1
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Murik O, Geffen O, Shotland Y, Fernandez-Pozo N, Ullrich KK, Walther D, Rensing SA, Treves H. Genomic imprints of unparalleled growth. THE NEW PHYTOLOGIST 2024; 241:1144-1160. [PMID: 38072860 DOI: 10.1111/nph.19444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023]
Abstract
Chlorella ohadii was isolated from desert biological soil crusts, one of the harshest habitats on Earth, and is emerging as an exciting new green model for studying growth, photosynthesis and metabolism under a wide range of conditions. Here, we compared the genome of C. ohadii, the fastest growing alga on record, to that of other green algae, to reveal the genomic imprints empowering its unparalleled growth rate and resistance to various stressors, including extreme illumination. This included the genome of its close relative, but slower growing and photodamage sensitive, C. sorokiniana UTEX 1663. A larger number of ribosome-encoding genes, high intron abundance, increased codon bias and unique genes potentially involved in metabolic flexibility and resistance to photodamage are all consistent with the faster growth of C. ohadii. Some of these characteristics highlight general trends in Chlorophyta and Chlorella spp. evolution, and others open new broad avenues for mechanistic exploration of their relationship with growth. This work entails a unique case study for the genomic adaptations and costs of exceptionally fast growth and sheds light on the genomic signatures of fast growth in photosynthetic cells. It also provides an important resource for future studies leveraging the unique properties of C. ohadii for photosynthesis and stress response research alongside their utilization for synthetic biology and biotechnology aims.
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Affiliation(s)
- Omer Murik
- Department of Plant and Environmental Sciences, Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- Medical Genetics Institute, Shaare Zedek Medical Center, 93722, Jerusalem, Israel
| | - Or Geffen
- School of Plant Sciences and Food Security, Tel-Aviv University, 39040, Tel-Aviv, Israel
| | - Yoram Shotland
- Chemical Engineering, Shamoon College of Engineering, 84100, Beer-Sheva, Israel
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, 35037, Marburg, Germany
| | - Kristian Karsten Ullrich
- Plant Cell Biology, Department of Biology, University of Marburg, 35037, Marburg, Germany
- Max-Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Dirk Walther
- Max-Planck Institute for Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Stefan Andreas Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, 35037, Marburg, Germany
- Center for Biological Signaling Studies (BIOSS), University of Freiburg, 79098, Freiburg, Germany
| | - Haim Treves
- School of Plant Sciences and Food Security, Tel-Aviv University, 39040, Tel-Aviv, Israel
- Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
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2
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Morlino MS, Serna García R, Savio F, Zampieri G, Morosinotto T, Treu L, Campanaro S. Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches. Biotechnol Adv 2023; 69:108264. [PMID: 37775073 DOI: 10.1016/j.biotechadv.2023.108264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.
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Affiliation(s)
- Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Rebecca Serna García
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Filippo Savio
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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3
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Ray A, Kundu P, Ghosh A. Reconstruction of a Genome-Scale Metabolic Model of Scenedesmus obliquus and Its Application for Lipid Production under Three Trophic Modes. ACS Synth Biol 2023; 12:3463-3481. [PMID: 37852251 DOI: 10.1021/acssynbio.3c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Green microalgae have emerged as beneficial feedstocks for biofuel production. A systems-level understanding of the biochemical network is needed to harness the microalgal metabolic capacity for bioproduction. Genome-scale metabolic modeling (GEM) showed immense potential in rational metabolic engineering, utilizing biochemical flux distribution analysis. Here, we report the first GEM for the green microalga, Scenedesmus obliquus (iAR632), a promising biodiesel feedstock with high lipid-storing capability. iAR632 comprises 1467 reactions, 734 metabolites, and 632 genes distributed among 7 compartments. The model was optimized under three different trophic modes of microalgal cultivation, i.e., autotrophy, mixotrophy, and heterotrophy. The robustness of the reconstructed network was confirmed by analyzing its sensitivity to the biomass components. Pathway-level flux profiles were analyzed, and significant flux space expansion was noticed majorly in reactions associated with lipid biosynthesis. In agreement with the experimental observation, iAR632 predicted about 3.8-fold increased biomass and almost 4-fold higher lipid under mixotrophy than the other trophic modes. Thus, the assessment of the condition-specific metabolic flux distribution of iAR632 suggested that mixotrophy is the preferred cultivation condition for improved microalgal growth and lipid production. Overall, the reconstructed GEM and subsequent analyses will provide a systematic framework for developing model-driven strategies to improve microalgal bioproduction.
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Affiliation(s)
- Ayusmita Ray
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Pritam Kundu
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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4
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Cecchin M, Simicevic J, Chaput L, Hernandez Gil M, Girolomoni L, Cazzaniga S, Remacle C, Hoeng J, Ivanov NV, Titz B, Ballottari M. Acclimation strategies of the green alga Chlorella vulgaris to different light regimes revealed by physiological and comparative proteomic analyses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4540-4558. [PMID: 37155956 DOI: 10.1093/jxb/erad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Acclimation to different light regimes is at the basis of survival for photosynthetic organisms, regardless of their evolutionary origin. Previous research efforts largely focused on acclimation events occurring at the level of the photosynthetic apparatus and often highlighted species-specific mechanisms. Here, we investigated the consequences of acclimation to different irradiances in Chlorella vulgaris, a green alga that is one of the most promising species for industrial application, focusing on both photosynthetic and mitochondrial activities. Moreover, proteomic analysis of cells acclimated to high light (HL) or low light (LL) allowed identification of the main targets of acclimation in terms of differentially expressed proteins. The results obtained demonstrate photosynthetic adaptation to HL versus LL that was only partially consistent with previous findings in Chlamydomonas reinhardtii, a model organism for green algae, but in many cases similar to vascular plant acclimation events. Increased mitochondrial respiration measured in HL-acclimated cells mainly relied on alternative oxidative pathway dissipating the excessive reducing power produced due to enhanced carbon flow. Finally, proteins involved in cell metabolism, intracellular transport, gene expression, and signaling-including a heliorhodopsin homolog-were identified as strongly differentially expressed in HL versus LL, suggesting their key roles in acclimation to different light regimes.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Jovan Simicevic
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Louise Chaput
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel Hernandez Gil
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Laura Girolomoni
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Stefano Cazzaniga
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, 4000 Liège, Belgium
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
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5
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Tec-Campos D, Posadas C, Tibocha-Bonilla JD, Thiruppathy D, Glonek N, Zuñiga C, Zepeda A, Zengler K. The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions. PLoS Comput Biol 2023; 19:e1011371. [PMID: 37556472 PMCID: PMC10441798 DOI: 10.1371/journal.pcbi.1011371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/21/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023] Open
Abstract
The purple non-sulfur bacterium Rhodopseudomonas palustris is recognized as a critical microorganism in the nitrogen and carbon cycle and one of the most common members in wastewater treatment communities. This bacterium is metabolically extremely versatile. It is capable of heterotrophic growth under aerobic and anaerobic conditions, but also able to grow photoautotrophically as well as mixotrophically. Therefore R. palustris can adapt to multiple environments and establish commensal relationships with other organisms, expressing various enzymes supporting degradation of amino acids, carbohydrates, nucleotides, and complex polymers. Moreover, R. palustris can degrade a wide range of pollutants under anaerobic conditions, e.g., aromatic compounds such as benzoate and caffeate, enabling it to thrive in chemically contaminated environments. However, many metabolic mechanisms employed by R. palustris to breakdown and assimilate different carbon and nitrogen sources under chemoheterotrophic or photoheterotrophic conditions remain unknown. Systems biology approaches, such as metabolic modeling, have been employed extensively to unravel complex mechanisms of metabolism. Previously, metabolic models have been reconstructed to study selected capabilities of R. palustris under limited experimental conditions. Here, we developed a comprehensive metabolic model (M-model) for R. palustris Bis A53 (iDT1294) consisting of 2,721 reactions, 2,123 metabolites, and comprising 1,294 genes. We validated the model using high-throughput phenotypic, physiological, and kinetic data, testing over 350 growth conditions. iDT1294 achieved a prediction accuracy of 90% for growth with various carbon and nitrogen sources and close to 80% for assimilation of aromatic compounds. Moreover, the M-model accurately predicts dynamic changes of growth and substrate consumption rates over time under nine chemoheterotrophic conditions and demonstrated high precision in predicting metabolic changes between photoheterotrophic and photoautotrophic conditions. This comprehensive M-model will help to elucidate metabolic processes associated with the assimilation of multiple carbon and nitrogen sources, anoxygenic photosynthesis, aromatic compound degradation, as well as production of molecular hydrogen and polyhydroxybutyrate.
