1
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Steichen S, Deshpande A, Mosey M, Loob J, Douchi D, Knoshaug EP, Brown S, Nielsen R, Weissman J, Carrillo LR, Laurens LML. Central transcriptional regulator controls photosynthetic growth and carbon storage in response to high light. Nat Commun 2024; 15:4842. [PMID: 38844786 PMCID: PMC11156908 DOI: 10.1038/s41467-024-49090-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Carbon capture and biochemical storage are some of the primary drivers of photosynthetic yield and productivity. To elucidate the mechanisms governing carbon allocation, we designed a photosynthetic light response test system for genetic and metabolic carbon assimilation tracking, using microalgae as simplified plant models. The systems biology mapping of high light-responsive photophysiology and carbon utilization dynamics between two variants of the same Picochlorum celeri species, TG1 and TG2 elucidated metabolic bottlenecks and transport rates of intermediates using instationary 13C-fluxomics. Simultaneous global gene expression dynamics showed 73% of the annotated genes responding within one hour, elucidating a singular, diel-responsive transcription factor, closely related to the CCA1/LHY clock genes in plants, with significantly altered expression in TG2. Transgenic P. celeri TG1 cells expressing the TG2 CCA1/LHY gene, showed 15% increase in growth rates and 25% increase in storage carbohydrate content, supporting a coordinating regulatory function for a single transcription factor.
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Affiliation(s)
- Seth Steichen
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Arnav Deshpande
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Megan Mosey
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Jessica Loob
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Damien Douchi
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Stuart Brown
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Robert Nielsen
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Joseph Weissman
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - L Ruby Carrillo
- ExxonMobil Technology and Engineering Co. (EMTEC), CLD286 Annandale, 1545 Route 22 East, Annandale, NJ, 08801, USA
| | - Lieve M L Laurens
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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2
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da Roza PA, Muller H, Sullivan GJ, Walker RSK, Goold HD, Willows RD, Palenik B, Paulsen IT. Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C 4 photosynthesis. Microb Genom 2024; 10. [PMID: 38625719 DOI: 10.1099/mgen.0.001223] [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: 04/17/2024] Open
Abstract
Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.
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Affiliation(s)
- Patrick A da Roza
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Héloïse Muller
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Roy S K Walker
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Hugh D Goold
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia
| | - Robert D Willows
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, Australia
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3
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Takusagawa M, Misumi O, Nozaki H, Kato S, Maruyama S, Tsujimoto-Inui Y, Yagisawa F, Ohnuma M, Kuroiwa H, Kuroiwa T, Matsunaga S. Complete mitochondrial and chloroplast DNA sequences of the freshwater green microalga Medakamo hakoo. Genes Genet Syst 2024; 98:353-360. [PMID: 38267054 DOI: 10.1266/ggs.23-00275] [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: 01/26/2024] Open
Abstract
We report the complete organellar genome sequences of an ultrasmall green alga, Medakamo hakoo strain M-hakoo 311, which has the smallest known nuclear genome in freshwater green algae. Medakamo hakoo has 90.8-kb chloroplast and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein-coding genes, respectively. The mitochondrial genome is the smallest in the Trebouxiophyceae algae studied so far. The GC content of the nuclear genome is 73%, but those of chloroplast and mitochondrial genomes are 41% and 35%, respectively. Codon usages in the organellar genomes have a different tendency from that in the nuclear genome. The organellar genomes have unique characteristics, such as the biased encoding of mitochondrial genes on a single strand and the absence of operon structures in chloroplast ribosomal genes. Medakamo hakoo will be helpful for understanding the evolution of the organellar genome and the regulation of gene expression in chloroplasts and mitochondria.
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Affiliation(s)
- Mari Takusagawa
- Department of Botany, Graduate School of Science, Kyoto University
- Department of Biology, Faculty of Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Osami Misumi
- Department of Biology, Faculty of Science, Graduate School of Sciences and Technology for Innovation, Yamaguchi University
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Shoichi Kato
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Shinichiro Maruyama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Yayoi Tsujimoto-Inui
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Fumi Yagisawa
- Research Facility Center, University of the Ryukyus
- Graduate School of Engineering and Science, University of the Ryukyus
| | - Mio Ohnuma
- National Institute of Technology (KOSEN), Hiroshima College
| | - Haruko Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University
| | - Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Science, Faculty of Science, Japan Women's University
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
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4
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Cano M, Krishnan A, Karns DA, Likhogrud MA, Weissman JC, Posewitz MC. Cas9 deletion of lutein biosynthesis in the marine alga Picochlorum celeri reduces photosynthetic pigments while sustaining high biomass productivity. Front Bioeng Biotechnol 2024; 11:1332461. [PMID: 38274009 PMCID: PMC10808502 DOI: 10.3389/fbioe.2023.1332461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Domestication of algae for food and renewable biofuels remains limited by the low photosynthetic efficiencies of processes that have evolved to be competitive for optimal light capture, incentivizing the development of large antennas in light-limiting conditions, thus decreasing efficient light utilization in cultivated ponds or photobioreactors. Reducing the pigment content to improve biomass productivity has been a strategy discussed for several decades and the ability to reduce pigment significantly is now fully at hand thanks to the widespread use of genome editing tools. Picochlorum celeri is one of the fastest growing marine algae identified and holds particular promise for outdoor cultivation, especially in saline water and warm climates. We show that while chlorophyll b is essential to sustain high biomass productivities under dense cultivation, removing Picochlorum celeri's main carotenoid, lutein, leads to a decreased total chlorophyll content, higher a/b ratio, reduced functional LHCII cross section and higher maximum quantum efficiencies at lower light intensities, resulting in an incremental increase in biomass productivity and increased PAR-to-biomass conversion efficiency. These findings further strengthen the existing strategies to improve photosynthetic efficiency and biomass production in algae.
