancton Marino, S.L., Dársena comercial s/n (Muelle pesquero), 11500 El Puerto de Santa María, Cádiz, Spain
| | - Svein Jarle Horn
- Norwegian University of Life Sciences (NMBU), Faculty of Chemistry, Biotechnology and Food Science, P.O. Box 5003, NO-1432 Ås, Norway
| | - Kari Skjånes
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, PO 115, NO-1431 Ås, Norway.
| | - Carlos Infante
- Fitoplancton Marino, S.L., Dársena comercial s/n (Muelle pesquero), 11500 El Puerto de Santa María, Cádiz, Spain
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5
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Grama SB, Liu Z, Li J. Emerging Trends in Genetic Engineering of Microalgae for Commercial Applications. Mar Drugs 2022; 20:285. [PMID: 35621936 PMCID: PMC9143385 DOI: 10.3390/md20050285] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
Recently, microalgal biotechnology has received increasing interests in producing valuable, sustainable and environmentally friendly bioproducts. The development of economically viable production processes entails resolving certain limitations of microalgal biotechnology, and fast evolving genetic engineering technologies have emerged as new tools to overcome these limitations. This review provides a synopsis of recent progress, current trends and emerging approaches of genetic engineering of microalgae for commercial applications, including production of pharmaceutical protein, lipid, carotenoids and biohydrogen, etc. Photochemistry improvement in microalgae and CO2 sequestration by microalgae via genetic engineering were also discussed since these subjects are closely entangled with commercial production of the above mentioned products. Although genetic engineering of microalgae is proved to be very effective in boosting performance of production in laboratory conditions, only limited success was achieved to be applicable to industry so far. With genetic engineering technologies advancing rapidly and intensive investigations going on, more bioproducts are expected to be produced by genetically modified microalgae and even much more to be prospected.
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Affiliation(s)
- Samir B. Grama
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, University of Oum El Bouaghi, Oum El Bouaghi 04000, Algeria;
| | - Zhiyuan Liu
- College of Marine Sciences, Hainan University, Haikou 570228, China;
| | - Jian Li
- College of Agricultural Sciences, Panzhihua University, Panzhihua 617000, China
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6
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Damoo DY, Durnford DG. Long-term survival of Chlamydomonas reinhardtii during conditional senescence. Arch Microbiol 2021; 203:5333-5344. [PMID: 34383108 DOI: 10.1007/s00203-021-02508-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/22/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022]
Abstract
Chlamydomonas reinhardtii undergoes conditional senescence when grown in batch culture due to nutrient limitation. Here, we explored plastid and photo-physiological adaptations in Chlamydomonas reinhardtii during a long-term ageing experiment by methodically sampling them over 22 weeks. Following exponential growth, Chlamydomonas entered an extended declining growth phase where cells continued to divide, although at a lower rate. Ultimately, this ongoing division was fueled by the recycling of macromolecules that was obvious in the rapidly declining protein and chlorophyll content in the cell during this phase. This process was sufficient to maintain a high level of cell viability as the culture entered stationary phase. Beyond that the cell viability starts to plummet. During the turnover of macromolecules after exponential growth that saw RuBisCO levels drop, the LHCII antenna was relatively stable. This, along with the upregulation of the light stress-related proteins (LHCSR), contributes to an efficient energy dissipation mechanism to protect the ageing cells from photooxidative stress during the senescence process. Ultimately, viability dropped to about 7% at 22 weeks in a batch culture. We anticipate that this research will help further understand the various acclimation strategies carried out by Chlamydomonas to maximize survival under conditional senescence.
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Affiliation(s)
- Djihane Yushrina Damoo
- Department of Biology, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada.,Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Dion G Durnford
- Department of Biology, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada.
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7
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8
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Petrova EV, Kukarskikh GP, Krendeleva TE, Antal TK. The Mechanisms and Role of Photosynthetic Hydrogen Production by Green Microalgae. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Transcriptomic analysis of hydrogen photoproduction in Chlorella pyrenoidosa under nitrogen deprivation. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101827] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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10
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Ran W, Wang H, Liu Y, Qi M, Xiang Q, Yao C, Zhang Y, Lan X. Storage of starch and lipids in microalgae: Biosynthesis and manipulation by nutrients. BIORESOURCE TECHNOLOGY 2019; 291:121894. [PMID: 31387839 DOI: 10.1016/j.biortech.2019.121894] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 05/28/2023]
Abstract
Microalgae accumulate starch and lipid as storage metabolites under nutrient depletion, which can be used as sustainable feedstock for biorefinery. Omics analysis coupled with enzymatic and genetic verifications uncovered a partial picture of pathways and important enzymes or regulators related to starch and lipid biosynthesis as well as the carbon partitioning between them under nutrient depletion conditions. Depletion of macronutrients (N, P, and S) resulted in considerable enhancement of starch and/or lipid content in microalgae, but the accompanying declined photosynthesis hampered the achievements of high concentrations. This review summarized the current knowledge on the pathways and the committed steps as well as their carbon allocation involved in starch and lipid biosynthesis, and focused on the manipulation of different nutrients and the alleviation of oxidative stress for enhanced storage metabolites production. The biological and engineering approaches to cope with the conflict between biomass production and storage metabolites accumulation are proposed.