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Affiliation(s)
- Diego Tec-Campos
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Camila Posadas
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Juan D. Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
| | - Deepan Thiruppathy
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Department of Bioengineering, University of California, San Diego, La Jolla California, United States of America
| | - Nathan Glonek
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
| | - Alejandro Zepeda
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- Department of Bioengineering, University of California, San Diego, La Jolla California, United States of America
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, United States of America
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6
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Cheng W, Hwang S, Guo Q, Qian L, Liu W, Yu Y, Liu L, Tao Y, Cao H. The Special and General Mechanism of Cyanobacterial Harmful Algal Blooms. Microorganisms 2023; 11:microorganisms11040987. [PMID: 37110410 PMCID: PMC10144548 DOI: 10.3390/microorganisms11040987] [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: 03/13/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Cyanobacterial harmful algal blooms (CyanoHABs) are longstanding aquatic hazards worldwide, of which the mechanism is not yet fully understood, i.e., the process in which cyanobacteria establish dominance over coexisting algae in the same eutrophic waters. The dominance of CyanoHABs represents a deviation from their low abundance under conventional evolution in the oligotrophic state, which has been the case since the origin of cyanobacteria on early Earth. To piece together a comprehensive mechanism of CyanoHABs, we revisit the origin and adaptive radiation of cyanobacteria in oligotrophic Earth, demonstrating ubiquitous adaptive radiation enabled by corresponding biological functions under various oligotrophic conditions. Next, we summarize the biological functions (ecophysiology) which drive CyanoHABs and ecological evidence to synthesize a working mechanism at the population level (the special mechanism) for CyanoHABs: CyanoHABs are the consequence of the synergistic interaction between superior cyanobacterial ecophysiology and elevated nutrients. Interestingly, these biological functions are not a result of positive selection by water eutrophication, but an adaptation to a longstanding oligotrophic state as all the genes in cyanobacteria are under strong negative selection. Last, to address the relative dominance of cyanobacteria over coexisting algae, we postulate a "general" mechanism of CyanoHABs at the community level from an energy and matter perspective: cyanobacteria are simpler life forms and thus have lower per capita nutrient demand for growth than coexisting eukaryotic algae. We prove this by comparing cyanobacteria and eukaryotic algae in cell size and structure, genome size, size of genome-scale metabolic networks, cell content, and finally the golden standard-field studies with nutrient supplementation in the same waters. To sum up, the comprehensive mechanism of CyanoHABs comprises a necessary condition, which is the general mechanism, and a sufficient condition, which is the special mechanism. One prominent prediction based on this tentative comprehensive mechanism is that eukaryotic algal blooms will coexist with or replace CyanoHABs if eutrophication continues and goes over the threshold nutrient levels for eukaryotic algae. This two-fold comprehensive mechanism awaits further theoretic and experimental testing and provides an important guide to control blooms of all algal species.
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Affiliation(s)
- Wenduo Cheng
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Somin Hwang
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Qisen Guo
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Leyuan Qian
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Weile Liu
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Li Liu
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
| | - Yi Tao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Huansheng Cao
- Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Ave, Kunshan 215316, China
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7
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Wendering P, Nikoloski Z. Toward mechanistic modeling and rational engineering of plant respiration. PLANT PHYSIOLOGY 2023; 191:2150-2166. [PMID: 36721968 PMCID: PMC10069892 DOI: 10.1093/plphys/kiad054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Plant respiration not only provides energy to support all cellular processes, including biomass production, but also plays a major role in the global carbon cycle. Therefore, modulation of plant respiration can be used to both increase the plant yield and mitigate the effects of global climate change. Mechanistic modeling of plant respiration at sufficient biochemical detail can provide key insights for rational engineering of this process. Yet, despite its importance, plant respiration has attracted considerably less modeling effort in comparison to photosynthesis. In this update review, we highlight the advances made in modeling of plant respiration, emphasizing the gradual but important change from phenomenological to models based on first principles. We also provide a detailed account of the existing resources that can contribute to resolving the challenges in modeling plant respiration. These resources point at tangible improvements in the representation of cellular processes that contribute to CO2 evolution and consideration of kinetic properties of underlying enzymes to facilitate mechanistic modeling. The update review emphasizes the need to couple biochemical models of respiration with models of acclimation and adaptation of respiration for their effective usage in guiding breeding efforts and improving terrestrial biosphere models tailored to future climate scenarios.
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Affiliation(s)
- Philipp Wendering
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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8
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Improvement of Lutein Production in Auxenochlorella protothecoides Using Its Genome-Scale Metabolic Model and a System-Oriented Approach. Appl Biochem Biotechnol 2023; 195:889-904. [PMID: 36222987 DOI: 10.1007/s12010-022-04186-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
Lutein is a valuable metabolite widely used in the food, pharmaceutical, cosmetic, and aquaculture industries. Marigold flowers are the most common source of commercial lutein, but cultivation area, weather conditions, and high manpower costs are among the disadvantages of lutein production from marigold flowers. Microalgae are an excellent alternative to plant sources of lutein as they do not have the limitations of plant extraction. Auxenochlorella protothecoides is a promising candidate for commercial production of lutein. In the present research, a genome-scale metabolic model was applied to introduce some strategies to improve lutein production in A. protothecoides. The effective reactions to improve lutein production were determined based on analysis of multiple optimal solutions. The enzymatic regulators of candidate reactions were identified using the BRENDA database. The effect of 13 activators was investigated experimentally. Our results showed that sodium citrate has the greatest effect on lutein production, so it was introduced as the most effective compound for increasing lutein production by A. protothecoides.
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9
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Yao H, Dahal S, Yang L. Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii. Microb Cell Fact 2023; 22:13. [PMID: 36650525 PMCID: PMC9847032 DOI: 10.1186/s12934-022-02004-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/17/2022] [Indexed: 01/19/2023] Open
Abstract
Gene expression data of cell cultures is commonly measured in biological and medical studies to understand cellular decision-making in various conditions. Metabolism, affected but not solely determined by the expression, is much more difficult to measure experimentally. Finding a reliable method to predict cell metabolism for expression data will greatly benefit metabolic engineering. We have developed a novel pipeline, OVERLAY, that can explore cellular fluxomics from expression data using only a high-quality genome-scale metabolic model. This is done through two main steps: first, construct a protein-constrained metabolic model (PC-model) by integrating protein and enzyme information into the metabolic model (M-model). Secondly, overlay the expression data onto the PC-model using a novel two-step nonconvex and convex optimization formulation, resulting in a context-specific PC-model with optionally calibrated rate constants. The resulting model computes proteomes and intracellular flux states that are consistent with the measured transcriptomes. Therefore, it provides detailed cellular insights that are difficult to glean individually from the omic data or M-model alone. We apply the OVERLAY to interpret triacylglycerol (TAG) overproduction by Chlamydomonas reinhardtii, using time-course RNA-Seq data. We show that OVERLAY can compute C. reinhardtii metabolism under nitrogen deprivation and metabolic shifts after an acetate boost. OVERLAY can also suggest possible 'bottleneck' proteins that need to be overexpressed to increase the TAG accumulation rate, as well as discuss other TAG-overproduction strategies.
