1
|
Ochiai KK, Hanawa D, Ogawa HA, Tanaka H, Uesaka K, Edzuka T, Shirae-Kurabayashi M, Toyoda A, Itoh T, Goshima G. Genome sequence and cell biological toolbox of the highly regenerative, coenocytic green feather alga Bryopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38642374 DOI: 10.1111/tpj.16764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 02/10/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Green feather algae (Bryopsidales) undergo a unique life cycle in which a single cell repeatedly executes nuclear division without cytokinesis, resulting in the development of a thallus (>100 mm) with characteristic morphology called coenocyte. Bryopsis is a representative coenocytic alga that has exceptionally high regeneration ability: extruded cytoplasm aggregates rapidly in seawater, leading to the formation of protoplasts. However, the genetic basis of the unique cell biology of Bryopsis remains poorly understood. Here, we present a high-quality assembly and annotation of the nuclear genome of Bryopsis sp. (90.7 Mbp, 27 contigs, N50 = 6.7 Mbp, 14 034 protein-coding genes). Comparative genomic analyses indicate that the genes encoding BPL-1/Bryohealin, the aggregation-promoting lectin, are heavily duplicated in Bryopsis, whereas homologous genes are absent in other ulvophyceans, suggesting the basis of regeneration capability of Bryopsis. Bryopsis sp. possesses >30 kinesins but only a single myosin, which differs from other green algae that have multiple types of myosin genes. Consistent with this biased motor toolkit, we observed that the bidirectional motility of chloroplasts in the cytoplasm was dependent on microtubules but not actin in Bryopsis sp. Most genes required for cytokinesis in plants are present in Bryopsis, including those in the SNARE or kinesin superfamily. Nevertheless, a kinesin crucial for cytokinesis initiation in plants (NACK/Kinesin-7II) is hardly expressed in the coenocytic part of the thallus, possibly underlying the lack of cytokinesis in this portion. The present genome sequence lays the foundation for experimental biology in coenocytic macroalgae.
Collapse
Affiliation(s)
- Kanta K Ochiai
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Daiki Hanawa
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Harumi A Ogawa
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kazuma Uesaka
- Centre for Gene Research, Nagoya University, Nagoya, 464-8602, Japan
| | - Tomoya Edzuka
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Maki Shirae-Kurabayashi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Gohta Goshima
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, 517-0004, Japan
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
He Y, Ma S, Yang Q, Lai H, Zhang J. Characterization of the mitochondrial genome of Chlorolobion braunii ITBB-AG6, an azolla-associated green alga isolated from sanitary sewage. Mitochondrial DNA B Resour 2023; 8:826-830. [PMID: 37545555 PMCID: PMC10402853 DOI: 10.1080/23802359.2023.2241573] [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: 01/05/2023] [Accepted: 07/23/2023] [Indexed: 08/08/2023] Open
Abstract
Sphaeropleales have the characteristics of rapid growth, high oil content, and efficient removal rates of nitrogen and phosphorus in sewage waters, and is potentially valuable in biodiesel production and environmental remediation. In this study, we isolated a strain of Sphaeropleales, Chlorolobion braunii strain ITBB-AG6 from an azolla community in a sewage pond. Its mitochondrial genome contains 110,124 bp and harbors at least 40 genes, including 15 protein-coding genes, 20 tRNA genes, and three rRNA genes. The protein-coding genes include two for ATP synthases, seven for NAD(P)H-quinone oxidoreductases (nad), three for cytochrome c oxidase subunits (coxs), and one for cytochrome b (cob). Transfer RNA genes for 18 amino acids were identified, in which the tRNA genes for leucine and serine are doubled, but the tRNA genes for threonine and valine are not annotated. Phylogenetic analysis using the mitochondrial genomes of seven families of Sphaeropleales indicated that ITBB-AG6 is closely related to Monoraphidium neglectum, and falls in the family Selenastraceae with 100% bootstrap support. Two species in the family Neochloridaceae are separated by a species in Hydrodictyaceae, indicating a polyphyletic nature. These findings revealed the complicated phylogenetic relationships of the Sphaeropleales and the necessity of genome sequences in the taxonomy of microalgae.
Collapse
Affiliation(s)
- Yiliang He
- College of Agriculture, Hainan University, Haikou, China
| | - Shuai Ma
- Institute of Tropical Bioscience and Biotechnology, Hainan Key Laboratory of Microbiological Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qiaoqiao Yang
- College of Agriculture, Hainan University, Haikou, China
| | - Huanggui Lai
- College of Agriculture, Hainan University, Haikou, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, Hainan Key Laboratory of Microbiological Resources, Hainan Bioenergy Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| |
Collapse
|
4
|
Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
Collapse
Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| |
Collapse
|
5
|
Kumar A, Baldia A, Rajput D, Kateriya S, Babu V, Dubey KK. Multiomics and optobiotechnological approaches for the development of microalgal strain for production of aviation biofuel and biorefinery. BIORESOURCE TECHNOLOGY 2023; 369:128457. [PMID: 36503094 DOI: 10.1016/j.biortech.2022.128457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Demand and consumption of fossil fuels is increasing daily, and oil reserves are depleting. Technological developments are required towards developing sustainable renewable energy sources and microalgae are emerging as a potential candidate for various application-driven research. Molecular understanding attained through omics and system biology approach empowering researchers to modify various metabolic pathways of microalgal system for efficient extraction of biofuel and important biomolecules. This review furnish insight into different "advanced approaches" like optogenetics, systems biology and multi-omics for enhanced production of FAS (Fatty Acid Synthesis) and lipids in microalgae and their associated challenges. These new approaches would be helpful in the path of developing microalgae inspired technological platforms for optobiorefinery, which could be explored as source material to produce biofuels and other valuable bio-compounds on a large scale.