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Affiliation(s)
- Melissa Cano
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States
| | - Anagha Krishnan
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States
| | - Devin A. Karns
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States
| | - Maria A. Likhogrud
- ExxonMobil Technology and Engineering Company, Annandale, NJ, United States
| | - Joseph C. Weissman
- ExxonMobil Technology and Engineering Company, Annandale, NJ, United States
| | - Matthew C. Posewitz
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States
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5
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Li X, Liu H, Lin Z, Richardson JJ, Xie W, Chen F, Lin W, Caruso F, Zhou J, Liu B. Cytoprotective Metal-Phenolic Network Sporulation to Modulate Microalgal Mobility and Division. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308026. [PMID: 38014599 PMCID: PMC10797472 DOI: 10.1002/advs.202308026] [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: 10/24/2023] [Indexed: 11/29/2023]
Abstract
Synthetic cell exoskeletons created from abiotic materials have attracted interest in materials science and biotechnology, as they can regulate cell behavior and create new functionalities. Here, a facile strategy is reported to mimic microalgal sporulation with on-demand germination and locomotion via responsive metal-phenolic networks (MPNs). Specifically, MPNs with tunable thickness and composition are deposited on the surface of microalgae cells via one-step coordination, without any loss of cell viability or intrinsic cell photosynthetic properties. The MPN coating keeps the cells in a dormant state, but can be disassembled on-demand in response to environmental pH or chemical stimulus, thereby reviving the microalgae within 1 min. Moreover, the artificial sporulation of microalgae resulted in resistance to environmental stresses (e.g., metal ions and antibiotics) akin to the function of natural sporulation. This strategy can regulate the life cycle of complex cells, providing a synthetic strategy for designing hybrid microorganisms.
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Affiliation(s)
- Xiaojie Li
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
| | - Hai Liu
- College of Biomass Science and EngineeringKey Laboratory of Leather Chemistry and Engineering of Ministry of EducationNational Engineering Laboratory for Clean Technology of Leather ManufactureSichuan UniversityChengdu610065China
| | - Zhixing Lin
- Department of Chemical EngineeringThe University of MelbourneParkvilleVictoria3010Australia
| | - Joseph J. Richardson
- Department of Chemical and Environmental EngineeringRMIT UniversityMelbourneVictoria3000Australia
| | - Weiying Xie
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
| | - Feng Chen
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
| | - Wei Lin
- College of Biomass Science and EngineeringKey Laboratory of Leather Chemistry and Engineering of Ministry of EducationNational Engineering Laboratory for Clean Technology of Leather ManufactureSichuan UniversityChengdu610065China
| | - Frank Caruso
- Department of Chemical EngineeringThe University of MelbourneParkvilleVictoria3010Australia
| | - Jiajing Zhou
- College of Biomass Science and EngineeringKey Laboratory of Leather Chemistry and Engineering of Ministry of EducationNational Engineering Laboratory for Clean Technology of Leather ManufactureSichuan UniversityChengdu610065China
| | - Bin Liu
- Shenzhen Key Laboratory of Marine Microbiome EngineeringShenzhen Key Laboratory of Food Nutrition and HealthInstitute for Advanced StudyCollege of Chemistry and Environmental EngineeringShenzhen UniversityShenzhen518060China
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6
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Groussman RD, Blaskowski S, Coesel SN, Armbrust EV. MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Sci Data 2023; 10:926. [PMID: 38129449 PMCID: PMC10739892 DOI: 10.1038/s41597-023-02842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.
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Affiliation(s)
- R D Groussman
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
| | - S Blaskowski
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Molecular Engineering & Sciences Building 3946 W Stevens Way NE, Seattle, WA, 98195, USA
| | - S N Coesel
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
| | - E V Armbrust
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
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7
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Wang B, Zuniga C, Guarnieri MT, Zengler K, Betenbaugh M, Young JD. Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis. Metab Eng 2023; 80:12-24. [PMID: 37678664 DOI: 10.1016/j.ymben.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/28/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
The capability of cyanobacteria to produce sucrose from CO2 and light has a remarkable societal and biotechnological impact since sucrose can serve as a carbon and energy source for a variety of heterotrophic organisms and can be converted into value-added products. However, most metabolic engineering efforts have focused on understanding local pathway alterations that drive sucrose biosynthesis and secretion in cyanobacteria rather than analyzing the global flux re-routing that occurs following induction of sucrose production by salt stress. Here, we investigated global metabolic flux alterations in a sucrose-secreting (cscB-overexpressing) strain relative to its wild-type Synechococcus elongatus 7942 parental strain. We used targeted metabolomics, 13C metabolic flux analysis (MFA), and genome-scale modeling (GSM) as complementary approaches to elucidate differences in cellular resource allocation by quantifying metabolic profiles of three cyanobacterial cultures - wild-type S. elongatus 7942 without salt stress (WT), wild-type with salt stress (WT/NaCl), and the cscB-overexpressing strain with salt stress (cscB/NaCl) - all under photoautotrophic conditions. We quantified the substantial rewiring of metabolic fluxes in WT/NaCl and cscB/NaCl cultures relative to WT and identified a metabolic bottleneck limiting carbon fixation and sucrose biosynthesis. This bottleneck was subsequently mitigated through heterologous overexpression of glyceraldehyde-3-phosphate dehydrogenase in an engineered sucrose-secreting strain. Our study also demonstrates that combining 13C-MFA and GSM is a useful strategy to both extend the coverage of MFA beyond central metabolism and to improve the accuracy of flux predictions provided by GSM.
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Affiliation(s)
- Bo Wang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Center for Microbiome Innovation, University of California, San Diego, CA, 92093, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA.