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Affiliation(s)
- Wenyi Ran
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Haitao Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning 116034, China
| | - Yinghui Liu
- Information Management Center of Sichuan University, Chengdu, Sichuan 610065, China
| | - Man Qi
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qi Xiang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Changhong Yao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Yongkui Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xianqiu Lan
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China
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11
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Góra-Sochacka A, Więsyk A, Fogtman A, Lirski M, Zagórski-Ostoja W. Root Transcriptomic Analysis Reveals Global Changes Induced by Systemic Infection of Solanum lycopersicum with Mild and Severe Variants of Potato Spindle Tuber Viroid. Viruses 2019; 11:v11110992. [PMID: 31671783 PMCID: PMC6893655 DOI: 10.3390/v11110992] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 12/11/2022] Open
Abstract
Potato spindle tuber viroid (PSTVd) causes systemic infection in plant hosts. There are many studies on viroid-host plant interactions, but they have predominantly focused on the aboveground part of the plant. Here, we investigated transcriptomic profile changes in tomato roots systemically infected with mild or severe PSTVd variants using a combined microarray/RNA-seq approach. Analysis indicated differential expression of genes related to various Gene Ontology categories depending on the stage of infection and PSTVd variant. A majority of cell-wall-related genes were down-regulated at early infection stages, but at the late stage, the number of up-regulated genes increased significantly. Along with observed alterations of many lignin-related genes, performed lignin quantification indicated their disrupted level in PSTVd-infected roots. Altered expression of genes related to biosynthesis and signaling of auxin and cytokinin, which are crucial for lateral root development, was also identified. Comparison of both PSTVd infections showed that transcriptional changes induced by the severe variant were stronger than those caused by the mild variant, especially at the late infection stage. Taken together, we showed that similarly to aboveground plant parts, PSTVd infection in the underground tissues activates the plant immune response.
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Affiliation(s)
- Anna Góra-Sochacka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
| | - Aneta Więsyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
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12
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Xu L, Fan J, Wang Q. Omics Application of Bio-Hydrogen Production Through Green Alga Chlamydomonas reinhardtii. Front Bioeng Biotechnol 2019; 7:201. [PMID: 31497598 PMCID: PMC6712067 DOI: 10.3389/fbioe.2019.00201] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022] Open
Abstract
This article summarizes the current knowledge regarding omics approaches, which include genomics, transcriptomics, proteomics and metabolomics, in the context of bio-hydrogen production in Chlamydomonas reinhardtii. In this paper, critical genes (HydA1, Hyd A2, Sulp, Tla1, Sta7, PFL1) involved in H2 metabolism were identified and analyzed for their function in H2 accumulation. Furthermore, the advantages of gene microarrays and RNA-seq were compared, as well as their applications in transcriptomic analysis of H2 production. Moreover, as a useful tool, proteomic analysis could identify different proteins that participate in H2 metabolism. This review provides fundamental theory and an experimental basis for H2 production, and further research effort is needed in this field.