Collapse
Affiliation(s)
- Akshay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Anshu Baldia
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepanshi Rajput
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vikash Babu
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Kashyap Kumar Dubey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
| |
Collapse
|
6
|
Barnum TP, Coates JD. Chlorine redox chemistry is widespread in microbiology. THE ISME JOURNAL 2023; 17:70-83. [PMID: 36202926 PMCID: PMC9751292 DOI: 10.1038/s41396-022-01317-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2-) by converting it to chloride (Cl-) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4-) or chlorate (ClO3-), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.
Collapse
Affiliation(s)
- Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
7
|
Ruffing AM, Davis RW, Lane TW. Advances in engineering algae for biofuel production. Curr Opin Biotechnol 2022; 78:102830. [PMID: 36332347 DOI: 10.1016/j.copbio.2022.102830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022]
Abstract
While algae demonstrate potential as a sustainable fuel source, low productivities limit the economic realization of algal biofuels. High-throughput strain engineering, omics-informed genome-scale modeling, and microbiome engineering are key technologies for enabling algal biofuels. High-throughput strain engineering efforts generate improved traits, including high biomass productivity and lipid content, in diverse algal species. Genome-scale models, constructed with the aid of omics data, provide insight into metabolic limitations and guide rational algal strain engineering efforts. As outdoor cultivation systems introduce exogenous organisms, microbiome engineering seeks to eliminate harmful organisms and introduce beneficial species. Optimizing algal biomass production and lipid content using these technologies may overcome the productivity barrier for the commercialization of algal biofuels.
Collapse
Affiliation(s)
- Anne M Ruffing
- Sandia National Laboratories, Molecular and Microbiology, P.O. Box 5800, MS 1413, Albuquerque, NM 87185, USA.
| | - Ryan W Davis
- Sandia National Laboratories, Bioresource and Environmental Security, P.O. Box 969, MS 9292, Livermore, CA 94551, USA
| | - Todd W Lane
- Sandia National Laboratories, Bioresource and Environmental Security, P.O. Box 969, MS 9292, Livermore, CA 94551, USA
| |
Collapse
|
8
|
Dvoretsky DS, Temnov MS, Markin IV, Ustinskaya YV, Es’kova MA. Problems in the Development of Efficient Biotechnology for the Synthesis of Valuable Components from Microalgae Biomass. THEORETICAL FOUNDATIONS OF CHEMICAL ENGINEERING 2022. [DOI: 10.1134/s0040579522040224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
Calhoun S, Kamel B, Bell TA, Kruse CP, Riley R, Singan V, Kunde Y, Gleasner CD, Chovatia M, Sandor L, Daum C, Treen D, Bowen BP, Louie KB, Northen TR, Starkenburg SR, Grigoriev IV. Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
10
|
Kirchner NJ, Hage A, Gomez J, Grayburn WS, Holbrook GP. Photosynthesis, competition, and wastewater treatment characteristics of the microalga Monoraphidium sp. Dek19 at cool temperatures. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
11
|
The Effects of Photobioreactor Type on Biomass and Lipid Production of the Green Microalga Monoraphidium pusillum in Laboratory Scale. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12042196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mass production of microorganisms, algae among them, for new bioactive compounds and renewable innovative products is a current issue in biotechnology. The greatest challenge of basic research on this topic is to find the best solution for both physiology and scalability. In this study, the main goal was to highlight the contradictions of physiological and technological optimization in the same, relatively small, laboratory scale. The green alga Monoraphidium pusillum (Printz) Komárková-Legnorová was cultured in a conventional Erlenmeyer flask (as air bubbled in a tank-type photobioreactor) and in a hybrid (fermenter type + helical tubular type) photobioreactor of the same volume (2.8 L). Higher cell numbers from 1.7–2.3-fold, 2–2.8-fold higher dry masses, and 1.9–2.6-fold higher total lipid contents (mg·L−1) were measured in the tank reactor than in the hybrid reactor. Cultures in the conventional tank reactor were characterized with better nutrient utilization (42.8–77.7% higher phosphate uptake) and more diverse lipid composition than in the hybrid reactor. The study highlights that well-scalable arrangements and settings could be not optimal (or unsuitable in some cases) from a physiological point of view. The results suggest certain developmental directions for complex, well-scalable devices and highlight the importance of testing the gained physiological optima on these systems.
Collapse
|
12
|
Wan Afifudeen CL, Aziz A, Wong LL, Takahashi K, Toda T, Abd Wahid ME, Cha TS. Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage. PHYTOCHEMISTRY 2021; 192:112936. [PMID: 34509143 DOI: 10.1016/j.phytochem.2021.112936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 08/26/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
The non-model microalga Messastrum gracile SE-MC4 is a potential species for biodiesel production. However, low biomass productivity hinders it from passing the life cycle assessment for biodiesel production. Therefore, the current study was aimed at uncovering the differences in the transcriptome profiles of the microalgae at early exponential and early stationary growth phases and dissecting the roles of specific differential expressed genes (DEGs) involved in cell division during M. gracile cultivation. The transcriptome analysis revealed that the photosynthetic integral membrane protein genes such as photosynthetic antenna protein were severely down-regulated during the stationary growth phase. In addition, the signaling pathways involving transcription, glyoxylate metabolism and carbon metabolism were also down-regulated during stationary growth phase. Current findings suggested that the coordination between photosynthetic integral membrane protein genes, signaling through transcription and carbon metabolism classified as prominent strategies during exponential growth stage. These findings can be applied in genetic improvement of M. gracile for biodiesel application.