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Affiliation(s)
- Haoyang Yao
- grid.410356.50000 0004 1936 8331Department of Chemical Engineering, Queen’s University, 19 Division St, Kingston, K7L 2N9 Canada
| | - Sanjeev Dahal
- grid.410356.50000 0004 1936 8331Department of Chemical Engineering, Queen’s University, 19 Division St, Kingston, K7L 2N9 Canada
| | - Laurence Yang
- grid.410356.50000 0004 1936 8331Department of Chemical Engineering, Queen’s University, 19 Division St, Kingston, K7L 2N9 Canada
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10
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Inwongwan S, Pekkoh J, Pumas C, Sattayawat P. Metabolic network reconstruction of Euglena gracilis: Current state, challenges, and applications. Front Microbiol 2023; 14:1143770. [PMID: 36937274 PMCID: PMC10018167 DOI: 10.3389/fmicb.2023.1143770] [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: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
A metabolic model, representing all biochemical reactions in a cell, is a prerequisite for several approaches in systems biology used to explore the metabolic phenotype of an organism. Despite the use of Euglena in diverse industrial applications and as a biological model, there is limited understanding of its metabolic network capacity. The unavailability of the completed genome data and the highly complex evolution of Euglena are significant obstacles to the reconstruction and analysis of its genome-scale metabolic model. In this mini-review, we discuss the current state and challenges of metabolic network reconstruction in Euglena gracilis. We have collated and present the available relevant data for the metabolic network reconstruction of E. gracilis, which could be used to improve the quality of the metabolic model of E. gracilis. Furthermore, we deliver the potential applications of the model in metabolic engineering. Altogether, it is supposed that this mini-review would facilitate the investigation of metabolic networks in Euglena and further lay out a direction for model-assisted metabolic engineering.
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Affiliation(s)
- Sahutchai Inwongwan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jeeraporn Pekkoh
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Chayakorn Pumas
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pachara Sattayawat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
- *Correspondence: Pachara Sattayawat,
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11
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Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Zou S, Huang Z, Wu X, Yu X. Physiological and Genetic Regulation for High Lipid Accumulation by Chlorella sorokiniana Strains from Different Environments of an Arctic Glacier, Desert, and Temperate Lake under Nitrogen Deprivation Conditions. Microbiol Spectr 2022; 10:e0039422. [PMID: 36200894 PMCID: PMC9603131 DOI: 10.1128/spectrum.00394-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
Microalgae can adapt to extreme environments with specialized metabolic mechanisms. Here, we report comparative physiological and genetic regulation analyses of Chlorella sorokiniana from different environmental regions of an arctic glacier, desert, and temperate native lake in response to N deprivation, for screening the optimal strain with high lipid accumulation. Strains from the three regions showed different growth and biochemical compositions under N deprivation. The arctic glacier and desert strains produced higher soluble sugar content than strains from the native lake. The arctic glacier strains produced the highest levels of lipid content and neutral lipids under N deprivation compared with strains from desert and native lake. At a molecular level, the arctic strain produced more differentially expressed genes related to fatty acid biosynthesis, glycolysis gluconeogenesis, and glycerolipid metabolism. The important functional genes acetyl coenzyme A (acetyl-CoA) carboxylase (ACCase), fatty acid synthase complex, pyruvate dehydrogenase component, and fatty acyl-acyl carrier protein (acyl-ACP) thioesterase were highly expressed in arctic strains. More acetyl-CoA was produced from glycolysis gluconeogenesis and glycerolipid metabolism, which then produced more fatty acid with the catalytic function of ACCase and acyl-ACP thioesterase in fatty acid biosynthesis. Our results indicated that the C. sorokiniana strains from the arctic region had the fullest potential for biodiesel production due to special genetic regulation related to fatty acid synthesis, glycolysis gluconeogenesis, and glycerolipid metabolism. IMPORTANCE It is important to reveal the physiological and genetic regulation mechanisms of microalgae for screening potential strains with high lipid production. Our results showed that Chlorella sorokiniana strains from arctic glacier, desert, and temperate native lake had different growth, biochemical composition, and genetic expression under N deprivation. The strains from an arctic glacier produced the highest lipid content (including neutral lipid), which was related to the genetic regulation of fatty acid biosynthesis, glycolysis gluconeogenesis, and glycerolipid metabolism. The functional genes for acetyl-CoA carboxylase, fatty acid synthase complex, pyruvate dehydrogenase component, and fatty acyl-ACP thioesterase in the three pathways were highly expressed in arctic strains. The revelation of physiological and genetic regulation of strains from different environmental regions will contribute to the microalgae selection for high lipid accumulation.
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Affiliation(s)
- Shanmei Zou
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Zheng Huang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xuemin Wu
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xinke Yu
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, P. R. China
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13
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Li T, Pang N, He L, Xu Y, Fu X, Tang Y, Shachar-Hill Y, Chen S. Re-Programing Glucose Catabolism in the Microalga Chlorella sorokiniana under Light Condition. Biomolecules 2022; 12:biom12070939. [PMID: 35883494 PMCID: PMC9313030 DOI: 10.3390/biom12070939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
The microalga Chlorella sorokiniana has attracted much attention for lipid production and wastewater treatment. It can perform photosynthesis and organic carbon utilization concurrently. To understand its phototrophic metabolism, a biomass compositional analysis, a 13C metabolic flux analysis, and metabolite pool size analyses were performed. Under dark condition, the oxidative pentose phosphate pathway (OPP) was the major route for glucose catabolism (88% carbon flux) and a cyclic OPP–glycolytic route for glucose catabolism was formed. Under light condition, fluxes in the glucose catabolism, tricarboxylic acid (TCA) cycle, and anaplerotic reaction (CO2 fixation via phosphoenolpyruvate carboxylase) were all suppressed. Meanwhile, the RuBisCO reaction became active and the ratio of its carbon fixation to glucose carbon utilization was determined as 7:100. Moreover, light condition significantly reduced the pool sizes of sugar phosphate metabolites (such as E4P, F6P, and S7P) and promoted biomass synthesis (which reached 0.155 h−1). In addition, light condition increased glucose consumption rates, leading to higher ATP and NADPH production and a higher protein content (43% vs. 30%) in the biomass during the exponential growth phase.
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Affiliation(s)
- Tingting Li
- Department of Immunology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China;
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA;
| | - Na Pang
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA;
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; (Y.X.); (Y.S.-H.)
| | - Lian He
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, USA; (L.H.); (Y.T.)
| | - Yuan Xu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; (Y.X.); (Y.S.-H.)
| | - Xinyu Fu
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48823, USA;
| | - Yinjie Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, USA; (L.H.); (Y.T.)
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; (Y.X.); (Y.S.-H.)
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA;
- Correspondence: ; Tel.: +509-335-3743; Fax: +509-335-2722
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14
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Briones-Baez MF, Aguilera-Vazquez L, Rangel-Valdez N, Martinez-Salazar AL, Zuñiga C. Multi-Objective Optimization of Microalgae Metabolism: An Evolutive Algorithm Based on FBA. Metabolites 2022; 12:metabo12070603. [PMID: 35888727 PMCID: PMC9325016 DOI: 10.3390/metabo12070603] [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: 05/21/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 12/07/2022] Open
Abstract
Studies enabled by metabolic models of different species of microalgae have become significant since they allow us to understand changes in their metabolism and physiological stages. The most used method to study cell metabolism is FBA, which commonly focuses on optimizing a single objective function. However, recent studies have brought attention to the exploration of simultaneous optimization of multiple objectives. Such strategies have found application in optimizing biomass and several other bioproducts of interest; they usually use approaches such as multi-level models or enumerations schemes. This work proposes an alternative in silico multiobjective model based on an evolutionary algorithm that offers a broader approximation of the Pareto frontier, allowing a better angle for decision making in metabolic engineering. The proposed strategy is validated on a reduced metabolic network of the microalgae Chlamydomonas reinhardtii while optimizing for the production of protein, carbohydrates, and CO2 uptake. The results from the conducted experimental design show a favorable difference in the number of solutions achieved compared to a classic tool solving FBA.