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Affiliation(s)
- Lili Xu
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jianhua Fan
- State Key Laboratory of South China Sea Marine Resource Utilization, Hainan University, Haikou, China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Quanxi Wang
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, China
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13
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Wirth R, Lakatos G, Böjti T, Maróti G, Bagi Z, Rákhely G, Kovács KL. Anaerobic gaseous biofuel production using microalgal biomass – A review. Anaerobe 2018; 52:1-8. [DOI: 10.1016/j.anaerobe.2018.05.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 12/17/2022]
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14
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Nagy V, Vidal-Meireles A, Podmaniczki A, Szentmihályi K, Rákhely G, Zsigmond L, Kovács L, Tóth SZ. The mechanism of photosystem-II inactivation during sulphur deprivation-induced H 2 production in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:548-561. [PMID: 29474754 DOI: 10.1111/tpj.13878] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/29/2018] [Accepted: 02/05/2018] [Indexed: 05/11/2023]
Abstract
Sulphur limitation may restrain cell growth and viability. In the green alga Chlamydomonas reinhardtii, sulphur limitation may induce H2 production lasting for several days, which can be exploited as a renewable energy source. Sulphur limitation causes a large number of physiological changes, including the inactivation of photosystem II (PSII), leading to the establishment of hypoxia, essential for the increase in hydrogenase expression and activity. The inactivation of PSII has long been assumed to be caused by the sulphur-limited turnover of its reaction center protein PsbA. Here we reinvestigated this issue in detail and show that: (i) upon transferring Chlamydomonas cells to sulphur-free media, the cellular sulphur content decreases only by about 25%; (ii) as demonstrated by lincomycin treatments, PsbA has a significant turnover, and other photosynthetic subunits, namely RbcL and CP43, are degraded more rapidly than PsbA. On the other hand, sulphur limitation imposes oxidative stress early on, most probably involving the formation of singlet oxygen in PSII, which leads to an increase in the expression of GDP-L-galactose phosphorylase, playing an essential role in ascorbate biosynthesis. When accumulated to the millimolar concentration range, ascorbate may inactivate the oxygen-evolving complex and provide electrons to PSII, albeit at a low rate. In the absence of a functional donor side and sufficient electron transport, PSII reaction centers are inactivated and degraded. We therefore demonstrate that the inactivation of PSII is a complex and multistep process, which may serve to mitigate the damaging effects of sulphur limitation.
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Affiliation(s)
- Valéria Nagy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - André Vidal-Meireles
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Anna Podmaniczki
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Klára Szentmihályi
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Laura Zsigmond
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - László Kovács
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Szilvia Z Tóth
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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15
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Xing J, Liu P, Zhao L, Huang F. Deletion of CGLD1 Impairs PSII and Increases Singlet Oxygen Tolerance of Green Alga Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2017; 8:2154. [PMID: 29326747 PMCID: PMC5736878 DOI: 10.3389/fpls.2017.02154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/05/2017] [Indexed: 05/24/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a key model organism for studying photosynthesis and oxidative stress in unicellular eukaryotes. Using a forward genetics approach, we have identified and characterized a mutant x32, which lacks a predicted protein named CGLD1 (Conserved in Green Lineage and Diatom 1) in GreenCut2, under normal and stress conditions. We show that loss of CGLD1 resulted in minimal photoautotrophic growth and PSII activity in the organism. We observed reduced amount of PSII complex and core subunits in the x32 mutant based on blue-native (BN)/PAGE and immunoblot analysis. Moreover, x32 exhibited increased sensitivity to high-light stress and altered tolerance to different reactive oxygenic species (ROS) stress treatments, i.e., decreased resistance to H2O2/or tert-Butyl hydroperoxide (t-BOOH) and increased tolerance to neutral red (NR) and rose bengal (RB) that induce the formation of singlet oxygen, respectively. Further analysis via quantitative real-time PCR (qRT-PCR) indicated that the increased singlet-oxygen tolerance of x32 was largely correlated with up-regulated gene expression of glutathione-S-transferases (GST). The phenotypical and physiological implications revealed from our experiments highlight the important roles of CGLD1 in maintaining structure and function of PSII as well as in protection of Chlamydomonas under photo-oxidative stress conditions.
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Affiliation(s)
- Jiale Xing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Zhao
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fang Huang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Scoma A, Hemschemeier A. The hydrogen metabolism of sulfur deprived Chlamydomonas reinhardtii cells involves hydrogen uptake activities. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Volgusheva AA, Jokel M, Allahverdiyeva Y, Kukarskikh GP, Lukashev EP, Lambreva MD, Krendeleva TE, Antal TK. Comparative analyses of H 2 photoproduction in magnesium- and sulfur-starved Chlamydomonas reinhardtii cultures. PHYSIOLOGIA PLANTARUM 2017; 161:124-137. [PMID: 28386962 DOI: 10.1111/ppl.12576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/09/2017] [Accepted: 02/27/2017] [Indexed: 05/27/2023]
Abstract
Magnesium (Mg)-deprived Chlamydomonas reinhardtii cells are capable to sustain hydrogen (H2 ) photoproduction at relatively high photosystem II (PSII) activity levels for an extended time period as compared with sulfur (S)-deprived cells. Herein, we present a comparative study of H2 photoproduction induced by Mg and S shortage to unravel the specific rearrangements of the photosynthetic machinery and cell metabolism occurring under the two deprivation protocols. The exhaustive analysis of photosynthetic activity and regulatory pathways, respiration and starch metabolism revealed the specific rearrangements of the photosynthetic machinery and cellular metabolism, which occur under the two deprivation conditions. The obtained results allowed us to conclude that the expanded time period of H2 production upon Mg-deprivation is due to the less harmful effects that Mg-depletion has on viability and metabolic performance of the cells. Unlike S-deprivation, the photosynthetic light and dark reactions in Mg-deprived cells remained active over the whole H2 production period. However, the elevated PSII activity in Mg-deprived cells was counteracted by the operation of pathways for O2 consumption that maintain anaerobic conditions in the presence of active water splitting.