Collapse
Affiliation(s)
- C L Wan Afifudeen
- Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Ahmad Aziz
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Li Lian Wong
- Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Tatsuki Toda
- Faculty of Science and Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan.
| | - Mohd Effendy Abd Wahid
- Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Thye San Cha
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| |
Collapse
|
13
|
Clark AD, Howell BK, Wilson AE, Schwartz TS. Draft genomes for one Microcystis-resistant and one Microcystis-sensitive strain of the water flea, Daphnia pulicaria. G3 (BETHESDA, MD.) 2021; 11:jkab266. [PMID: 34849790 PMCID: PMC8527513 DOI: 10.1093/g3journal/jkab266] [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] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022]
Abstract
Daphnia species are well-suited for studying local adaptation and evolutionary responses to stress(ors) including those caused by algal blooms. Algal blooms, characterized by an overgrowth (bloom) of cyanobacteria, are detrimental to the health of aquatic and terrestrial members of freshwater ecosystems. Some strains of Daphnia pulicaria have demonstrated resistance to toxic algae and the ability to mitigate toxic algal blooms. Understanding the genetic mechanism associated with this toxin resistance requires adequate genomic resources. Using whole-genome sequence data mapped to the Daphnia pulex reference genome (PA42), we present reference-guided draft assemblies from one tolerant and one sensitive strain of D. pulicaria, Wintergreen-6 (WI-6), and Bassett-411 (BA-411), respectively. Assessment of the draft assemblies reveal low contamination levels, and high levels (95%) of genic content. Reference scaffolds had coverage breadths of 98.9-99.4%, and average depths of 33X and 29X for BA-411 and WI-6, respectively. Within, we discuss caveats and suggestions for improving these draft assemblies. These genomic resources are presented with a goal of contributing to the resources necessary to understand the genetic mechanisms and associations of toxic prey resistance observed in this species.
Collapse
Affiliation(s)
- Amanda D Clark
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Bailey K Howell
- Bioinformatics REU Program, Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alan E Wilson
- Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
14
|
Calixto Mancipe N, McLaughlin EM, Barney BM. Genomic analysis and characterization of Scenedesmus glucoliberatum PABB004: An unconventional sugar-secreting green alga. J Appl Microbiol 2021; 132:2004-2019. [PMID: 34599635 DOI: 10.1111/jam.15311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/02/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022]
Abstract
AIMS In this report, we present Scenedesmus glucoliberatum PABB004, a microalga that was isolated from an association with Paramecium bursaria with the potential for application in fermentative processes and co-culture schemes due to its advantageous high sugar secretion phenotype. METHODS AND RESULTS We sequenced, assembled and annotated the draft genome and transcriptome for this newly reported strain. The nuclear genome has an exceptionally high GC content of 78%. Our results revealed significant sugar accumulation over a range from 6.2 to 7.8 pH units. The predicted proteome was compared with other green algae that show different sugar secretion phenotypes aiming to help uncover their common features for simple sugar secretion and those unique to S. glucoliberatum PABB004. CONCLUSIONS The evolutionary history of this organism, inferred from its genomic traits, expands our current understanding of algal mutualistic relationships involving photosynthate exchanges. S. glucoliberatum PABB004 secreted ready-to-use fermentable sugars (glucose and maltose) directly to the extracellular media achieving concentrations greater than 2.7 g/L of free glucose and 1.2 g/L of maltose in batch cultures. SIGNIFICANCE AND IMPACT OF THE STUDY A draft genome is provided for a new member of an important class of green algae. Scenedesmus glucoliberatum PABB004 secretes high levels of simple sugars over a broad pH range.
Collapse
Affiliation(s)
- Natalia Calixto Mancipe
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Evelyn M McLaughlin
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Brett M Barney
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA.,BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
15
|
Agathokleous E, Zhou B, Xu J, Ioannou A, Feng Z, Saitanis CJ, Frei M, Calabrese EJ, Fotopoulos V. Exogenous application of melatonin to plants, algae, and harvested products to sustain agricultural productivity and enhance nutritional and nutraceutical value: A meta-analysis. ENVIRONMENTAL RESEARCH 2021; 200:111746. [PMID: 34302829 DOI: 10.1016/j.envres.2021.111746] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 05/27/2023]
Abstract
Melatonin is produced by plants, algae, and animals. Worldwide studies show diverse positive effects of exogenous melatonin on plants, edible plant products, and algae, but the potential of melatonin to enhance food and feed systems through these positive effects remains largely unexplored. Through a meta-analysis of about 25,000 observations, we show for the first time that exogenous application of melatonin significantly increases crop productivity and yields, and enhances the nutritional and nutraceutical value of edible plant products and algae by regulating diverse biological functions. We demonstrate that melatonin can improve plants, edible plant products, and algae under various current climate change scenarios, environmental pollution factors, and other stresses by about 7% to nearly 30%, on average, depending on the stressor. We also analyze various technical/methodological factors influencing the desired outcomes and identify conditions that offer optimal enhancement. We show that the positive effect of melatonin on plants and edible plant products varies among species, genera, and families, and strongly depends on the concentration of melatonin and treatment duration. The effect of melatonin is slightly lower on the monocot clade Commelinids than on the eudicot clades Asterids and Rosids. We also show that its stimulatory effect on plants depends on cultivation system, with a larger effect obtained in hydroponic systems. However, it does not depend on application stage (seed or vegetative), application route (foliage, roots, or seed), and whether the cultivation system is ex vivo or in vivo. This is the first meta-analysis examining the effects of melatonin on plants, edible plant products, and algae, and offers a scientific and technical roadmap facilitating sustainable food and feed production through the application of exogenous melatonin.