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Affiliation(s)
- Monica Fabiola Briones-Baez
- TECNM/Instituto Tecnológico de Ciudad Madero, División de Estudios de Posgrado e Investigación, Los Mangos 89440, Mexico; (M.F.B.-B.); (L.A.-V.)
| | - Luciano Aguilera-Vazquez
- TECNM/Instituto Tecnológico de Ciudad Madero, División de Estudios de Posgrado e Investigación, Los Mangos 89440, Mexico; (M.F.B.-B.); (L.A.-V.)
| | - Nelson Rangel-Valdez
- CONACyT—TECNM/Instituto Tecnológico de Ciudad Madero, División de Estudios de Posgrado e Investigación, Los Mangos 89440, Mexico;
| | - Ana Lidia Martinez-Salazar
- TECNM/Instituto Tecnológico de Ciudad Madero, División de Estudios de Posgrado e Investigación, Los Mangos 89440, Mexico; (M.F.B.-B.); (L.A.-V.)
- Correspondence:
| | - Cristal Zuñiga
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA;
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15
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Srivastava A, Kalwani M, Chakdar H, Pabbi S, Shukla P. Biosynthesis and biotechnological interventions for commercial production of microalgal pigments: A review. BIORESOURCE TECHNOLOGY 2022; 352:127071. [PMID: 35351568 DOI: 10.1016/j.biortech.2022.127071] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Microalgae are photosynthetic eukaryotes that serve as microbial cell factories for the production of useful biochemicals, including pigments. These pigments are eco-friendly alternatives to synthetic dyes and reduce environmental and health risks. They also exhibit excellent anti-oxidative properties, making them a useful commodity in the nutrition and pharmaceutical industries. Light-harvesting pigments such as chlorophylls and phycobilins, and photoprotective carotenoids are some of the most common microalgal pigments. The increasing demand for these pigments in industrial applications has prompted a need to improve their metabolic yield in microalgal cells. So far, expensive cultivation methods and sensitivity to microbial contamination remain the main obstacles to the large-scale production of these pigments. This review highlights current issues and future prospects related to the production of microalgal pigments. The review also emphasizes the use of engineering approaches such as genetic engineering, and optimization of media components and physical parameters to increase their commercial-scale production.
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Affiliation(s)
- Amit Srivastava
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mohneesh Kalwani
- School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India; Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh 275103, India
| | - Sunil Pabbi
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Pratyoosh Shukla
- School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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16
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Xie Z, Wu F, Lin W, Luo J. The utilization of photophosphorylation uncoupler to improve lipid production of Chlorella, a case study using transcriptome and functional gene expression analysis to reveal its mechanism. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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17
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Passi A, Tibocha-Bonilla JD, Kumar M, Tec-Campos D, Zengler K, Zuniga C. Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data. Metabolites 2021; 12:14. [PMID: 35050136 PMCID: PMC8778254 DOI: 10.3390/metabo12010014] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.
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Affiliation(s)
- Anurag Passi
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
| | - Juan D. Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA;
| | - Manish Kumar
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
| | - Diego Tec-Campos
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán, Merida 97203, Yucatan, Mexico
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0403, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
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18
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Wen J, Rapp K, Dahlin LR, Li CT, Sebesta J, Barry AN, Guarnieri MT, Peebles C, Betenbaugh M. Mapping the path forward to next generation algal technologies: Workshop on understanding the rules of life and complexity in algal systems. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Examining the impact of carbon dioxide levels and modulation of resulting hydrogen peroxide in Chlorella vulgaris. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Wang Q, Yu Z, Wei D, Chen W, Xie J. Mixotrophic Chlorella pyrenoidosa as cell factory for ultrahigh-efficient removal of ammonium from catalyzer wastewater with valuable algal biomass coproduction through short-time acclimation. BIORESOURCE TECHNOLOGY 2021; 333:125151. [PMID: 33892430 DOI: 10.1016/j.biortech.2021.125151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
To achieve ultrahigh-efficient ammonium removal and valuable biomass coproduction, Chlorella-mediated short-time acclimation was implemented in photo-fermentation. The results demonstrated short-time acclimation of mixotrophic Chlorella pyrenoidosa could significantly improve NH4+ removal and biomass production in shake flasks. After acclimation through two batch cultures in 5-L photo-fermenter, the maximum NH4+ removal rate (1,400 mg L-1 d-1) were achieved under high NH4+ level (4,750 mg L-1) in batch 3. In 50-L photo-fermenter, through one batch acclimated culture, the maximum NH4+ removal rate (2,212 mg L-1 d-1) and biomass concentration (58.4 g L-1) were achieved in batch 2, with the highest productivities of protein (5.56 g L-1 d-1) and total lipids (5.66 g L-1 d-1). The hypothetical pathway of nutrients assimilation in mixotrophic cells as cell factory was proposed with detailed discussion. This study provided a novel strategy for high-ammonium wastewater treatment without dilution, facilitating the algae-based "waste-to-treasure" bioconversion process for green manufacturing.
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Affiliation(s)
- Qingke Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zongyi Yu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Dong Wei
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Research Institute for Food Nutrition and Human Health, Guangzhou, China.
| | - Weining Chen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Chinese Academy of Fishery Sciences Pearl River Fisheries Research Institute, Guangzhou, China
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21
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Norena-Caro DA, Zuniga C, Pete AJ, Saemundsson SA, Donaldson MR, Adams AJ, Dooley KM, Zengler K, Benton MG. Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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22
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Insights into the physiology of Chlorella vulgaris cultivated in sweet sorghum bagasse hydrolysate for sustainable algal biomass and lipid production. Sci Rep 2021; 11:6779. [PMID: 33762646 PMCID: PMC7991646 DOI: 10.1038/s41598-021-86372-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/15/2021] [Indexed: 02/06/2023] Open
Abstract
Supplementing cultivation media with exogenous carbon sources enhances biomass and lipid production in microalgae. Utilization of renewable organic carbon from agricultural residues can potentially reduce the cost of algae cultivation, while enhancing sustainability. In the present investigation a medium was developed from sweet sorghum bagasse for cultivation of Chlorella under mixotrophic conditions. Using response surface methodology, the optimal values of critical process parameters were determined, namely inoculum cell density (O.D.750) of 0.786, SSB hydrolysate content of the medium 25% v/v, and zero medium salinity, to achieve maximum lipid productivity of 120 mg/L/d. Enhanced biomass (3.44 g/L) and lipid content (40% of dry cell weight) were observed when the alga was cultivated in SSB hydrolysate under mixotrophic conditions compared to heterotrophic and photoautotrophic conditions. A time course investigation revealed distinct physiological responses in terms of cellular growth and biochemical composition of C. vulgaris cultivated in the various trophic modes. The determined carbohydrate and lipid profiles indicate that sugar addition to the cultivation medium boosts neutral lipid synthesis compared to structural lipids, suggesting that carbon flux is channeled towards triacylglycerol synthesis in the cells. Furthermore, the fatty acid profile of lipids extracted from mixotrophically grown cultures contained more saturated and monosaturated fatty acids, which are suitable for biofuel manufacturing. Scale-up studies in a photobioreactor using SSB hydrolysate achieved a biomass concentration of 2.83 g/L consisting of 34% lipids and 26% carbohydrates. These results confirmed that SSB hydrolysate is a promising feedstock for mixotrophic cultivation of Chlorella and synthesis of algal bioproducts and biofuels.
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23
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The carbon partitioning of glucose and DIC in mixotrophic, heterotrophic and photoautotrophic cultures of Tetraselmis suecica. Biotechnol Lett 2021; 43:729-743. [PMID: 33459952 DOI: 10.1007/s10529-020-03073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/17/2020] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Changes in the partitioning of dissolved inorganic (DIC) and glucose were elucidated by utilising 13C labelled DIC or glucose, and quantifying the biochemical profile of mixotrophic, heterotrophic and photoautotrophic cultures of the microalga Tetraselmis suecica. RESULTS Mixotrophic cultivation increases microalgal productivity and changes their biochemical profile, due to an alteration in the partitioning of carbon within the cell. When cultured mixotrophically and heterotrophically, there is enhanced incorporation of carbon into shorter chain saturated fatty acids and non-lipid biomass, compared to photoautotrophic cultivation. Autotrophic culture results in increased total fatty acid content of cultures (4.19% dry weight compared to 2.13%) and shifts the fatty acid profile in favour of long-chain unsaturated fatty acids, such as 18:2 n-(9,12), compared to mixotrophic culture. Quantifying the changes in partitioning between DIC and glucose facilitates tailoring of the biochemical profile to develop "designer" algae. CONCLUSIONS There is a condition specific shift in carbon partitioning into different fatty acid and biochemical fractions in T. suecica, with more inorganic carbon partitioned into 18:2 n-(9,12) in photoautotrophic rather than mixotrophic cultures.