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Affiliation(s)
- Alena A Volgusheva
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Martina Jokel
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, FI-20014, Finland
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, FI-20014, Finland
| | - Galina P Kukarskikh
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugeni P Lukashev
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maya D Lambreva
- Institute of Crystallography, National Research Council of Italy, Rome, Italy
| | - Tatayana E Krendeleva
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Taras K Antal
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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18
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Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O. Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:197. [PMID: 28814974 PMCID: PMC5556983 DOI: 10.1186/s13068-017-0882-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/03/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering. RESULTS An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum. Transcript data were correlated with metabolic data for cellular contents of starch and of different lipid fractions. A pronounced transcriptional down-regulation of photosynthesis became apparent in response to nitrogen starvation, whereas glucose catabolism was found to be up-regulated. An in-depth reconstruction and analysis of the pathways for glycerolipid, central carbon, and starch metabolism revealed that distinct transcriptional changes were generally found only for specific steps within a metabolic pathway. In addition to pathway analyses, the transcript data were also used to refine the current genome annotation. The transcriptome data were integrated into a database and complemented with data for other microalgae which were also subjected to nitrogen starvation. It is available at https://tdbmn.cebitec.uni-bielefeld.de. CONCLUSIONS Based on the transcriptional responses to different stages of nitrogen availability, a model for triacylglycerol and lipid hyperaccumulation is proposed, which involves transcriptional induction of thioesterases, differential regulation of lipases, and a re-routing of the central carbon metabolism. Over-expression of distinct thioesterases was identified to be a potential strategy to increase the oleaginous phenotype of M. neglectum, and furthermore specific lipases were identified as potential targets for future metabolic engineering approaches.
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Affiliation(s)
- Daniel Jaeger
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Jan H. Mussgnug
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, 35392 Gießen, Germany
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 27, 33615 Bielefeld, Germany
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Banerjee A, Banerjee C, Negi S, Chang JS, Shukla P. Improvements in algal lipid production: a systems biology and gene editing approach. Crit Rev Biotechnol 2017; 38:369-385. [DOI: 10.1080/07388551.2017.1356803] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Avik Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | - Chiranjib Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | | | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Pratyoosh Shukla
- Department of Microbiology, Enzyme Technology and Protein Bioinformatics Laboratory, Maharshi Dayanand University, Rohtak, India
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20
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Venkanna D, Südfeld C, Baier T, Homburg SV, Patel AV, Wobbe L, Kruse O. Knock-Down of the IFR1 Protein Perturbs the Homeostasis of Reactive Electrophile Species and Boosts Photosynthetic Hydrogen Production in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2017; 8:1347. [PMID: 28824682 PMCID: PMC5540887 DOI: 10.3389/fpls.2017.01347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/19/2017] [Indexed: 05/26/2023]
Abstract
The protein superfamily of short-chain dehydrogenases/reductases (SDR), including members of the atypical type (aSDR), covers a huge range of catalyzed reactions and in vivo substrates. This superfamily also comprises isoflavone reductase-like (IRL) proteins, which are aSDRs highly homologous to isoflavone reductases from leguminous plants. The molecular function of IRLs in non-leguminous plants and green microalgae has not been identified as yet, but several lines of evidence point at their implication in reactive oxygen species homeostasis. The Chlamydomonas reinhardtii IRL protein IFR1 was identified in a previous study, analyzing the transcriptomic changes occurring during the acclimation to sulfur deprivation and anaerobiosis, a condition that triggers photobiological hydrogen production in this microalgae. Accumulation of the cytosolic IFR1 protein is induced by sulfur limitation as well as by the exposure of C. reinhardtii cells to reactive electrophile species (RES) such as reactive carbonyls. The latter has not been described for IRL proteins before. Over-accumulation of IFR1 in the singlet oxygen response 1 (sor1) mutant together with the presence of an electrophile response element, known to be required for SOR1-dependent gene activation as a response to RES, in the promoter of IFR1, indicate that IFR1 expression is controlled by the SOR1-dependent pathway. An implication of IFR1 into RES homeostasis, is further implied by a knock-down of IFR1, which results in a diminished tolerance toward RES. Intriguingly, IFR1 knock-down has a positive effect on photosystem II (PSII) stability under sulfur-deprived conditions used to trigger photobiological hydrogen production, by reducing PSII-dependent oxygen evolution, in C. reinhardtii. Reduced PSII photoinhibition in IFR1 knock-down strains prolongs the hydrogen production phase resulting in an almost doubled final hydrogen yield compared to the parental strain. Finally, IFR1 knock-down could be successfully used to further increase hydrogen yields of the high hydrogen-producing mutant stm6, demonstrating that IFR1 is a promising target for genetic engineering approaches aiming at an increased hydrogen production capacity of C. reinhardtii cells.