Collapse
Affiliation(s)
- Evgenios Agathokleous
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology (NUIST), Nanjing, 210044, China.
| | - Boya Zhou
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology (NUIST), Nanjing, 210044, China
| | - Jianing Xu
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology (NUIST), Nanjing, 210044, China
| | - Andreas Ioannou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, 3603, Cyprus
| | - Zhaozhong Feng
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology (NUIST), Nanjing, 210044, China.
| | - Costas J Saitanis
- Lab of Ecology and Environmental Science, Agricultural University of Athens, Iera Odos 75, Athens, 11855, Greece
| | - Michael Frei
- Institute of Agronomy and Crop Physiology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Edward J Calabrese
- Department of Environmental Health Sciences, Morrill I, N344, University of Massachusetts, Amherst, MA, 01003, USA
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos, 3603, Cyprus
| |
Collapse
|
16
|
Metabolic pathway analysis of walnut endophytic bacterium Bacillus subtilis HB1310 related to lipid production from fermentation of cotton stalk hydrolysate based on genome sequencing. Biotechnol Lett 2021; 43:1883-1894. [PMID: 34228235 DOI: 10.1007/s10529-021-03160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/28/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVES In this study, genome sequencing and metabolic analysis were used to identify and verify the key metabolic pathways for glucose and xylose utilization and fatty acid synthesis in the walnut endophytic bacterium (WEB) Bacillus subtilis HB1310. RESULTS The genome sequence of WEB HB1310 was generated with a size of 4.1 Mb and GC content of 43.5%. Genome annotation indicated that the Embden-Meyerhof-Parnas, pentose phosphate, and fatty acid synthesis pathways were mainly involved in mixed sugar utilization and lipid production. In particular, diverse and abundant fatty acid synthesis genes were observed in a higher number than in other Bacillus strains. The tricarboxylic acid cycle competitively shared the carbon flux flowing before 48 h, and the acetic acid fermentation competed after 72 h. Moreover, fatty acid synthase activity was highly correlated with lipid titer with a correlation coefficient of 0.9626, and NADPH might be more utilized for the lipid synthesis within 48 h. CONCLUSIONS This study is the first attempt to explain the metabolic mechanism of mixed sugar utilization and lipid production based on genomic information, which provides a theoretical basis for the metabolic regulation of bacterial lipid production from lignocellulosic hydrolysates.
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Teng SY, Yew GY, Sukačová K, Show PL, Máša V, Chang JS. Microalgae with artificial intelligence: A digitalized perspective on genetics, systems and products. Biotechnol Adv 2020; 44:107631. [PMID: 32931875 DOI: 10.1016/j.biotechadv.2020.107631] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022]
Abstract
With recent advances in novel gene-editing tools such as RNAi, ZFNs, TALENs, and CRISPR-Cas9, the possibility of altering microalgae toward designed properties for various application is becoming a reality. Alteration of microalgae genomes can modify metabolic pathways to give elevated yields in lipids, biomass, and other components. The potential of such genetically optimized microalgae can give a "domino effect" in further providing optimization leverages down the supply chain, in aspects such as cultivation, processing, system design, process integration, and revolutionary products. However, the current level of understanding the functional information of various microalgae gene sequences is still primitive and insufficient as microalgae genome sequences are long and complex. From this perspective, this work proposes to link up this knowledge gap between microalgae genetic information and optimized bioproducts using Artificial Intelligence (AI). With the recent acceleration of AI research, large and complex data from microalgae research can be properly analyzed by combining the cutting-edge of both fields. In this work, the most suitable class of AI algorithms (such as active learning, semi-supervised learning, and meta-learning) are discussed for different cases of microalgae applications. This work concisely reviews the current state of the research milestones and highlight some of the state-of-art that has been carried out, providing insightful future pathways. The utilization of AI algorithms in microalgae cultivation, system optimization, and other aspects of the supply chain is also discussed. This work opens the pathway to a digitalized future for microalgae research and applications.
Collapse
Affiliation(s)
- Sin Yong Teng
- Brno University of Technology, Institute of Process Engineering, Technická 2896/2, 616 69, Brno, Czech Republic.
| | - Guo Yong Yew
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
| | - Kateřina Sukačová
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, Brno 603 00, Czech Republic.
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
| | - Vítězslav Máša
- Brno University of Technology, Institute of Process Engineering, Technická 2896/2, 616 69, Brno, Czech Republic.
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, College of Engineering, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan.
| |
Collapse
|
19
|
Polle JE, Calhoun S, McKie-Krisberg Z, Prochnik S, Neofotis P, Yim WC, Hathwaik LT, Jenkins J, Molina H, Bunkenborg J, Grigoriev IV, Barry K, Schmutz J, Jin E, Cushman JC, Magnusson JK. Genomic adaptations of the green alga Dunaliella salina to life under high salinity. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101990] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
20
|
Liu C, Shi X, Wu F, Ren M, Gao G, Wu Q. Genome analyses provide insights into the evolution and adaptation of the eukaryotic Picophytoplankton Mychonastes homosphaera. BMC Genomics 2020; 21:477. [PMID: 32652928 PMCID: PMC7354681 DOI: 10.1186/s12864-020-06891-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
Background Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used third-generation sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China. Result The 24.23 Mbp nuclear genome of M.homosphaera, harboring 6649 protein-coding genes, is more compact than the genomes of the closely related Sphaeropleales species. This genome streamlining may be caused by a reduction in gene family number, intergenic size and introns. The genome sequence of M.homosphaera reveals the strategies adopted by this organism for environmental adaptation in the eutrophic lake. Analysis of cultures and the protein complement highlight the metabolic flexibility of M.homosphaera, the genome of which encodes genes involved in light harvesting, carbohydrate metabolism, and nitrogen and microelement metabolism, many of which form functional gene clusters. Reconstruction of the bioenergetic metabolic pathways of M.homosphaera, such as the lipid, starch and isoprenoid pathways, reveals characteristics that make this species suitable for biofuel production. Conclusion The analysis of the whole genome of M. homosphaera provides insights into the genome streamlining, the high lipid yield, the environmental adaptation and phytoplankton evolution.