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber M, Best AA, DeJongh M, Kimbrel JA, D’haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D575-D588. [PMID: 32986834 PMCID: PMC7778927 DOI: 10.1093/nar/gkaa746] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical 'Rosetta Stone' to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D’haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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25
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D1555. [PMID: 33179751 DOI: 10.1101/2020.03.31.018663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
ABSTRACTFor over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions;; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical “Rosetta Stone” to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies, and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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Girolomoni L, Bellamoli F, de la Cruz Valbuena G, Perozeni F, D'Andrea C, Cerullo G, Cazzaniga S, Ballottari M. Evolutionary divergence of photoprotection in the green algal lineage: a plant-like violaxanthin de-epoxidase enzyme activates the xanthophyll cycle in the green alga Chlorella vulgaris modulating photoprotection. THE NEW PHYTOLOGIST 2020; 228:136-150. [PMID: 32442330 PMCID: PMC7539987 DOI: 10.1111/nph.16674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/13/2020] [Indexed: 05/05/2023]
Abstract
The xanthophyll cycle is the metabolic process by which the carotenoid violaxanthin is de-epoxidated to zeaxanthin, a xanthophyll with a crucial photoprotective role in higher plants and mosses. The role of zeaxanthin is still unclear in green algae, and a peculiar violaxanthin de-epoxidating enzyme was found in the model organism Chlamydomonas reinhardtii. Here, we investigated the molecular details and functions of the xanthophyll cycle in the case of Chlorella vulgaris, one of the green algae most considered for industrial cultivation, where resistance to high light stress is a prerequisite for sustainable biomass production. Identification of the violaxanthin de-epoxidase enzyme in C. vulgaris was performed by genome mining and in vitro analysis of the catalytic activity of the gene product identified. The photoprotective role of zeaxanthin was then investigated in vivo and in isolated pigment-binding complexes. The results obtained demonstrate the functioning, even though with a different pH sensitivity, of a plant-like violaxanthin de-epoxidase enzyme in C. vulgaris. Differently from C. reinhardtii, zeaxanthin accumulation in C. vulgaris was found to be crucial for photoprotective quenching of excitation energy harvested by both photosystem I and II. These findings demonstrate an evolutionary divergence of photoprotective mechanisms among Chlorophyta.
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Affiliation(s)
- Laura Girolomoni
- Department of BiotechnologyUniversity of VeronaStrada le Grazie 15Verona37134Italy
| | - Francesco Bellamoli
- Department of BiotechnologyUniversity of VeronaStrada le Grazie 15Verona37134Italy
| | | | - Federico Perozeni
- Department of BiotechnologyUniversity of VeronaStrada le Grazie 15Verona37134Italy
| | - Cosimo D'Andrea
- IFN‐CNRDepartment of PhysicsPolitecnico di MilanoPiazza Leonardo da Vinci 32Milan20133Italy
- Center for NanoScience and Technology @PoliMiIstituto Italiano di Tecnologiavia Pascoli 70/3Milan20133Italy
| | - Giulio Cerullo
- IFN‐CNRDepartment of PhysicsPolitecnico di MilanoPiazza Leonardo da Vinci 32Milan20133Italy
| | - Stefano Cazzaniga
- Department of BiotechnologyUniversity of VeronaStrada le Grazie 15Verona37134Italy
| | - Matteo Ballottari
- Department of BiotechnologyUniversity of VeronaStrada le Grazie 15Verona37134Italy
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27
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Vidotti AD, Riaño-Pachón DM, Mattiello L, Giraldi LA, Winck FV, Franco TT. Analysis of autotrophic, mixotrophic and heterotrophic phenotypes in the microalgae Chlorella vulgaris using time-resolved proteomics and transcriptomics approaches. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Wirth R, Pap B, Böjti T, Shetty P, Lakatos G, Bagi Z, Kovács KL, Maróti G. Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. Front Bioeng Biotechnol 2020; 8:557572. [PMID: 33072721 PMCID: PMC7537789 DOI: 10.3389/fbioe.2020.557572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/28/2020] [Indexed: 11/24/2022] Open
Abstract
Microalgae-based bioenergy production is a promising field with regard to the wide variety of algal species and metabolic potential. The use of liquid wastes as nutrient clearly improves the sustainability of microalgal biofuel production. Microalgae and bacteria have an ecological inter-kingdom relationship. This microenvironment called phycosphere has a major role in the ecosystem productivity and can be utilized both in bioremediation and biomass production. However, knowledge on the effects of indigenous bacteria on microalgal growth and the characteristics of bacterial communities associated with microalgae are limited. In this study municipal, industrial and agricultural liquid waste derivatives were used as cultivation media. Chlorella vulgaris green microalgae and its bacterial partners efficiently metabolized the carbon, nitrogen and phosphorous content available in these wastes. The read-based metagenomics approach revealed a diverse microbial composition at the start point of cultivations in the different types of liquid wastes. The relative abundance of the observed taxa significantly changed over the cultivation period. The genome-centric reconstruction of phycospheric bacteria further explained the observed correlations between the taxonomic composition and biomass yield of the various waste-based biodegradation systems. Functional profile investigation of the reconstructed microbes revealed a variety of relevant biological processes like organic acid oxidation and vitamin B synthesis. Thus, liquid wastes were shown to serve as valuable resources of nutrients as well as of growth promoting bacteria enabling increased microalgal biomass production.
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Affiliation(s)
- Roland Wirth
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Bernadett Pap
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Tamás Böjti
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Gergely Lakatos
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Kornél L. Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Faculty of Water Sciences, National University of Public Service, Baja, Hungary
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Ahmad A, Tiwari A, Srivastava S. A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential. Microorganisms 2020; 8:microorganisms8091396. [PMID: 32932853 PMCID: PMC7563145 DOI: 10.3390/microorganisms8091396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 01/27/2023] Open
Abstract
Thalassiosira pseudonana is a transformable and biotechnologically promising model diatom with an ability to synthesise nutraceuticals such as fucoxanthin and store a significant amount of polyglucans and lipids including omega-3 fatty acids. While it was the first diatom to be sequenced, a systems-level analysis of its metabolism has not been done yet. This work presents first comprehensive, compartmentalized, and functional genome-scale metabolic model of the marine diatom Thalassiosira pseudonana CCMP 1335, which we have termed iThaps987. The model includes 987 genes, 2477 reactions, and 2456 metabolites. Comparison with the model of another diatom Phaeodactylum tricornutum revealed presence of 183 unique enzymes (belonging primarily to amino acid, carbohydrate, and lipid metabolism) in iThaps987. Model simulations showed a typical C3-type photosynthetic carbon fixation and suggested a preference of violaxanthin-diadinoxanthin pathway over violaxanthin-neoxanthin pathway for the production of fucoxanthin. Linear electron flow was found be active and cyclic electron flow was inactive under normal phototrophic conditions (unlike green algae and plants), validating the model predictions with previous reports. Investigation of the model for the potential of Thalassiosira pseudonana CCMP 1335 to produce other industrially useful compounds suggest iso-butanol as a foreign compound that can be synthesized by a single-gene addition. This work provides novel insights about the metabolism and potential of the organism and will be helpful to further investigate its metabolism and devise metabolic engineering strategies for the production of various compounds.
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Affiliation(s)
- Ahmad Ahmad
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India;
- Department of Biotechnology, Noida International University (NIU), Noida 203201, India
| | - Archana Tiwari
- Department of Biotechnology, Noida International University (NIU), Noida 203201, India
- Correspondence: (A.T.); (S.S.); Tel.: +91-958-264-9114 (A.T.); +91-11-2674-1361 (S.S.)
| | - Shireesh Srivastava
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India;
- Correspondence: (A.T.); (S.S.); Tel.: +91-958-264-9114 (A.T.); +91-11-2674-1361 (S.S.)