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Affiliation(s)
- Deepak Venkanna
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Christian Südfeld
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Thomas Baier
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Sarah V. Homburg
- Faculty of Engineering and Mathematics, Fermentation and Formulation of Biologicals and Chemicals, Bielefeld University of Applied SciencesBielefeld, Germany
| | - Anant V. Patel
- Faculty of Engineering and Mathematics, Fermentation and Formulation of Biologicals and Chemicals, Bielefeld University of Applied SciencesBielefeld, Germany
| | - Lutz Wobbe
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
| | - Olaf Kruse
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld UniversityBielefeld, Germany
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Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S. Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:387-99. [DOI: 10.1089/omi.2016.0065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Debasish Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
| | - Santosh Noronha
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P. Wangikar
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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22
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Nagy V, Vidal-Meireles A, Tengölics R, Rákhely G, Garab G, Kovács L, Tóth SZ. Ascorbate accumulation during sulphur deprivation and its effects on photosystem II activity and H2 production of the green alga Chlamydomonas reinhardtii. PLANT, CELL & ENVIRONMENT 2016; 39:1460-72. [PMID: 26714836 DOI: 10.1111/pce.12701] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/25/2015] [Accepted: 12/18/2015] [Indexed: 05/10/2023]
Abstract
In nature, H2 production in Chlamydomonas reinhardtii serves as a safety valve during the induction of photosynthesis in anoxia, and it prevents the over-reduction of the photosynthetic electron transport chain. Sulphur deprivation of C. reinhardtii also triggers a complex metabolic response resulting in the induction of various stress-related genes, down-regulation of photosynthesis, the establishment of anaerobiosis and expression of active hydrogenase. Photosystem II (PSII) plays dual role in H2 production because it supplies electrons but the evolved O2 inhibits the hydrogenase. Here, we show that upon sulphur deprivation, the ascorbate content in C. reinhardtii increases about 50-fold, reaching the mM range; at this concentration, ascorbate inactivates the Mn-cluster of PSII, and afterwards, it can donate electrons to tyrozin Z(+) at a slow rate. This stage is followed by donor-side-induced photoinhibition, leading to the loss of charge separation activity in PSII and reaction centre degradation. The time point at which maximum ascorbate concentration is reached in the cell is critical for the establishment of anaerobiosis and initiation of H2 production. We also show that ascorbate influenced H2 evolution via altering the photosynthetic electron transport rather than hydrogenase activity and starch degradation.