Collapse
Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingdong Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
21
|
Reshma R, Kumari S, Arumugam M. Structural elucidation of selenocysteine insertion machinery of microalgal selenoprotein T and its transcriptional analysis. Biotechnol Appl Biochem 2020; 68:636-647. [PMID: 32579774 DOI: 10.1002/bab.1974] [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: 04/10/2020] [Accepted: 06/21/2020] [Indexed: 11/06/2022]
Abstract
Essential trace element selenium in association with selenoproteins, which is found in almost all organisms except higher plants and fungi, is involved in various biological functions. Advancement in the field of whole genome sequencing and data analyzing bioinformatic tools led to the accumulation of genome information of organisms. However, selenoproteins are unique and it needs specialized genomics tool for its identification as well as characterization. In this study, the presence of selenoprotein T (SelT) from Scenedesmus quadricauda was shown for the first time with experimental evidence and compared with SelT of marine microalgae Nannochloropsis oceanica. Along with SelT, all the associated machineries required to synthesize the selenoproteins were also identified. Also, the present study tried to explicate the evolutionary relatedness of SelT of these two organisms with other known bacteria and eukaryotes. Transcript level analysis in S. quadricauda under endoplasmic reticulum stress showed a 1.2 ± 0.28-fold increase in SelT expression. Thus, it provided the first experimental evidence on SelT expression from microalgae.
Collapse
Affiliation(s)
- Ragini Reshma
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR), Trivandrum, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sunitha Kumari
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR), Trivandrum, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Muthu Arumugam
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR), Trivandrum, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
22
|
Zhang Z, Qu C, Zhang K, He Y, Zhao X, Yang L, Zheng Z, Ma X, Wang X, Wang W, Wang K, Li D, Zhang L, Zhang X, Su D, Chang X, Zhou M, Gao D, Jiang W, Leliaert F, Bhattacharya D, De Clerck O, Zhong B, Miao J. Adaptation to Extreme Antarctic Environments Revealed by the Genome of a Sea Ice Green Alga. Curr Biol 2020; 30:3330-3341.e7. [PMID: 32619486 DOI: 10.1016/j.cub.2020.06.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023]
Abstract
The unicellular green alga Chlamydomonas sp. ICE-L thrives in polar sea ice, where it tolerates extreme low temperatures, high salinity, and broad seasonal fluctuations in light conditions. Despite the high interest in biotechnological uses of this species, little is known about the adaptations that allow it to thrive in this harsh and complex environment. Here, we assembled a high-quality genome sequence of ∼542 Mb and found that retrotransposon proliferation contributed to the relatively large genome size of ICE-L when compared to other chlorophytes. Genomic features that may support the extremophilic lifestyle of this sea ice alga include massively expanded gene families involved in unsaturated fatty acid biosynthesis, DNA repair, photoprotection, ionic homeostasis, osmotic homeostasis, and reactive oxygen species detoxification. The acquisition of multiple ice binding proteins through putative horizontal gene transfer likely contributed to the origin of the psychrophilic lifestyle in ICE-L. Additional innovations include the significant upregulation under abiotic stress of several expanded ICE-L gene families, likely reflecting adaptive changes among diverse metabolic processes. Our analyses of the genome, transcriptome, and functional assays advance general understanding of the Antarctic green algae and offer potential explanations for how green plants adapt to extreme environments.
Collapse
Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Changfeng Qu
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Kaijian Zhang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Yingying He
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Zhou Zheng
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xixi Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Wenyu Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Kai Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Dan Li
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Liping Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xin Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Danyan Su
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Dan Gao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Frederik Leliaert
- Biology Department, Ghent University, 9000 Ghent, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China.
| | - Jinlai Miao
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China.
| |
Collapse
|
23
|
Derilus D, Rahman MZ, Pinero F, Massey SE. Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes. Sci Rep 2020; 10:8918. [PMID: 32488045 PMCID: PMC7265537 DOI: 10.1038/s41598-020-65476-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/05/2020] [Indexed: 01/01/2023] Open
Abstract
The photosynthetic picoeukaryotes (PPEs) comprise a rare example of free-living eukaryotes that have undergone genome reduction. Here, we examine a duality in the process; the proposed driver of genome reduction (the Black Queen hypothesis, BQH), and the resultant impact of genome information loss (the Proteomic Constraint hypothesis, PCH). The BQH predicts that some metabolites may be shared in the open ocean, thus driving loss of redundant metabolic pathways in individual genomes. In contrast, the PCH predicts that as the information content of a genome is reduced, the total mutation load is also reduced, leading to loss of DNA repair genes due to the resulting reduction in selective constraint. Consistent with the BQH, we observe that biosynthetic pathways involved with soluble metabolites such as amino acids and carotenoids are preferentially lost from the PPEs, in contrast to biosynthetic pathways involved with insoluble metabolites, such as lipids, which are retained. Consistent with the PCH, a correlation between proteome size and the number of DNA repair genes, and numerous other informational categories, is observed. While elevated mutation rates resulting from the loss of DNA repair genes have been linked to reduced effective population sizes in intracellular bacteria, this remains to be established. This study shows that in microbial species with large population sizes, an underlying factor in modulating their DNA repair capacity appears to be information content.