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30
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Zuñiga C, Peacock B, Liang B, McCollum G, Irigoyen SC, Tec-Campos D, Marotz C, Weng NC, Zepeda A, Vidalakis G, Mandadi KK, Borneman J, Zengler K. Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts. NPJ Syst Biol Appl 2020; 6:24. [PMID: 32753656 PMCID: PMC7403731 DOI: 10.1038/s41540-020-00142-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
Candidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.
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Affiliation(s)
- Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Beth Peacock
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Bo Liang
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Greg McCollum
- USDA, ARS, US Horticultural Research Laboratory, 2001 S. Rock Road, Fort Pierce, FL, 34945, USA
| | - Sonia C Irigoyen
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Weslaco, TX, USA
| | - Diego Tec-Campos
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Campus de Ciencias Exactas e Ingenierías, Mérida, 97203, Yucatán, México
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Nien-Chen Weng
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Alejandro Zepeda
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Campus de Ciencias Exactas e Ingenierías, Mérida, 97203, Yucatán, México
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Weslaco, TX, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093-0412, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0403, USA.
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31
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Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. Nat Commun 2020; 11:3803. [PMID: 32732991 PMCID: PMC7393147 DOI: 10.1038/s41467-020-17612-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 07/02/2020] [Indexed: 01/23/2023] Open
Abstract
Microbial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.
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32
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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Campos DT, Zuñiga C, Passi A, Del Toro J, Tibocha-Bonilla JD, Zepeda A, Betenbaugh MJ, Zengler K. Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ. Metab Eng Commun 2020; 11:e00132. [PMID: 32551229 PMCID: PMC7292883 DOI: 10.1016/j.mec.2020.e00132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 01/28/2023] Open
Abstract
Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH3). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. Azotobacter vinelandii is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in A. vinelandii remain unknown to date. Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium A. vinelandii DJ (iDT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. iDT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism. Genome-scale metabolic model of Azotobacter vinelandii DJ achives over 90% accuracy. iDT1278 is the most comprehensive model to simulate diazotrophy. Determining the most suitable culture conditions to produce polymers A. vinelandii. Constraint-based modeling unravels links among nitrogen fixation and production of organic nitrogen.
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Affiliation(s)
- Diego Tec Campos
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.,Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Anurag Passi
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - John Del Toro
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Juan D Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093-0412, USA
| | - Alejandro Zepeda
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093-0412, USA.,Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0403, USA
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Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes. NPJ Syst Biol Appl 2020; 6:14. [PMID: 32415097 PMCID: PMC7229059 DOI: 10.1038/s41540-020-0135-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
Cells can sense changes in their extracellular environment and subsequently adapt their biomass composition. Nutrient abundance defines the capability of the cell to produce biomass components. Under nutrient-limited conditions, resource allocation dramatically shifts to carbon-rich molecules. Here, we used dynamic biomass composition data to predict changes in growth and reaction flux distributions using the available genome-scale metabolic models of five eukaryotic organisms (three heterotrophs and two phototrophs). We identified temporal profiles of metabolic fluxes that indicate long-term trends in pathway and organelle function in response to nitrogen depletion. Surprisingly, our calculations of model sensitivity and biosynthetic cost showed that free energy of biomass metabolites is the main driver of biosynthetic cost and not molecular weight, thus explaining the high costs of arginine and histidine. We demonstrated how metabolic models can accurately predict the complexity of interwoven mechanisms in response to stress over the course of growth.
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35
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Ahmad A, Pathania R, Srivastava S. Biochemical Characteristics and a Genome-Scale Metabolic Model of an Indian Euryhaline Cyanobacterium with High Polyglucan Content. Metabolites 2020; 10:metabo10050177. [PMID: 32365713 PMCID: PMC7281201 DOI: 10.3390/metabo10050177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Marine cyanobacteria are promising microbes to capture and convert atmospheric CO2 and light into biomass and valuable industrial bio-products. Yet, reports on metabolic characteristics of non-model cyanobacteria are scarce. In this report, we show that an Indian euryhaline Synechococcus sp. BDU 130192 has biomass accumulation comparable to a model marine cyanobacterium and contains approximately double the amount of total carbohydrates, but significantly lower protein levels compared to Synechococcus sp. PCC 7002 cells. Based on its annotated chromosomal genome sequence, we present a genome scale metabolic model (GSMM) of this cyanobacterium, which we have named as iSyn706. The model includes 706 genes, 908 reactions, and 900 metabolites. The difference in the flux balance analysis (FBA) predicted flux distributions between Synechococcus sp. PCC 7002 and Synechococcus sp. BDU130192 strains mimicked the differences in their biomass compositions. Model-predicted oxygen evolution rate for Synechococcus sp. BDU130192 was found to be close to the experimentally-measured value. The model was analyzed to determine the potential of the strain for the production of various industrially-useful products without affecting growth significantly. This model will be helpful to researchers interested in understanding the metabolism as well as to design metabolic engineering strategies for the production of industrially-relevant compounds.
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Affiliation(s)
- Ahmad Ahmad
- DBT-ICGEB Center for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, Noida International University, Noida, U.P. 203201, India
| | - Ruchi Pathania
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| | - Shireesh Srivastava
- DBT-ICGEB Center for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Correspondence: ; Tel.: +91-11-26741361 (ext. 450)
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Lavoie M, Saint-Béat B, Strauss J, Guérin S, Allard A, V. Hardy S, Falciatore A, Lavaud J. Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness. BIOLOGY 2020; 9:biology9020030. [PMID: 32079178 PMCID: PMC7168318 DOI: 10.3390/biology9020030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/31/2020] [Accepted: 02/08/2020] [Indexed: 12/15/2022]
Abstract
Diatoms are major primary producers in polar environments where they can actively grow under extremely variable conditions. Integrative modeling using a genome-scale model (GSM) is a powerful approach to decipher the complex interactions between components of diatom metabolism and can provide insights into metabolic mechanisms underlying their evolutionary success in polar ecosystems. We developed the first GSM for a polar diatom, Fragilariopsis cylindrus, which enabled us to study its metabolic robustness using sensitivity analysis. We find that the predicted growth rate was robust to changes in all model parameters (i.e., cell biochemical composition) except the carbon uptake rate. Constraints on total cellular carbon buffer the effect of changes in the input parameters on reaction fluxes and growth rate. We also show that single reaction deletion of 20% to 32% of active (nonzero flux) reactions and single gene deletion of 44% to 55% of genes associated with active reactions affected the growth rate, as well as the production fluxes of total protein, lipid, carbohydrate, DNA, RNA, and pigments by less than 1%, which was due to the activation of compensatory reactions (e.g., analogous enzymes and alternative pathways) with more highly connected metabolites involved in the reactions that were robust to deletion. Interestingly, including highly divergent alleles unique for F. cylindrus increased its metabolic robustness to cellular perturbations even more. Overall, our results underscore the high robustness of metabolism in F. cylindrus, a feature that likely helps to maintain cell homeostasis under polar conditions.
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Affiliation(s)
- Michel Lavoie
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
- Correspondence:
| | - Blanche Saint-Béat
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
| | - Jan Strauss
- Department of Biology, University of Hamburg, D-22607 Hamburg, Germany;
- CSSB Centre for Structural Systems Biology, c/o Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Sébastien Guérin
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC G1V 0A6, Canada;
- Centre interdisciplinaire de modélisation mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Simon V. Hardy
- Département d’informatique et génie logiciel, Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada;
- Unité des Neurosciences cellulaires et moléculaires, Centre de recherche CERVO, Québec, QC G1V 0A6, Canada
| | - Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141, Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France;
| | - Johann Lavaud
- Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada; (B.S.-B.); (S.G.); (J.L.)