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8
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Krishnan A, Cano M, Karns DA, Burch TA, Likhogrud M, Aqui M, Bailey S, Verruto J, Lambert W, Kuzminov F, Naghipor M, Wang Y, Ebmeier CC, Weissman JC, Posewitz MC. Simultaneous CAS9 editing of cp SRP43, LHCA6, and LHCA7 in Picochlorum celeri lowers chlorophyll levels and improves biomass productivity. PLANT DIRECT 2023; 7:e530. [PMID: 37711644 PMCID: PMC10497401 DOI: 10.1002/pld3.530] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
High cellular pigment levels in dense microalgal cultures contribute to excess light absorption. To improve photosynthetic yields in the marine microalga Picochlorum celeri, CAS9 gene editing was used to target the molecular chaperone cpSRP43. Depigmented strains (>50% lower chlorophyll) were generated, with proteomics showing attenuated levels of most light harvesting complex (LHC) proteins. Gene editing generated two types of cpSRP43 transformants with distinct lower pigment phenotypes: (i) a transformant (Δsrp43) with both cpSRP43 diploid alleles modified to encode non-functional polypeptides and (ii) a transformant (STR30309) with a 3 nt in-frame insertion in one allele at the CAS9 cut site (non-functional second allele), leading to expression of a modified cpSRP43. STR30309 has more chlorophyll than Δsrp43 but substantially less than wild type. To further decrease light absorption by photosystem I in STR30309, CAS9 editing was used to stack in disruptions of both LHCA6 and LHCA7 to generate STR30843, which has higher (5-24%) productivities relative to wild type in solar-simulating bioreactors. Maximal productivities required frequent partial harvests throughout the day. For STR30843, exemplary diel bioreactor yields of ~50 g m-2 day-1 were attained. Our results demonstrate diel productivity gains in P. celeri by lowering pigment levels.
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Affiliation(s)
- Anagha Krishnan
- Department of ChemistryColorado School of MinesGoldenColoradoUSA
| | - Melissa Cano
- Department of ChemistryColorado School of MinesGoldenColoradoUSA
| | - Devin A. Karns
- Department of ChemistryColorado School of MinesGoldenColoradoUSA
| | - Tyson A. Burch
- Department of ChemistryColorado School of MinesGoldenColoradoUSA
| | - Maria Likhogrud
- ExxonMobil Technology and Engineering CompanyAnnandaleNew JerseyUSA
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9
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Dahlin LR, Meyers AW, Stefani SW, Webb EG, Wachter B, Subramanian V, Guarnieri MT. Heterologous expression of formate dehydrogenase enables photoformatotrophy in the emerging model microalga, Picochlorum renovo. Front Bioeng Biotechnol 2023; 11:1162745. [PMID: 37706077 PMCID: PMC10497104 DOI: 10.3389/fbioe.2023.1162745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/04/2023] [Indexed: 09/15/2023] Open
Abstract
Rising global greenhouse gas emissions and the impacts of resultant climate change necessitate development and deployment of carbon capture and conversion technologies. Amongst the myriad of bio-based conversion approaches under evaluation, a formate bio-economy has recently been proposed, wherein CO2-derived formate serves as a substrate for concurrent carbon and energy delivery to microbial systems. To date, this approach has been explored in chemolithotrophic and heterotrophic organisms via native or engineered formatotrophy. However, utilization of this concept in phototrophic organisms has yet to be reported. Herein, we have taken the first steps to establish formate utilization in Picochlorum renovo, a recently characterized eukaryotic microalga with facile genetic tools and promising applied biotechnology traits. Plastidial heterologous expression of a formate dehydrogenase (FDH) enabled P. renovo growth on formate as a carbon and energy source. Further, FDH expression enhanced cultivation capacity on ambient CO2, underscoring the potential for bypass of conventional CO2 capture and concentration limitations. This work establishes a photoformatotrophic cultivation regime that leverages light energy-driven formate utilization. The resultant photosynthetic formate platform has widespread implications for applied phototrophic cultivation systems and the bio-economy at large.
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Affiliation(s)
- Lukas R. Dahlin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Alex W. Meyers
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Skylar W. Stefani
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Ellsbeth G. Webb
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Benton Wachter
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Michael T. Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, United States
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, United States
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10
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Barbosa MJ, Janssen M, Südfeld C, D'Adamo S, Wijffels RH. Hypes, hopes, and the way forward for microalgal biotechnology. Trends Biotechnol 2023; 41:452-471. [PMID: 36707271 DOI: 10.1016/j.tibtech.2022.12.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/26/2023]
Abstract
The urge for food security and sustainability has advanced the field of microalgal biotechnology. Microalgae are microorganisms able to grow using (sun)light, fertilizers, sugars, CO2, and seawater. They have high potential as a feedstock for food, feed, energy, and chemicals. Microalgae grow faster and have higher areal productivity than plant crops, without competing for agricultural land and with 100% efficiency uptake of fertilizers. In comparison with bacterial, fungal, and yeast single-cell protein production, based on hydrogen or sugar, microalgae show higher land-use efficiency. New insights are provided regarding the potential of microalgae replacing soy protein, fish oil, and palm oil and being used as cell factories in modern industrial biotechnology to produce designer feed, recombinant proteins, biopharmaceuticals, and vaccines.
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Affiliation(s)
- Maria J Barbosa
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700, AA, The Netherlands.
| | - Marcel Janssen
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700, AA, The Netherlands
| | - Christian Südfeld
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700, AA, The Netherlands
| | - Sarah D'Adamo
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700, AA, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700, AA, The Netherlands; Biosciences and Aquaculture, Nord University, Bodø, N-8049,Norway
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11
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Patel VK, Das A, Kumari R, Kajla S. Recent progress and challenges in CRISPR-Cas9 engineered algae and cyanobacteria. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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12
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Gao S, Edmundson S, Huesemann M, Gutknecht A, Laurens LM, Van Wychen S, Pittman K, Greer M. DISCOVR strain screening pipeline – Part III: Strain evaluation in outdoor raceway ponds. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.102990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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13
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LaPanse AJ, Burch TA, Tamburro JM, Traller JC, Pinowska A, Posewitz MC. Adaptive laboratory evolution for increased temperature tolerance of the diatom Nitzschia inconspicua. Microbiologyopen 2022; 12:e1343. [PMID: 36825881 PMCID: PMC9791160 DOI: 10.1002/mbo3.1343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022] Open
Abstract
Outdoor microalgal cultivation for the production of valuable biofuels and bioproducts typically requires high insolation and strains with high thermal (>37°C) tolerance. While some strains are naturally thermotolerant, other strains of interest require improved performance at elevated temperatures to enhance industrial viability. In this study, adaptive laboratory evolution (ALE) was performed for over 300 days using consecutive 0.5°C temperature increases in a constant temperature incubator to attain greater thermal tolerance in the industrially relevant diatom Nitzschia inconspicua str. Hildebrandi. The adapted strain was able to grow at a constant temperature of 37.5°C; whereas this constant temperature was lethal to the parental control, which had an upper-temperature boundary of 35.5°C before adaptive evolution. Several high-temperature clonal isolates were obtained from the evolved population following ALE, and increased temperature tolerance was observed in the clonal, parent, and non-clonal adapted cultures. This ALE method demonstrates the development of enhanced industrial algal strains without the production of genetically modified organisms (GMOs).