Collapse
Affiliation(s)
- D Derilus
- Environmental Sciences Department, University of Puerto Rico - Rio Piedras, San Juan, Puerto Rico
| | - M Z Rahman
- Biology Department, University of Puerto Rico - Rio Piedras, San Juan, Puerto Rico
| | - F Pinero
- Mathematics Department, University of Puerto Rico - Ponce, Ponce, Puerto Rico
| | - S E Massey
- Biology Department, University of Puerto Rico - Rio Piedras, San Juan, Puerto Rico.
| |
Collapse
|
24
|
Li Y, Ye Q, He D, Bai H, Wen J. The ubiquity and coexistence of two FBPases in chloroplasts of photosynthetic eukaryotes and its evolutionary and functional implications. PLANT DIVERSITY 2020; 42:120-125. [PMID: 32373770 PMCID: PMC7195585 DOI: 10.1016/j.pld.2019.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 05/24/2023]
Abstract
In photosynthetic eukaryotes, there are two well-characterized fructose-1,6-bisphosphatases (FBPases): the redox-insensitive cytosolic FBPase (cyFBPase), which participates in gluconeogenesis, and the redox-sensitive chloroplastic FBPase (cpFBPase1), which is a critical enzyme in the Calvin cycle. Recent studies have identified a new chloroplastic FBPase, cpFBPase2; however, its phylogenetic distribution, evolutionary origin, and physiological function remain unclear. In this study, we identified and characterized these three FBPase isoforms in diverse, representative photosynthetic lineages and analyzed their phylogeny. In contrast to previous hypotheses, we found that cpFBPase2 is ubiquitous in photosynthetic eukaryotes. Additionally, all cpFBPase2s from diverse lineages form a monophyly, suggesting cpFBPase2 is not a recently evolved enzyme restricted to land plants but rather evolved early in the evolution of photosynthetic organisms, and most likely, in the common ancestor of photosynthetic eukaryotes. cyFBPase was probably first duplicated to produce cpFBPase2, and then the latter duplicated to produce cpFBPase1. The ubiquitous coexistence of these two cpFBPases in chloroplasts is most likely the consequence of adaptation to different redox conditions of photosynthesis, especially those caused by recurrent changes in light conditions.
Collapse
Affiliation(s)
- Yujin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Qingqing Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - De He
- College of Life Sciences, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Huixian Bai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jianfan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| |
Collapse
|
25
|
Draft Genome Sequence of the Biofuel-Relevant Microalga Desmodesmus armatus. Microbiol Resour Announc 2020; 9:9/6/e00896-19. [PMID: 32029566 PMCID: PMC7005114 DOI: 10.1128/mra.00896-19] [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] [Indexed: 11/20/2022] Open
Abstract
A draft genome of 906 scaffolds of 115.8 Mb was assembled for Desmodesmus armatus, a diploid, lipid- and storage carbohydrate-accumulating microalga proven relevant for large-scale, outdoor cultivation, and serves as a model alga platform for improving photosynthetic efficiency and carbon assimilation for next-generation bioenergy production. A draft genome of 906 scaffolds of 115.8 Mb was assembled for Desmodesmus armatus, a diploid, lipid- and storage carbohydrate-accumulating microalga proven relevant for large-scale, outdoor cultivation, and serves as a model alga platform for improving photosynthetic efficiency and carbon assimilation for next-generation bioenergy production.
Collapse
|
26
|
Wichmann J, Lauersen KJ, Kruse O. Green algal hydrocarbon metabolism is an exceptional source of sustainable chemicals. Curr Opin Biotechnol 2020; 61:28-37. [DOI: 10.1016/j.copbio.2019.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/25/2019] [Indexed: 10/25/2022]
|
27
|
He Y, Ao Y, Yin Y, Yuan A, Che T, Li L, Shen S. Comparative transcriptome analysis between floating and attached Ulva prolifera in studying green tides in the Yellow Sea. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
28
|
Green Production and Biotechnological Applications of Cell Wall Lytic Enzymes. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9235012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
: Energy demand is constantly growing, and, nowadays, fossil fuels still play a dominant role in global energy production, despite their negative effects on air pollution and the emission of greenhouse gases, which are the main contributors to global warming. An alternative clean source of energy is represented by the lignocellulose fraction of plant cell walls, the most abundant carbon source on Earth. To obtain biofuels, lignocellulose must be efficiently converted into fermentable sugars. In this regard, the exploitation of cell wall lytic enzymes (CWLEs) produced by lignocellulolytic fungi and bacteria may be considered as an eco-friendly alternative. These organisms evolved to produce a variety of highly specific CWLEs, even if in low amounts. For an industrial use, both the identification of novel CWLEs and the optimization of sustainable CWLE-expressing biofactories are crucial. In this review, we focus on recently reported advances in the heterologous expression of CWLEs from microbial and plant expression systems as well as some of their industrial applications, including the production of biofuels from agricultural feedstock and of value-added compounds from waste materials. Moreover, since heterologous expression of CWLEs may be toxic to plant hosts, genetic strategies aimed in converting such a deleterious effect into a beneficial trait are discussed.
Collapse
|
29
|
Mishra A, Medhi K, Malaviya P, Thakur IS. Omics approaches for microalgal applications: Prospects and challenges. BIORESOURCE TECHNOLOGY 2019; 291:121890. [PMID: 31378447 DOI: 10.1016/j.biortech.2019.121890] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
In recent impetus of phycological research, microalgae have emerged as a potential candidate for various arena of application-driven research. Omics-based tactics are used for disentangling the regulation and network integration for biosynthesis/degradation of metabolic precursors, intermediates, end products, and identifying the networks that regulate the metabolic flux. Multi-omics coupled with data analytics have facilitated understanding of biological processes and allow ample access to diverse metabolic pathways utilized for genetic manipulations making microalgal factories more efficient. The present review discusses state-of-art "Algomics" and the prospect of microalgae and their role in symbiotic association by using omics approaches including genomics, transcriptomics, proteomics and metabolomics. Microalgal based uni- and multi-omics approaches are critically analyzed in wastewater treatment, metal toxicity and remediation, biofuel production, and therapeutics to provide an imminent outlook for an array of environmentally sustainable and economically viable microalgal applications.