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Affiliation(s)
- Valéria Nagy
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - André Vidal-Meireles
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Roland Tengölics
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Győző Garab
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - László Kovács
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Szilvia Z Tóth
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári krt. 62, H-6726, Szeged, Hungary
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23
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Luesse DR, Wilson ME, Haswell ES. RNA Sequencing Analysis of the msl2msl3, crl, and ggps1 Mutants Indicates that Diverse Sources of Plastid Dysfunction Do Not Alter Leaf Morphology Through a Common Signaling Pathway. FRONTIERS IN PLANT SCIENCE 2015; 6:1148. [PMID: 26734046 PMCID: PMC4686620 DOI: 10.3389/fpls.2015.01148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/02/2015] [Indexed: 05/20/2023]
Abstract
Determining whether individual genes function in the same or in different pathways is an important aspect of genetic analysis. As an alternative to the construction of higher-order mutants, we used contemporary expression profiling methods to perform pathway analysis on several Arabidopsis thaliana mutants, including the mscS-like (msl)2msl3 double mutant. MSL2 and MSL3 are implicated in plastid ion homeostasis, and msl2msl3 double mutants exhibit leaves with a lobed periphery, a rumpled surface, and disturbed mesophyll cell organization. Similar developmental phenotypes are also observed in other mutants with defects in a range of other chloroplast or mitochondrial functions, including biogenesis, gene expression, and metabolism. We wished to test the hypothesis that the common leaf morphology phenotypes of these mutants are the result of a characteristic nuclear expression pattern that is generated in response to organelle dysfunction. RNA-Sequencing was performed on aerial tissue of msl2msl3 geranylgeranyl diphosphate synthase 1 (ggps1), and crumpled leaf (crl) mutants. While large groups of co-expressed genes were identified in pairwise comparisons between genotypes, we were only able to identify a small set of genes that showed similar expression profiles in all three genotypes. Subsequent comparison to the previously published gene expression profiles of two other mutants, yellow variegated 2 (var2) and scabra3 (sca3), failed to reveal a common pattern of gene expression associated with superficially similar leaf morphology defects. Nor did we observe overlap between genes differentially expressed in msl2msl3, crl, and ggps1 and a previously identified retrograde core response module. These data suggest that a common retrograde signaling pathway initiated by organelle dysfunction either does not exist in these mutants or cannot be identified through transcriptomic methods. Instead, the leaf developmental defects observed in these mutants may be achieved through a number of independent pathways.
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Affiliation(s)
- Darron R. Luesse
- Department of Biological Sciences, Southern Illinois University EdwardsvilleEdwardsville, IL, USA
| | - Margaret E. Wilson
- Department of Biology, Washington University in Saint LouisSaint Louis, MO, USA
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Gonzalez-Ballester D, Jurado-Oller JL, Fernandez E. Relevance of nutrient media composition for hydrogen production in Chlamydomonas. PHOTOSYNTHESIS RESEARCH 2015; 125:395-406. [PMID: 25952745 DOI: 10.1007/s11120-015-0152-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 04/29/2015] [Indexed: 05/23/2023]
Abstract
Microalgae are capable of biological H2 photoproduction from water, solar energy, and a variety of organic substrates. Acclimation responses to different nutrient regimes finely control photosynthetic activity and can influence H2 production. Hence, nutrient stresses are an interesting scenario to study H2 production in photosynthetic organisms. In this review, we mainly focus on the H2-production mechanisms in Chlamydomonas reinhardtii and the physiological relevance of the nutrient media composition when producing H2.
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Affiliation(s)
- David Gonzalez-Ballester
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Edif. Severo Ochoa, 14071, Córdoba, Spain,
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25
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Guarnieri MT, Pienkos PT. Algal omics: unlocking bioproduct diversity in algae cell factories. PHOTOSYNTHESIS RESEARCH 2015; 123:255-63. [PMID: 24627032 DOI: 10.1007/s11120-014-9989-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/17/2014] [Indexed: 05/10/2023]
Abstract
Rapid advances in "omic" technologies are helping to unlock the full potential of microalgae as multi-use feedstocks, with utility in an array of industrial biotechnology, biofuel, and biomedical applications. In turn, algae are emerging as highly attractive candidates for development as microbial cell factories. In this review, we examine the wide array of potential algal bioproducts, with a focus upon the role of omic technologies in driving bioproduct discovery and optimization in microalgal systems.