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Affiliation(s)
| | - Tyson A. Burch
- Department of ChemistryColorado School of MinesGoldenColoradoUSA
| | - Jacob M. Tamburro
- Department of Quantitative Biosciences and EngineeringColorado School of MinesGoldenColoradoUSA
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14
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Barten R, van Workum DJM, de Bakker E, Risse J, Kleisman M, Navalho S, Smit S, Wijffels RH, Nijveen H, Barbosa MJ. Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution. BMC Biol 2022; 20:242. [PMID: 36303154 PMCID: PMC9615354 DOI: 10.1186/s12915-022-01431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptive laboratory evolution (ALE) is a powerful method for strain optimization towards abiotic stress factors and for identifying adaptation mechanisms. In this study, the green microalga Picochlorum sp. BPE23 was cultured under supra-optimal temperature to force genetic adaptation. The robustness and adaptive capacity of Picochlorum strains turned them into an emerging model for evolutionary studies on abiotic stressors such as temperature, salinity, and light. RESULTS Mutant strains showed an expanded maximal growth temperature of 44.6 °C, whereas the maximal growth temperature of the wild-type strain was 42 °C. Moreover, at the optimal growth temperature of 38 °C, the biomass yield on light was 22.3% higher, and the maximal growth rate was 70.5% higher than the wild type. Genome sequencing and transcriptome analysis were performed to elucidate the mechanisms behind the improved phenotype. A de novo assembled phased reference genome allowed the identification of 21 genic mutations involved in various processes. Moreover, approximately half of the genome contigs were found to be duplicated or even triplicated in all mutants, suggesting a causal role in adaptation. CONCLUSIONS The developed tools and mutant strains provide a strong framework from whereupon Picochlorum sp. BPE23 can be further developed. Moreover, the extensive strain characterization provides evidence of how microalgae evolve to supra-optimal temperature and to photobioreactor growth conditions. With this study, microalgal evolutionary mechanisms were identified by combining ALE with genome sequencing.
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Affiliation(s)
- Robin Barten
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands.
| | - Dirk-Jan M van Workum
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Emma de Bakker
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
| | - Judith Risse
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Michelle Kleisman
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Sofia Navalho
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands.,Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Maria J Barbosa
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
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15
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Minimum nitrogen cell quota for maximal growth rate in cycloturbidostat cultures of Picochlorum oklahomense. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Sanders CK, Hanschen ER, Biondi TC, Hovde BT, Kunde YA, Eng WL, Kwon T, Dale T. Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. "desiccata" (Trebouxiophyceae, Chlorophyta), formerly Chlorella desiccata, supported by a high-quality genome assembly. JOURNAL OF PHYCOLOGY 2022; 58:436-448. [PMID: 35262191 DOI: 10.1111/jpy.13242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Microalgae are diverse, with many gaps remaining in phylogenetic and physiological understanding. Thus, studying new microalgae species increases our broader comprehension of biological diversity, and evaluation of new candidates as algal production platforms can lead to improved productivity under a variety of cultivation conditions. Chlorella is a genus of fast-growing species often isolated from freshwater habitats and cultivated as a source of nutritional supplements. However, the use of freshwater increases competition with other freshwater needs. We identified Chlorella desiccata to be worthy of further investigation as a potential algae production strain, due to its isolation from a marine environment and its promising growth and biochemical composition properties. Long-read genomic sequencing was conducted for C. desiccata UTEX 2526, resulting in a high-quality, near chromosome level, diploid genome with an assembly length of 21.55 Mbp in only 18 contigs. We also report complete circular mitochondrial and chloroplast genomes. Phylogenomic and phylogenetic analyses using nuclear, chloroplast, 18S rRNA, and actin sequences revealed that this species clades within strains currently identified as Nannochloris (Trebouxiophyceae, Chlorophyta), leading to its reclassification as Nannochloris sp. "desiccata" UTEX 2526. The mode of cell division for this species is autosporulation, differing from the type species N. bacillaris. As has occurred across multiple microalgae genera, there are repeated examples of Nannochloris species reclassification in the literature. This high-quality genome assembly and phylogenetic analysis of the potential algal production strain Nannochloris sp. "desiccata" UTEX 2526 provides an important reference and useful tool for further studying this region of the phylogenetic tree.
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Affiliation(s)
- Claire K Sanders
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Erik R Hanschen
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Thomas C Biondi
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Blake T Hovde
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Yuliya A Kunde
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Wyatt L Eng
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Taehyung Kwon
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
| | - Taraka Dale
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico, 87545, USA
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17
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Harnessing the Algal Chloroplast for Heterologous Protein Production. Microorganisms 2022; 10:microorganisms10040743. [PMID: 35456794 PMCID: PMC9025058 DOI: 10.3390/microorganisms10040743] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
Photosynthetic microbes are gaining increasing attention as heterologous hosts for the light-driven, low-cost production of high-value recombinant proteins. Recent advances in the manipulation of unicellular algal genomes offer the opportunity to establish engineered strains as safe and viable alternatives to conventional heterotrophic expression systems, including for their use in the feed, food, and biopharmaceutical industries. Due to the relatively small size of their genomes, algal chloroplasts are excellent targets for synthetic biology approaches, and are convenient subcellular sites for the compartmentalized accumulation and storage of products. Different classes of recombinant proteins, including enzymes and peptides with therapeutical applications, have been successfully expressed in the plastid of the model organism Chlamydomonas reinhardtii, and of a few other species, highlighting the emerging potential of transplastomic algal biotechnology. In this review, we provide a unified view on the state-of-the-art tools that are available to introduce protein-encoding transgenes in microalgal plastids, and discuss the main (bio)technological bottlenecks that still need to be addressed to develop robust and sustainable green cell biofactories.