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Effect of Delays on the Response of Microalgae When Exposed to Dynamic Environmental Conditions. Processes (Basel) 2020. [DOI: 10.3390/pr8010087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
During mathematical representation of microbial cultures, it is normally assumed that changes in the environment produce instantaneous effects on growth. However, reports are available indicating that sometimes this may not be the case. This work studied the existence of delays on the response of a population of microalgae when subjected to changes in energy and carbon sources, and when exposed to a growth inhibitor. Results show that no appreciable delays exist when microalgae undergo changes in the incident light intensity. For changes in carbon source concentration (inorganic carbon), a small delay in the range of minutes was detected. Finally, when exposing microalgae to inhibitory concentrations of ammonia, a significant delay of several hours was observed.
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Cecchin M, Marcolungo L, Rossato M, Girolomoni L, Cosentino E, Cuine S, Li‐Beisson Y, Delledonne M, Ballottari M. Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1289-1305. [PMID: 31437318 PMCID: PMC6972661 DOI: 10.1111/tpj.14508] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 05/05/2023]
Abstract
Chlorella vulgaris is a fast-growing fresh-water microalga cultivated on the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed us to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seq data obtained at two different irradiances of growth (high light, HL versus low light, LL) enabled us to identify 10 724 nuclear genes, coding for 11 082 transcripts. Moreover, 121 and 48 genes, respectively, were found in the chloroplast and mitochondrial genome. Functional annotation and expression analysis of nuclear, chloroplast and mitochondrial genome sequences revealed particular features of Chlorella vulgaris. Evidence of horizontal gene transfers from chloroplast to mitochondrial genome was observed. Furthermore, comparative transcriptomic analyses of LL versus HL provided insights into the molecular basis for metabolic rearrangement under HL versus LL conditions leading to enhanced de novo fatty acid biosynthesis and triacylglycerol accumulation. The occurrence of a cytosolic fatty acid biosynthetic pathway could be predicted and its upregulation upon HL exposure was observed, consistent with the increased lipid amount under HL conditions. These data provide a rich genetic resource for future genome editing studies, and potential targets for biotechnological manipulation of Chlorella vulgaris or other microalgae species to improve biomass and lipid productivity.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Luca Marcolungo
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Marzia Rossato
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Laura Girolomoni
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Emanuela Cosentino
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Stephan Cuine
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Yonghua Li‐Beisson
- Institute of Biosciences and Biotechnologies of Aix‐Marseille, UMR7265Aix‐Marseille UniversityCEACNRSCEA CadaracheSaint‐Paul‐lez DuranceF‐13108France
| | - Massimo Delledonne
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
| | - Matteo Ballottari
- Dipartimento di BiotecnologieUniversità di VeronaStrada Le Grazie 1537134Verona, Italy
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Buchmann L, Brändle I, Haberkorn I, Hiestand M, Mathys A. Pulsed electric field based cyclic protein extraction of microalgae towards closed-loop biorefinery concepts. BIORESOURCE TECHNOLOGY 2019; 291:121870. [PMID: 31382092 DOI: 10.1016/j.biortech.2019.121870] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Microalgae-based biorefinery concepts can contribute to providing sufficient resources for a growing world population. However, the performance needs to be improved, which requires innovative technologies and processes. Continuous extraction from Chlorella vulgaris cultures via pulsed electric field (PEF) processing might be a viable process to increase the performance of microalgae-based biorefinery concepts. In this study, increasing protein extraction rates were observed with increasing electric field strength, up to 96.6 ± 4.8% of the free protein in the microalgae. However, increased extraction rates negatively influenced microalgae growth after PEF treatment. A free protein extraction rate up to 29.1 ± 1.1% without a significant influence on microalgal growth after 168 h was achieved (p = 0.788). Within the scope of this work, a protocol for continuous protein extraction during microalgae cultivation by PEF processing was developed. The incorporation of innovative downstream into upstream processing could be a viable future concept.
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Affiliation(s)
- Leandro Buchmann
- ETH Zurich, Department of Health Sciences and Technology, Institute of Food Nutrition and Health, IFNH, Laboratory of Sustainable Food Processing, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Ivraina Brändle
- ETH Zurich, Department of Health Sciences and Technology, Institute of Food Nutrition and Health, IFNH, Laboratory of Sustainable Food Processing, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Iris Haberkorn
- ETH Zurich, Department of Health Sciences and Technology, Institute of Food Nutrition and Health, IFNH, Laboratory of Sustainable Food Processing, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Michèle Hiestand
- ETH Zurich, Department of Health Sciences and Technology, Institute of Food Nutrition and Health, IFNH, Laboratory of Sustainable Food Processing, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Alexander Mathys
- ETH Zurich, Department of Health Sciences and Technology, Institute of Food Nutrition and Health, IFNH, Laboratory of Sustainable Food Processing, Schmelzbergstrasse 9, Zurich 8092, Switzerland.
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40
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Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities. Nat Microbiol 2019; 4:2184-2191. [PMID: 31591554 DOI: 10.1038/s41564-019-0567-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 08/21/2019] [Indexed: 12/28/2022]
Abstract
Phototrophic communities of photosynthetic algae or cyanobacteria and heterotrophic bacteria or fungi are pervasive throughout the environment1. How interactions between members contribute to the resilience and affect the fitness of phototrophic communities is not fully understood2,3. Here, we integrated metatranscriptomics, metabolomics and phenotyping with computational modelling to reveal condition-dependent secretion and cross-feeding of metabolites in a synthetic community. We discovered that interactions between members are highly dynamic and are driven by the availability of organic and inorganic nutrients. Environmental factors, such as ammonia concentration, influenced community stability by shifting members from collaborating to competing. Furthermore, overall fitness was dependent on genotype and streamlined genomes improved growth of the entire community. Our mechanistic framework provides insights into the physiology and metabolic response to environmental and genetic perturbation of these ubiquitous microbial associations.
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41
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Liu X, Wang K, Wang J, Zuo J, Peng F, Wu J, San E. Carbon dioxide fixation coupled with ammonium uptake by immobilized Scenedesmus obliquus and its potential for protein production. BIORESOURCE TECHNOLOGY 2019; 289:121685. [PMID: 31323715 DOI: 10.1016/j.biortech.2019.121685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
In this study, immobilized Scenedesmus obliquus (S. obliquus) was proposed to simultaneously alleviate the carbon dioxide (CO2) and ammonium (NH4+-N). Two trophic modes of autotrophy and mixotrophy were conducted by batch experiments with a period of 5 days. The results shown that NH4+-N could be removed more efficiently if algal cells were immobilized, and the trophic mode change had no significant effect on immobilized S. obliquus to NH4+-N removal under 5% CO2 sparging. Specifically, immobilized S. obliquus could remove NH4+-N completely at initial concentrations of 30 and 50 mg/L and reached about 80% removal rate of NH4+-N at the concentration of 70 mg/L under both trophic modes. The protein synthesis was its main removal mechanism and the dominant amino acid components including glutamic acid (Glu), cystine (Cys), arginine (Arg), methionine (Met) and lysine (Lys) were sensitive to NH4+-N assimilation.
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Affiliation(s)
- Xiang Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Kaijun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
| | - Jingyao Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Jiane Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Fei Peng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Jing Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Erfu San
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
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42
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Li CT, Yelsky J, Chen Y, Zuñiga C, Eng R, Jiang L, Shapiro A, Huang KW, Zengler K, Betenbaugh MJ. Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity. NPJ Syst Biol Appl 2019; 5:33. [PMID: 31583115 PMCID: PMC6760154 DOI: 10.1038/s41540-019-0110-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 08/21/2019] [Indexed: 11/09/2022] Open
Abstract
Nutrient availability is critical for growth of algae and other microbes used for generating valuable biochemical products. Determining the optimal levels of nutrient supplies to cultures can eliminate feeding of excess nutrients, lowering production costs and reducing nutrient pollution into the environment. With the advent of omics and bioinformatics methods, it is now possible to construct genome-scale models that accurately describe the metabolism of microorganisms. In this study, a genome-scale model of the green alga Chlorella vulgaris (iCZ946) was applied to predict feeding of multiple nutrients, including nitrate and glucose, under both autotrophic and heterotrophic conditions. The objective function was changed from optimizing growth to instead minimizing nitrate and glucose uptake rates, enabling predictions of feed rates for these nutrients. The metabolic model control (MMC) algorithm was validated for autotrophic growth, saving 18% nitrate while sustaining algal growth. Additionally, we obtained similar growth profiles by simultaneously controlling glucose and nitrate supplies under heterotrophic conditions for both high and low levels of glucose and nitrate. Finally, the nitrate supply was controlled in order to retain protein and chlorophyll synthesis, albeit at a lower rate, under nitrogen-limiting conditions. This model-driven cultivation strategy doubled the total volumetric yield of biomass, increased fatty acid methyl ester (FAME) yield by 61%, and enhanced lutein yield nearly 3 fold compared to nitrogen starvation. This study introduces a control methodology that integrates omics data and genome-scale models in order to optimize nutrient supplies based on the metabolic state of algal cells in different nutrient environments. This approach could transform bioprocessing control into a systems biology-based paradigm suitable for a wide range of species in order to limit nutrient inputs, reduce processing costs, and optimize biomanufacturing for the next generation of desirable biotechnology products.