Collapse
Affiliation(s)
- Arti Mishra
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kristina Medhi
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Piyush Malaviya
- Department of Environmental Science, University of Jammu, Jammu (J&K), India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
30
|
A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus. Nat Commun 2019; 10:4061. [PMID: 31492891 PMCID: PMC6731263 DOI: 10.1038/s41467-019-12014-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 08/16/2019] [Indexed: 12/11/2022] Open
Abstract
Tiny marine green algae issued from two deep branches of the Chlorophyta, the Mamiellophyceae and Chloropicophyceae, dominate different regions of the oceans and play key roles in planktonic communities. Considering that the Mamiellophyceae is the sole lineage of prasinophyte algae that has been intensively investigated, the extent to which these two algal groups differ in their metabolic capacities and cellular processes is currently unknown. To address this gap of knowledge, we investigate here the nuclear genome sequence of a member of the Chloropicophyceae, Chloropicon primus. Among the main biological insights that emerge from this 17.4 Mb genome, we find an unexpected diploid structure for most chromosomes and a propionate detoxification pathway in green algae. Our results support the notion that separate events of genome minimization, which entailed differential losses of genes/pathways, have occurred in the Chloropicophyceae and Mamiellophyceae, suggesting different strategies of adaptation to oceanic environments.
Collapse
|
31
|
Kugler A, Zorin B, Didi-Cohen S, Sibiryak M, Gorelova O, Ismagulova T, Kokabi K, Kumari P, Lukyanov A, Boussiba S, Solovchenko A, Khozin-Goldberg I. Long-Chain Polyunsaturated Fatty Acids in the Green Microalga Lobosphaera incisa Contribute to Tolerance to Abiotic Stresses. PLANT & CELL PHYSIOLOGY 2019; 60:1205-1223. [PMID: 30668793 DOI: 10.1093/pcp/pcz013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/15/2019] [Indexed: 05/16/2023]
Abstract
Lobosphaera incisa is a green microalga that accumulates high levels of the valuable omega-6 long-chain polyunsaturated fatty acids (LC-PUFA) arachidonic acid (ARA, 20:4n-6) in triacylglycerols (TAG) under nitrogen (N) starvation. LC-PUFA accumulation is a rare trait in photosynthetic microalgae with insufficiently understood physiological significance. In this study, RNAi was attempted, for the first time in L. incisa, to produce knockdown lines for the Δ5 desaturase gene. Two lines, termed modified lines, which were isolated during screening for transgenic events, demonstrated alterations in their LC-PUFA profile, ARA-biosynthesis gene expression and lipid class distribution. In line M5-78, which appeared to carry a mutation in the Δ6 elongase gene, LC-PUFA were substituted by 18:3n-6 in all glycerolipids. Line M2-35, for which the exact genetic background has not been established, displayed a dramatic reduction in 20:4n-6, concomitant with an augmented proportion of 18:1n-9, in particular in the extraplastidial membrane lipids and TAG. The physiological responses of the modified lines to stressful conditions were compared with the wild type and the Δ5 desaturase mutant. In the N-replete cells of modified lines, the frequency of lipid droplets was reduced, while a number of starch grains increased, suggesting altered partitioning of assimilated carbon into reserve products. Furthermore, both lines exhibited reduced ability to accumulate TAG under N deprivation and recover from N starvation. Both lines demonstrated lower photosynthetic pigment contents, impairments in photosynthesis under a range of stressful conditions, and less efficient functioning of photoprotection under optimal conditions. Possible implications of fatty acids modifications in the stress response of L. incisa are addressed.
Collapse
Affiliation(s)
- Amit Kugler
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Boris Zorin
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Shoshana Didi-Cohen
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Maria Sibiryak
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Olga Gorelova
- Faculty of Biology, Department of Bioengineering, Moscow State University, GSP-1, Moscow, Russia
| | - Tatiana Ismagulova
- Faculty of Biology, Department of Bioengineering, Moscow State University, GSP-1, Moscow, Russia
| | - Kamilya Kokabi
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Puja Kumari
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Alexander Lukyanov
- Faculty of Biology, Department of Bioengineering, Moscow State University, GSP-1, Moscow, Russia
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Alexei Solovchenko
- Faculty of Biology, Department of Bioengineering, Moscow State University, GSP-1, Moscow, Russia
- Institute of Agriculture and Technology, Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology for Drylands, The J. Blaustein Institutes for Desert Research Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Israel
| |
Collapse
|
32
|
Abstract
Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.
Collapse
Affiliation(s)
| | - Sabeeha S Merchant
- Departments of Plant and Microbial Biology and Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
| |
Collapse
|
33
|
Kalapos B, Hlavová M, Nádai TV, Galiba G, Bišová K, Dóczi R. Early Evolution of the Mitogen-Activated Protein Kinase Family in the Plant Kingdom. Sci Rep 2019; 9:4094. [PMID: 30858468 PMCID: PMC6411719 DOI: 10.1038/s41598-019-40751-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/04/2019] [Indexed: 01/23/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathways are central cellular signalling mechanisms in all eukaryotes. They are key regulators of the cell cycle and stress responses, yet evolution of MAPK families took markedly different paths in the animal and plant kingdoms. Instead of the characteristic divergence of MAPK types in animals, in plants an expanded network of ERK-like MAPKs has emerged. To gain insight into the early evolution of the plant MAPK family we identified and analysed MAPKs in 13 representative species across green algae, a large and diverse early-diverging lineage within the plant kingdom. Our results reveal that the plant MAPK gene family emerged from three types of progenitor kinases, which are ubiquitously present in algae, implying their formation in an early ancestor. Low number of MAPKs is characteristic across algae, the few losses or duplications are associated with genome complexity rather than habitat ecology, despite the importance of MAPKs in environmental signalling in flowering plants. ERK-type MAPKs are associated with cell cycle regulation in opisthokont models, yet in plants their stress-signalling function is more prevalent. Unicellular microalgae offer an excellent experimental system to study the cell cycle, and MAPK gene expression profiles show CDKB-like peaks around S/M phase in synchronised Chlamydomonas reinhardtii cultures, suggesting their participation in cell cycle regulation, in line with the notion that the ancestral eukaryotic MAPK was a cell cycle regulator ERK-like kinase. Our work also highlights the scarcity of signalling knowledge in microalgae, in spite of their enormous ecological impact and emerging economic importance.