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Affiliation(s)
- Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, MS 3323, Golden, CO, 80401, USA,
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26
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Weber J, Krujatz F, Hilpmann G, Grützner S, Herrmann J, Thierfelder S, Bienert G, Illing R, Helbig K, Hurtado A, Cuniberti G, Mertig M, Lange R, Günther E, Opitz J, Lippmann W, Bley T, Haufe N. Biotechnological hydrogen production by photosynthesis. Eng Life Sci 2014. [DOI: 10.1002/elsc.201400056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jost Weber
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Felix Krujatz
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Gerd Hilpmann
- Chair of Chemical Engineering and Process Plants; Technische Universität Dresden; Dresden Germany
| | - Sara Grützner
- Institute of Power Engineering; Chair of Hydrogen and Nuclear Energy, Technische Universität Dresden; Dresden Germany
| | - Jana Herrmann
- Chair of Environmental Management and Accounting; Technische Universität Dresden; Dresden Germany
| | - Simone Thierfelder
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Georg Bienert
- Chair of Environmental Management and Accounting; Technische Universität Dresden; Dresden Germany
| | - Rico Illing
- Chair of Materials Science and Nanotechnology; Technische Universität Dresden; Dresden Germany
| | - Karsten Helbig
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Antonio Hurtado
- Institute of Power Engineering; Chair of Hydrogen and Nuclear Energy, Technische Universität Dresden; Dresden Germany
| | - Gianaurelio Cuniberti
- Chair of Materials Science and Nanotechnology; Technische Universität Dresden; Dresden Germany
- Institute for Material Science and Max Bergmann Center of Biomaterials; Technische Universität Dresden; Dresden Germany
- Center for Advancing Electronics; Technische Universität Dresden; Dresden Germany
| | - Michael Mertig
- Institute of Physical Chemistry; Technische Universität Dresden; Dresden Germany
- Kurt Schwabe Institute; Meinsberg Germany
| | - Rüdiger Lange
- Chair of Chemical Engineering and Process Plants; Technische Universität Dresden; Dresden Germany
| | - Edeltraud Günther
- Chair of Environmental Management and Accounting; Technische Universität Dresden; Dresden Germany
| | - Jörg Opitz
- Institute for Material Science and Max Bergmann Center of Biomaterials; Technische Universität Dresden; Dresden Germany
- Fraunhofer Institute for Ceramic Technologies and Systems; Material Diagnostics, IKTS-MD Dresden; Dresden Germany
- Electronics Packaging Lab; Technische Universität Dresden; Dresden Germany
| | - Wolfgang Lippmann
- Institute of Power Engineering; Chair of Hydrogen and Nuclear Energy, Technische Universität Dresden; Dresden Germany
| | - Thomas Bley
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden Germany
| | - Nora Haufe
- Institute for Material Science and Max Bergmann Center of Biomaterials; Technische Universität Dresden; Dresden Germany
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Ye M, Wang Z, Wang Y, Wu R. A multi-Poisson dynamic mixture model to cluster developmental patterns of gene expression by RNA-seq. Brief Bioinform 2014; 16:205-15. [PMID: 24817567 DOI: 10.1093/bib/bbu013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Dynamic changes of gene expression reflect an intrinsic mechanism of how an organism responds to developmental and environmental signals. With the increasing availability of expression data across a time-space scale by RNA-seq, the classification of genes as per their biological function using RNA-seq data has become one of the most significant challenges in contemporary biology. Here we develop a clustering mixture model to discover distinct groups of genes expressed during a period of organ development. By integrating the density function of multivariate Poisson distribution, the model accommodates the discrete property of read counts characteristic of RNA-seq data. The temporal dependence of gene expression is modeled by the first-order autoregressive process. The model is implemented with the Expectation-Maximization algorithm and model selection to determine the optimal number of gene clusters and obtain the estimates of Poisson parameters that describe the pattern of time-dependent expression of genes from each cluster. The model has been demonstrated by analyzing a real data from an experiment aimed to link the pattern of gene expression to catkin development in white poplar. The usefulness of the model has been validated through computer simulation. The model provides a valuable tool for clustering RNA-seq data, facilitating our global view of expression dynamics and understanding of gene regulation mechanisms.
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Grewe S, Ballottari M, Alcocer M, D'Andrea C, Blifernez-Klassen O, Hankamer B, Mussgnug JH, Bassi R, Kruse O. Light-Harvesting Complex Protein LHCBM9 Is Critical for Photosystem II Activity and Hydrogen Production in Chlamydomonas reinhardtii. THE PLANT CELL 2014; 26:1598-1611. [PMID: 24706511 PMCID: PMC4036574 DOI: 10.1105/tpc.114.124198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Photosynthetic organisms developed multiple strategies for balancing light-harvesting versus intracellular energy utilization to survive ever-changing environmental conditions. The light-harvesting complex (LHC) protein family is of paramount importance for this function and can form light-harvesting pigment protein complexes. In this work, we describe detailed analyses of the photosystem II (PSII) LHC protein LHCBM9 of the microalga Chlamydomonas reinhardtii in terms of expression kinetics, localization, and function. In contrast to most LHC members described before, LHCBM9 expression was determined to be very low during standard cell cultivation but strongly increased as a response to specific stress conditions, e.g., when nutrient availability was limited. LHCBM9 was localized as part of PSII supercomplexes but was not found in association with photosystem I complexes. Knockdown cell lines with 50 to 70% reduced amounts of LHCBM9 showed reduced photosynthetic activity upon illumination and severe perturbation of hydrogen production activity. Functional analysis, performed on isolated PSII supercomplexes and recombinant LHCBM9 proteins, demonstrated that presence of LHCBM9 resulted in faster chlorophyll fluorescence decay and reduced production of singlet oxygen, indicating upgraded photoprotection. We conclude that LHCBM9 has a special role within the family of LHCII proteins and serves an important protective function during stress conditions by promoting efficient light energy dissipation and stabilizing PSII supercomplexes.