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Affiliation(s)
- Chien-Ting Li
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Jacob Yelsky
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Yiqun Chen
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Cristal Zuñiga
- 2Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760 USA
- 3Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412 USA
| | - Richard Eng
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Liqun Jiang
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
- 4School of Environmental Science and Engineering, Shandong University, No.27 Shanda Nan Road, Jinan, 250100 China
| | - Alison Shapiro
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Kai-Wen Huang
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Karsten Zengler
- 2Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760 USA
- 3Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412 USA
- 5Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0436 USA
| | - Michael J Betenbaugh
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
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Gupta A, Ahmad A, Chothwe D, Madhu MK, Srivastava S, Sharma VK. Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotroph Methylococcus capsulatus str. Bath. PeerJ 2019; 7:e6685. [PMID: 31316867 PMCID: PMC6613435 DOI: 10.7717/peerj.6685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/13/2019] [Indexed: 12/27/2022] Open
Abstract
The increase in greenhouse gases with high global warming potential such as methane is a matter of concern and requires multifaceted efforts to reduce its emission and increase its mitigation from the environment. Microbes such as methanotrophs can assist in methane mitigation. To understand the metabolic capabilities of methanotrophs, a complete genome-scale metabolic model (GSMM) of an obligate methanotroph, Methylococcus capsulatus str. Bath was reconstructed. The model contains 535 genes, 899 reactions and 865 metabolites and is named iMC535. The predictive potential of the model was validated using previously-reported experimental data. The model predicted the Entner–Duodoroff pathway to be essential for the growth of this bacterium, whereas the Embden–Meyerhof–Parnas pathway was found non-essential. The performance of the model was simulated on various carbon and nitrogen sources and found that M. capsulatus can grow on amino acids. The analysis of network topology of the model identified that six amino acids were in the top-ranked metabolic hubs. Using flux balance analysis, 29% of the metabolic genes were predicted to be essential, and 76 double knockout combinations involving 92 unique genes were predicted to be lethal. In conclusion, we have reconstructed a GSMM of a methanotroph Methylococcus capsulatus str. Bath. This is the first high quality GSMM of a Methylococcus strain which can serve as an important resource for further strain-specific models of the Methylococcus genus, as well as identifying the biotechnological potential of M. capsulatus Bath.
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Affiliation(s)
- Ankit Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Ahmad Ahmad
- Systems Biology for Biofuels Group, International Centre For Genetic Engineering And Biotechnology, New Delhi, India.,Department of Biotechnology, Noida International University, Noida, India
| | - Dipesh Chothwe
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Midhun K Madhu
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre For Genetic Engineering And Biotechnology, New Delhi, India
| | - Vineet K Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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Fu W, Gudmundsson S, Wichuk K, Palsson S, Palsson BO, Salehi-Ashtiani K, Brynjólfsson S. Sugar-stimulated CO 2 sequestration by the green microalga Chlorella vulgaris. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:275-283. [PMID: 30445327 DOI: 10.1016/j.scitotenv.2018.11.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
To convert waste CO2 from flue gases of power plants into value-added products, bio-mitigation technologies show promise. In this study, we cultivated a fast-growing species of green microalgae, Chlorella vulgaris, in different sizes of photobioreactors (PBRs) and developed a strategy using small doses of sugars for enhancing CO2 sequestration under light-emitting diode illumination. Glucose supplementation at low levels resulted in an increase of photoautotrophic growth-driven biomass generation as well as CO2 capture by 10% and its enhancement corresponded to an increase of supplied photon flux. The utilization of urea instead of nitrate as the sole nitrogen source increased photoautotrophic growth by 14%, but change of nitrogen source didn't compromise glucose-induced enhancement of photoautotrophic growth. The optimized biomass productivity achieved was 30.4% higher than the initial productivity of purely photoautotrophic culture. The major pigments in the obtained algal biomass were found comparable to its photoautotrophic counterpart and a high neutral lipids productivity of 516.6 mg/(L·day) was achieved after optimization. A techno-economic model was also developed, indicating that LED-based PBRs represent a feasible strategy for converting CO2 into value-added algal biomass.
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Affiliation(s)
- Weiqi Fu
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavík, Iceland; Division of Science and Math, Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Steinn Gudmundsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavík, Iceland
| | - Kristine Wichuk
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavík, Iceland
| | - Sirus Palsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavík, Iceland
| | - Bernhard O Palsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavík, Iceland; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Sigurður Brynjólfsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, 101 Reykjavík, Iceland
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45
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Rincon SM, Urrego NF, Avila KJ, Romero HM, Beyenal H. Photosynthetic activity assessment in mixotrophically cultured Chlorella vulgaris biofilms at various developmental stages. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101408] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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46
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Sforza E, Pastore M, Barbera E, Bertucco A. Respirometry as a tool to quantify kinetic parameters of microalgal mixotrophic growth. Bioprocess Biosyst Eng 2019; 42:839-851. [DOI: 10.1007/s00449-019-02087-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/30/2019] [Indexed: 10/27/2022]
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47
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Parichehreh R, Gheshlaghi R, Mahdavi MA, Elkamel A. Optimization of lipid production in Chlorella vulgaris for biodiesel production using flux balance analysis. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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48
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Metabolomic profiles of tropical Chlorella and Parachlorella species in response to physiological changes during exponential and stationary growth phase. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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49
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Tibocha-Bonilla JD, Zuñiga C, Godoy-Silva RD, Zengler K. Advances in metabolic modeling of oleaginous microalgae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:241. [PMID: 30202436 PMCID: PMC6124020 DOI: 10.1186/s13068-018-1244-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Production of biofuels and bioenergy precursors by phototrophic microorganisms, such as microalgae and cyanobacteria, is a promising alternative to conventional fuels obtained from non-renewable resources. Several species of microalgae have been investigated as potential candidates for the production of biofuels, for the most part due to their exceptional metabolic capability to accumulate large quantities of lipids. Constraint-based modeling, a systems biology approach that accurately predicts the metabolic phenotype of phototrophs, has been deployed to identify suitable culture conditions as well as to explore genetic enhancement strategies for bioproduction. Core metabolic models were employed to gain insight into the central carbon metabolism in photosynthetic microorganisms. More recently, comprehensive genome-scale models, including organelle-specific information at high resolution, have been developed to gain new insight into the metabolism of phototrophic cell factories. Here, we review the current state of the art of constraint-based modeling and computational method development and discuss how advanced models led to increased prediction accuracy and thus improved lipid production in microalgae.
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Affiliation(s)
- Juan D. Tibocha-Bonilla
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Av. Carrera 30 No. 45-03, Bogotá, D.C. Colombia
| | - Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760 USA
| | - Rubén D. Godoy-Silva
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Av. Carrera 30 No. 45-03, Bogotá, D.C. Colombia
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760 USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412 USA
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0436 USA
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Arora N, Pienkos PT, Pruthi V, Poluri KM, Guarnieri MT. Leveraging algal omics to reveal potential targets for augmenting TAG accumulation. Biotechnol Adv 2018; 36:1274-1292. [PMID: 29678388 DOI: 10.1016/j.biotechadv.2018.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 02/08/2023]
Abstract
Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.
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Affiliation(s)
- Neha Arora
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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