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18
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Goswami RK, Mehariya S, Karthikeyan OP, Verma P. Influence of Carbon Sources on Biomass and Biomolecule Accumulation in Picochlorum sp. Cultured under the Mixotrophic Condition. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19063674. [PMID: 35329358 PMCID: PMC8954116 DOI: 10.3390/ijerph19063674] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/12/2022] [Accepted: 03/17/2022] [Indexed: 11/18/2022]
Abstract
The major downfalls of the microalgal biorefinery are low volume of high value product accumulation, low biomass productivity and high cultivation costs. Here, we aimed to improve the biomass productivity of the industrially relevant Picochlorum sp. BDUG 100241 strain. The growth of Picochlorum sp. BDUG 100241 was investigated under different cultivations conditions, including photoautotrophic (with light), mixotrophic (1% glucose, with light) and heterotrophic (1% glucose, without light). Among them, Picochlorum sp. BDUG100241 showed the highest growth in the mixotrophic condition. Under different (1%) carbon sources’ supplementation, including glucose, sodium acetate, glycerol, citric acid and methanol, Picochlorum sp. BDUG100241 growth was tested. Among them, sodium acetate was found to be most suitable carbon source for Picochlorum sp. BDUG 100241 growth, biomass (1.67 ± 0.18 g/L) and biomolecule productivity. From the different concentrations of sodium acetate (0, 2.5, 5.0, 7.5 and 10 g/L) tested, the maximum biomass production of 2.40 ± 0.20 g/L with the biomass productivity of 95 ± 5.00 mg/L/d was measured from 7.5 g/L in sodium acetate. The highest total lipid (53.50 ± 1.70%) and total carotenoids (0.75 ± 0.01 µg/mL) contents were observed at the concentration of 7.5 g/L and 5.0 g/L of sodium acetate as a carbon source, respectively. In conclusion, the mixotrophic growth condition containing 7.5 g/L of sodium acetate showed the maximum biomass yield and biomolecule accumulation compared to other organic carbon sources.
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Affiliation(s)
- Rahul Kumar Goswami
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, Kishangarh 305817, India;
| | - Sanjeet Mehariya
- Department of Engineering, University of Campania “Luigi Vanvitelli”, Real Casa dell’Annunziata, Via Roma 29, 81031 Aversa, Italy;
| | - Obulisamy Parthiba Karthikeyan
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX 77400, USA;
- Institute of Bioresource and Agriculture, Hong Kong Baptist University, Hong Kong, China
- Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, Kishangarh 305817, India;
- Correspondence: ; Tel.: +91-1463-238734
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19
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Heterologous expression of phosphite dehydrogenase in the chloroplast or nucleus enables phosphite utilization and genetic selection in Picochlorum spp. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Short-term physiologic response of the green microalga Picochlorum sp. (BPE23) to supra-optimal temperature. Sci Rep 2022; 12:3290. [PMID: 35228560 PMCID: PMC8885816 DOI: 10.1038/s41598-022-06954-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/08/2022] [Indexed: 11/09/2022] Open
Abstract
Photobioreactors heat up significantly during the day due to irradiation by sunlight. High temperatures affect cell physiology negatively, causing reduced growth and productivity. To elucidate the microalgal response to stressful supra-optimal temperature, we studied the physiology of Picochlorum sp. (BPE23) after increasing the growth temperature from 30 °C to 42 °C, whereas 38 °C is its optimal growth temperature. Cell growth, cell composition and mRNA expression patterns were regularly analyzed for 120 h after increasing the temperature. The supra-optimal temperature caused cell cycle arrest for 8 h, with concomitant changes in metabolic activity. Accumulation of fatty acids was observed during this period to store unspent energy which was otherwise used for growth. In addition, the microalgae changed their pigment and fatty acid composition. For example, palmitic acid (C16:0) content in the polar fatty acid fraction increased by 30%, hypothetically to reduce membrane fluidity to counteract the effect of increased temperature. After the relief of cell cycle arrest, the metabolic activity of Picochlorum sp. (BPE23) reduced significantly over time. A strong response in gene expression was observed directly after the increase in temperature, which was dampened in the remainder of the experiment. mRNA expression levels associated with pathways associated with genes acting in photosynthesis, carbon fixation, ribosome, citrate cycle, and biosynthesis of metabolites and amino acids were downregulated, whereas the proteasome, autophagy and endocytosis were upregulated.
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21
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Pang M, Liu K, Liu H. Evidence for mixotrophy in pico-chlorophytes from a new Picochlorum (Trebouxiophyceae) strain. JOURNAL OF PHYCOLOGY 2022; 58:80-91. [PMID: 34676899 DOI: 10.1111/jpy.13218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Mixotrophs are increasingly recognized for their wide distribution in aquatic ecosystems and significant contributions to biogeochemical cycling. Many taxa within the phyla Chrysophyta, Cryptophyta, and Haptophyta are capable of phago-mixotrophy, however, phagotrophy in the Chlorophyta remains controversial due to insufficient research and solid evidence. In this study, we identified a new strain, Picochlorum sp. GLMF1 (Trebouxiophyceae), using 18S rRNA gene analysis and morphological observations. It displayed multi-cell division through autosporulation (two- or four-cell daughters) and has two unequal flagella that have never been reported in the genus Picochlorum. By using multiple methods, including 3D bioimaging analysis, acidic food vacuole-like compartment staining, and prey reduction calculation, we discovered and confirmed bacterivory in Picochlorum, which provided strong evidence for phago-mixotrophy in this green alga. In addition, we found that Picochlorum sp. GLMF1 cannot grow under complete darkness or prey-depleted conditions, suggesting that both light and bacteria are indispensable for this strain, and its mixotrophic nutrition mode is obligate. Like other phago-phototrophs, Picochlorum sp. GLMF1 is capable of regulating their growth and ingestion rates according to light intensity and inorganic nutrient concentration. The confirmation of mixotrophy in this Picochlorum strain advances our understanding of the trophic roles of green algae, as well as the photosynthetic picoeukaryotes, in marine microbial food webs.