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Affiliation(s)
- Sabrina Grewe
- Algae Biotechnology and Bioenergy Group, Department of Biology, Center for Biotechnology, Bielefeld University, D-33615 Bielefeld, Germany
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, I-37134 Verona, Italy
| | - Marcelo Alcocer
- INF-CNR, Dipartimento di Fisica, Politecnico di Milano, 20133 Milan, Italy Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, 20133 Milan, Italy
| | - Cosimo D'Andrea
- INF-CNR, Dipartimento di Fisica, Politecnico di Milano, 20133 Milan, Italy Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, 20133 Milan, Italy
| | - Olga Blifernez-Klassen
- Algae Biotechnology and Bioenergy Group, Department of Biology, Center for Biotechnology, Bielefeld University, D-33615 Bielefeld, Germany
| | - Ben Hankamer
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jan H Mussgnug
- Algae Biotechnology and Bioenergy Group, Department of Biology, Center for Biotechnology, Bielefeld University, D-33615 Bielefeld, Germany
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, I-37134 Verona, Italy
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy Group, Department of Biology, Center for Biotechnology, Bielefeld University, D-33615 Bielefeld, Germany
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Wecker MSA, Ghirardi ML. High-throughput biosensor discriminates between different algal H2 -photoproducing strains. Biotechnol Bioeng 2014; 111:1332-40. [PMID: 24578287 DOI: 10.1002/bit.25206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/15/2014] [Accepted: 01/28/2014] [Indexed: 12/24/2022]
Abstract
A number of species of microalgae and cyanobacteria photosynthetically produce H2 gas by coupling water oxidation with the reduction of protons to molecular hydrogen, generating renewable energy from sunlight and water. Photosynthetic H2 production, however, is transitory, and there is considerable interest in increasing and extending it for commercial applications. Here we report a Petri-plate version of our previous, microplate-based assay that detects photosynthetic H2 production by algae. The assay consists of an agar overlay of H2 -sensing Rhodobacter capsulatus bacteria carrying a green fluorescent protein that responds to H2 produced by single algal colonies in the bottom agar layer. The assay distinguishes between algal strains that photoproduce H2 at different levels under high light intensities, and it does so in a simple, inexpensive, and high-throughput manner. The assay will be useful for screening both natural populations and mutant libraries for strains having increased H2 production, and useful for identifying various genetic factors that physiologically or genetically alter algal hydrogen production.
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Yang S, Guarnieri MT, Smolinski S, Ghirardi M, Pienkos PT. De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:118. [PMID: 23971877 PMCID: PMC3846465 DOI: 10.1186/1754-6834-6-118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular H2 under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of H2 photoproduction in this organism. RESULTS In this work, RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of H2 photoproduction. 156 million reads generated from 7 samples were then used for de novo assembly after data trimming. BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 34,136 contigs, which were then used as the reference contigs for RNA-Seq analysis. Our results indicated that more contigs were differentially expressed during the period of early and higher H2 photoproduction, and fewer contigs were differentially expressed when H2-photoproduction rates decreased. In addition, C. moewusii and C. reinhardtii share core functional pathways, and transcripts for H2 photoproduction and anaerobic metabolite production were identified in both organisms. C. moewusii also possesses similar metabolic flexibility as C. reinhardtii, and the difference between C. moewusii and C. reinhardtii on hydrogenase expression and anaerobic fermentative pathways involved in redox balancing may explain their different profiles of hydrogenase activity and secreted anaerobic metabolites. CONCLUSIONS Herein, we have described a workflow using commercial software to analyze RNA-Seq data without reference genome sequence information, which can be applied to other unsequenced microorganisms. This study provided biological insights into the anaerobic fermentation and H2 photoproduction of C. moewusii, and the first transcriptomic RNA-Seq dataset of C. moewusii generated in this study also offer baseline data for further investigation (e.g. regulatory proteins related to fermentative pathway discussed in this study) of this organism as a H2-photoproduction strain.
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Affiliation(s)
| | | | - Sharon Smolinski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Maria Ghirardi
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
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