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Affiliation(s)
- Mengwen Pang
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong, China
| | - Kailin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Clear Water Bay Road, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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22
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Barten R, Peeters T, Navalho S, Fontowicz L, Wijffels RH, Barbosa M. Expanding the upper‐temperature boundary for the microalga
Picochlorum sp. (BPE23)
by adaptive laboratory evolution. Biotechnol J 2022; 17:e2100659. [DOI: 10.1002/biot.202100659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Robin Barten
- Bioprocess Engineering & AlgaePARC Wageningen University and Research Wageningen PO Box 16, 6700 AA The Netherlands
| | - Teun Peeters
- Bioprocess Engineering & AlgaePARC Wageningen University and Research Wageningen PO Box 16, 6700 AA The Netherlands
| | - Sofia Navalho
- Bioprocess Engineering & AlgaePARC Wageningen University and Research Wageningen PO Box 16, 6700 AA The Netherlands
| | - Louis Fontowicz
- Bioprocess Engineering & AlgaePARC Wageningen University and Research Wageningen PO Box 16, 6700 AA The Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering & AlgaePARC Wageningen University and Research Wageningen PO Box 16, 6700 AA The Netherlands
- Biosciences and Aquaculture Nord University Bodø N‐8049 Norway
| | - Maria Barbosa
- Bioprocess Engineering & AlgaePARC Wageningen University and Research Wageningen PO Box 16, 6700 AA The Netherlands
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23
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Kselíková V, Singh A, Bialevich V, Čížková M, Bišová K. Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet. Biotechnol Adv 2021; 58:107885. [PMID: 34906670 DOI: 10.1016/j.biotechadv.2021.107885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.
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Affiliation(s)
- Veronika Kselíková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anjali Singh
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Vitali Bialevich
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Mária Čížková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic.
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24
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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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25
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da Roza PA, Goold HD, Paulsen IT. Picochlorum sp. SENEW3. Trends Genet 2021; 38:209-210. [PMID: 34711424 DOI: 10.1016/j.tig.2021.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick A da Roza
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Hugh D Goold
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; New South Wales Department of Primary Industries, Orange, NSW 2800, Australia
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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26
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Abstract
A number of technological challenges need to be overcome if algae are to be utilized for commercial fuel production. Current economic assessment is largely based on laboratory scale up or commercial systems geared to the production of high value products, since no industrial scale plant exits that are dedicated to algal biofuel. For macroalgae (‘seaweeds’), the most promising processes are anaerobic digestion for biomethane production and fermentation for bioethanol, the latter with levels exceeding those from sugar cane. Currently, both processes could be enhanced by increasing the rate of degradation of the complex polysaccharide cell walls to generate fermentable sugars using specifically tailored hydrolytic enzymes. For microalgal biofuel production, open raceway ponds are more cost-effective than photobioreactors, with CO2 and harvesting/dewatering costs estimated to be ~50% and up to 15% of total costs, respectively. These costs need to be reduced by an order of magnitude if algal biodiesel is to compete with petroleum. Improved economics could be achieved by using a low-cost water supply supplemented with high glucose and nutrients from food grade industrial wastewater and using more efficient flocculation methods and CO2 from power plants. Solar radiation of not <3000 h·yr−1 favours production sites 30° north or south of the equator and should use marginal land with flat topography near oceans. Possible geographical sites are discussed. In terms of biomass conversion, advances in wet technologies such as hydrothermal liquefaction, anaerobic digestion, and transesterification for algal biodiesel are presented and how these can be integrated into a biorefinery are discussed.
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27
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Pigment modulation in response to irradiance intensity in the fast-growing alga Picochlorum celeri. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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Kumar Patel A, Tseng YS, Rani Singhania R, Chen CW, Chang JS, Di Dong C. Novel application of microalgae platform for biodesalination process: A review. BIORESOURCE TECHNOLOGY 2021; 337:125343. [PMID: 34120057 DOI: 10.1016/j.biortech.2021.125343] [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: 05/04/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
Freshwater demand is rising worldwide due to largely increasing population and industrialization. Latest focus is to explore the Ocean and saline effluent from industries to produce freshwater in a sustainable way via algal desalination. Current physicochemical desalination technology is not only an energy-intensive and expensive process but also gives severe environmental impact from brine and GHGs emissions. Therefore, it is neither environmentally-friendly nor feasible to countries with limited resources. Biodesalination could be an attractive technology with recent breakthroughs in algal bioprocess with fast growth rate under highly saline conditions to effectively remove salts optimally 50-67% from saline water. Algal desalination mainly occurs through biosorption and bioaccumulation which governs by biotic and abiotic factors e.g., strain, temperature, pH, light and nutrients etc. This review provides a current scenario of this novel technology by an in-depth assessment of technological advancement, social impact, possible risks and scope for policy implications.
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Affiliation(s)
- Anil Kumar Patel
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City 81157 Taiwan
| | - Yi-Sheng Tseng
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City 81157 Taiwan
| | - Reeta Rani Singhania
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City 81157 Taiwan
| | - Chiu-Wen Chen
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City 81157 Taiwan
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, Tunghai University, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng Di Dong
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City 81157 Taiwan.
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29
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Goswami RK, Agrawal K, Verma P. Phycoremediation of nitrogen and phosphate from wastewater using Picochlorum sp.: A tenable approach. J Basic Microbiol 2021; 62:279-295. [PMID: 34312905 DOI: 10.1002/jobm.202100277] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/22/2021] [Accepted: 07/04/2021] [Indexed: 11/11/2022]
Abstract
The wastewater originates from different industrial, municipal, and agriculture processes and contains different nitrogen sources, for example, nitrate, ammonium, nitrite, and phosphate such as inorganic and organic sources. The discharge of high nitrate and phosphate to the ecosystem or nearby water bodies can cause eutrophication which disbalances the aquatic ecosystem. Furthermore, ingestion of these pollutants can cause severe toxicity and disease to humans and animals. Thus, from an environmental and social perspective, its treatment is essential with no negative impact on the ecosystem. Microalgae are fundamental, mixotrophic microorganisms that treat different wastewater and utilize nitrate and phosphate in the medium as a source of nutrients. Among them, Picochlorum sp., have the potential to remove nitrogen and phosphate from wastewater. The biomass produced by Picochlorum sp. can be a promising candidate as a sustainable feedstock for biofuel and bioproducts formation. Thus, the present review provides a brief knowledge and understanding about the concentration of nitrogen and phosphate in different wastewater, their negative impacts, and the uptake mechanism of microalgae. Furthermore, the review also provides an insight into Picochlorum sp., and the effects of different physiological and nutritional factors on their growth, wastewater treatment efficacy, and biomass for value-added products and biorefinery applications. In addition, the review is useful to understand the potential of Picochlorum sp. for a tenable wastewater treatment process.
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Affiliation(s)
- Rahul K Goswami
- Department of Microbiology, Bioprocess, and Bioenergy Laboratory, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Komal Agrawal
- Department of Microbiology, Bioprocess, and Bioenergy Laboratory, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Pradeep Verma
- Department of Microbiology, Bioprocess, and Bioenergy Laboratory, Central University of Rajasthan, Ajmer, Rajasthan, India
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30
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Krishnan A, Likhogrud M, Cano M, Edmundson S, Melanson JB, Huesemann M, McGowen J, Weissman JC, Posewitz MC. Picochlorum celeri as a model system for robust outdoor algal growth in seawater. Sci Rep 2021; 11:11649. [PMID: 34079003 PMCID: PMC8172913 DOI: 10.1038/s41598-021-91106-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 11/08/2022] Open
Abstract
With fast growth rates, broad halotolerance and the ability to thrive at high temperatures, algae in the genus Picochlorum are emerging as promising biomass producers. Recently, we isolated a remarkably productive strain, Picochlorum celeri, that attains > 40 g m-2 day-1 productivities using simulated outdoor light. To test outdoor productivities, Picochlorum celeri was cultivated in 820 L raceway ponds at the Arizona Center for Algae Technology and Innovation. Picochlorum celeri demonstrated the highest outdoor biomass productivities reported to date at this testbed averaging ~ 31 g m-2 day-1 over four months with a monthly (August) high of ~ 36 g m-2 day-1. Several single day productivities were > 40 g m-2 day-1. Importantly for sustainability, Picochlorum celeri achieved these productivities in saline water ranging from seawater to 50 parts per thousand sea salts, without any biocides or pond crashes, for over 143 days. Lastly, we report robust genetic engineering tools for future strain improvements.
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Affiliation(s)
- Anagha Krishnan
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Maria Likhogrud
- Corporate Strategic Research, ExxonMobil, Annandale, NJ, 08801, USA
| | - Melissa Cano
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Scott Edmundson
- Marine and Coastal Research Laboratory, Pacific Northwest National Laboratory, Sequim, WA, 98382, USA
| | - Jenna B Melanson
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Michael Huesemann
- Marine and Coastal Research Laboratory, Pacific Northwest National Laboratory, Sequim, WA, 98382, USA
| | - John McGowen
- Arizona Center for Algae Technology and Innovation, Arizona State University, Mesa, AZ, 85212, USA
| | - Joseph C Weissman
- Corporate Strategic Research, ExxonMobil, Annandale, NJ, 08801, USA.
| | - Matthew C Posewitz
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA.
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31
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Lafarga T, Sánchez‐Zurano A, Morillas‐España A, Acién‐Fernández FG. Extremophile microalgae as feedstock for high‐value carotenoids: A review. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomás Lafarga
- Department of Chemical Engineering University of Almería Almería 04120 Spain
| | - Ana Sánchez‐Zurano
- Department of Chemical Engineering University of Almería Almería 04120 Spain
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32
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Kashiyama Y, Ishizuka Y, Terauchi I, Matsuda T, Maeda Y, Yoshino T, Matsumoto M, Yabuki A, Bowler C, Tanaka T. Engineered chlorophyll catabolism conferring predator resistance for microalgal biomass production. Metab Eng 2021; 66:79-86. [PMID: 33862197 DOI: 10.1016/j.ymben.2021.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/27/2020] [Accepted: 03/27/2021] [Indexed: 01/27/2023]
Abstract
Production of valuable compounds including biofuels and pharmaceutical precursors derived from microalgae has garnered significant interest. Stable production of algal biomass is essential to make the microalgal industry commercially feasible. However, one of the largest issues is severe biological contamination by predators grazing the algal biomass, resulting in the crash of outdoor cultures. In the present study, we propose a novel engineering strategy for microalgae to cope with predators. The overexpression of plant chlorophyllase (CLH) in a microalga resulted in the enhancement of resistance to the predator. This result supported our hypothesis that CLH promotes chlorophyll breakdown in the chloroplasts of the microalgae when they are digested by the predator, generating the phototoxic catabolite chlorophyllide that damages the predator. To the best of our knowledge, this is the first study to establish predator-resistant microalgae by enhancing the CLH activity.
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Affiliation(s)
- Yuichiro Kashiyama
- Department of Applied Science and Engineering, Graduate School of Engineering, Fukui University of Technology, 3-6-1, Gakuen, Fukui, Fukui, 910-8505, Japan
| | - Yuki Ishizuka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Issei Terauchi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Toshiki Matsuda
- Department of Applied Science and Engineering, Graduate School of Engineering, Fukui University of Technology, 3-6-1, Gakuen, Fukui, Fukui, 910-8505, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Mitsufumi Matsumoto
- Biotechnology Laboratory, Electric Power Development Co., Ltd, 1, Yanagisaki-machi, Wakamatsu-ku, Kitakyusyu, Fukuoka, 808-0111, Japan
| | - Akinori Yabuki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Dahlin LR, Guarnieri MT. Development of the high-productivity marine microalga, Picochlorum renovo, as a photosynthetic protein secretion platform. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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Mosey M, Douchi D, Knoshaug EP, Laurens LM. Methodological review of genetic engineering approaches for non-model algae. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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35
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Calhoun S, Bell TAS, Dahlin LR, Kunde Y, LaButti K, Louie KB, Kuftin A, Treen D, Dilworth D, Mihaltcheva S, Daum C, Bowen BP, Northen TR, Guarnieri MT, Starkenburg SR, Grigoriev IV. A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. Commun Biol 2021; 4:333. [PMID: 33712730 PMCID: PMC7955037 DOI: 10.1038/s42003-021-01859-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalga Scenedesmus sp. NREL 46B-D3 demonstrating peak growth near 25 °C that reaches 30 g/m2/day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.
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Affiliation(s)
- Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tisza Ann Szeremy Bell
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Division of Biological Sciences, Genome Core, University of Montana, Missoula, MT, USA
| | - Lukas R Dahlin
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Yuliya Kunde
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine B Louie
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrea Kuftin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Treen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Dilworth
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sirma Mihaltcheva
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin P Bowen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Shawn R Starkenburg
- Applied Genomics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
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Douchi D, Mosey M, Astling DP, Knoshaug EP, Nag A, McGowen J, Laurens LM. Nuclear and chloroplast genome engineering of a productive non-model alga Desmodesmus armatus: Insights into unusual and selective acquisition mechanisms for foreign DNA. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Steadman CR, Banerjee S, Kunde YA, Sanders CK, Marrone BL, Twary SN. Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity. Front Genet 2020; 11:560444. [PMID: 33193644 PMCID: PMC7593850 DOI: 10.3389/fgene.2020.560444] [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: 05/08/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022] Open
Abstract
Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism's molecular adaptation to the environment, resulting in distinctive phenotypes. Epigenetic manipulation of algae holds yet untapped potential for the optimization of biofuel production and bioproduct formation; however, epigenetic machinery and modes-of-action have not been well characterized in algae. We sought to determine the extent to which the biofuel platform species Picochlorum soloecismus utilizes DNA methylation to regulate its genome. We found candidate genes with domains for DNA methylation in the P. soloecismus genome. Whole-genome bisulfite sequencing revealed DNA methylation in all three cytosine contexts (CpG, CHH, and CHG). While global DNA methylation is low overall (∼1.15%), it occurs in appreciable quantities (12.1%) in CpG dinucleotides in a bimodal distribution in all genomic contexts, though terminators contain the greatest number of CpG sites per kilobase. The P. soloecismus genome becomes hypomethylated during the growth cycle in response to nitrogen starvation. Algae cultures were treated daily across the growth cycle with 20 μM 5-aza-2'-deoxycytidine (5AZA) to inhibit propagation of DNA methylation in daughter cells. 5AZA treatment significantly increased optical density and forward and side scatter of cells across the growth cycle (16 days). This increase in cell size and complexity correlated with a significant increase (∼66%) in lipid accumulation. Site specific CpG DNA methylation was significantly altered with 5AZA treatment over the time course, though nitrogen starvation itself induced significant hypomethylation in CpG contexts. Genes involved in several biological processes, including fatty acid synthesis, had altered methylation ratios in response to 5AZA; we hypothesize that these changes are potentially responsible for the phenotype of early induction of carbon storage as lipids. This is the first report to utilize epigenetic manipulation strategies to alter algal physiology and phenotype. Collectively, these data suggest these strategies can be utilized to fine-tune metabolic responses, alter growth, and enhance environmental adaption of microalgae for desired outcomes.
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Affiliation(s)
- Christina R Steadman
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Shounak Banerjee
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Yuliya A Kunde
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Claire K Sanders
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Babetta L Marrone
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
| | - Scott N Twary
- Los Alamos National Laboratory, Bioenergy and Biome Sciences, Los Alamos, NM, United States
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Yadav G, Fabiano LA, Soh L, Zimmerman J, Sen R, Seider WD.
CO
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process intensification of algae oil extraction to biodiesel. AIChE J 2020. [DOI: 10.1002/aic.16992] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Geetanjali Yadav
- Department of Chemical and Biomolecular Engineering University of Pennsylvania Philadelphia Pennsylvania USA
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | - Leonard A. Fabiano
- Department of Chemical and Biomolecular Engineering University of Pennsylvania Philadelphia Pennsylvania USA
| | - Lindsay Soh
- Department of Chemical and Biomolecular Engineering Lafayette University Easton Pennsylvania USA
| | - Julie Zimmerman
- Department of Chemical and Environmental Engineering Yale University New Haven Connecticut USA
| | - Ramkrishna Sen
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | - Warren D. Seider
- Department of Chemical and Biomolecular Engineering University of Pennsylvania Philadelphia Pennsylvania USA
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40
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Barten RJ, Wijffels RH, Barbosa MJ. Bioprospecting and characterization of temperature tolerant microalgae from Bonaire. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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41
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Krishnan A, Cano M, Burch TA, Weissman JC, Posewitz MC. Genome editing using Cas9-RNA ribonucleoprotein complexes in the high-productivity marine alga Picochlorum celeri. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101944] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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42
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Phased Diploid Genome Sequence for the Fast-Growing Microalga Picochlorum celeri. Microbiol Resour Announc 2020; 9:9/20/e00087-20. [PMID: 32409528 PMCID: PMC7225527 DOI: 10.1128/mra.00087-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Picochlorum celeri is a fast-growing marine microalga with high biomass productivity. Here, we report the use of PacBio sequencing to assemble the phased diploid genome of P. celeri.
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