Collapse
Affiliation(s)
- Balázs Kalapos
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.,Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Hungary
| | - Monika Hlavová
- Centre Algatech, Institute of Microbiology Academy of Sciences of the Czech Republic, Opatovicky mlyn, CZ 379 81, Třeboň, Czech Republic
| | - Tímea V Nádai
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.,Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Hungary
| | - Gábor Galiba
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.,Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Hungary
| | - Kateřina Bišová
- Centre Algatech, Institute of Microbiology Academy of Sciences of the Czech Republic, Opatovicky mlyn, CZ 379 81, Třeboň, Czech Republic
| | - Róbert Dóczi
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.
| |
Collapse
|
34
|
Ye J, Liu M, He M, Ye Y, Huang J. Illustrating and Enhancing the Biosynthesis of Astaxanthin and Docosahexaenoic Acid in Aurantiochytrium sp. SK4. Mar Drugs 2019; 17:md17010045. [PMID: 30634667 PMCID: PMC6357005 DOI: 10.3390/md17010045] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/01/2019] [Accepted: 01/03/2019] [Indexed: 12/22/2022] Open
Abstract
The marine thraustochytrids are a promising source of docosahexaenoic acid (DHA) and the ketocarotenoid astaxanthin. In this study, the biosynthetic pathways of these two important metabolites in Aurantiochytrium sp. SK4 was illustrated by the analyses of the genome, transcriptome, key enzymes, and pathway products. Two sets of genes were involved in two pathways for the biosynthesis of fatty acids. The absence of Δ-15 desaturase genes and the presence of docosapentaenoic acid (DPA), up to 12% of total fatty acids suggest that Aurantiochytrium sp. SK4 may synthesize DHA mainly via a polyketide synthase (PKS) pathway. Three enzymes, namely geranyl diphosphate synthase (GPPS), farnysyl diphosphate synthase (FPPS), and geranylgeranyle diphosphate synthase (GGPPS) were found to be involved in the formation of GGPP that was subsequently catalyzed to β-carotene by a trifunctional CrtIBY enzyme. β-Carotene might be ketolated and then hydroxylated into astaxanthin based on the carotenoid profiles. The formation of GGPP was proposed to be the limiting steps for carotenoid production. Overexpression of the Archaeoglobus GPS together with the Escherichia coli isopentenyl pyrophosphate isomerase, and Vitreoscilla hemoglobin resulted in not only 1.85- and 5.02-fold increases of total carotenoids and astaxanthin, but also 2.40- and 2.74-fold increases of total fatty acids and DHA. This study provides insights into the biosynthesis of carotenoids and fatty acids in Aurantiochytrium.
Collapse
Affiliation(s)
- Jingrun Ye
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Mengmeng Liu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Mingxia He
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Ying Ye
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junchao Huang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| |
Collapse
|
35
|
Lauersen KJ. Eukaryotic microalgae as hosts for light-driven heterologous isoprenoid production. PLANTA 2019; 249:155-180. [PMID: 30467629 DOI: 10.1007/s00425-018-3048-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/14/2018] [Indexed: 05/21/2023]
Abstract
Eukaryotic microalgae hold incredible metabolic potential for the sustainable production of heterologous isoprenoid products. Recent advances in algal engineering have enabled the demonstration of prominent examples of heterologous isoprenoid production. Isoprenoids, also known as terpenes or terpenoids, are the largest class of natural chemicals, with a vast diversity of structures and biological roles. Some have high-value in human-use applications, although may be found in their native contexts in low abundance or be difficult to extract and purify. Heterologous production of isoprenoid compounds in heterotrophic microbial hosts such as bacteria or yeasts has been an active area of research for some time and is now a mature technology. Eukaryotic microalgae represent sustainable alternatives to these hosts for biotechnological production processes as their cultivation can be driven by light and freely available CO2 as a carbon source. Their photosynthetic lifestyles require metabolic architectures structured towards the generation of associated isoprenoids (carotenoids, phytol) which participate in photon capture, energy dissipation, and electron transfer. Eukaryotic microalgae should, therefore, contain inherently high capacities for the generation of heterologous isoprenoid products. Although engineering strategies in eukaryotic microalgae have lagged behind the more genetically tractable bacteria and yeasts, recent advances in algal engineering concepts have demonstrated prominent examples of light-driven heterologous isoprenoid production from these photosynthetic hosts. This work seeks to provide practical insights into the choice of eukaryotic microalgae as biotechnological chassis. Recent reports of advances in algal engineering for heterologous isoprenoid production are highlighted as encouraging examples that promote their expanded use as sustainable green-cell factories. Current state of the art, limitations, and future challenges are also discussed.
Collapse
Affiliation(s)
- Kyle J Lauersen
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615, Bielefeld, Germany.
| |
Collapse
|
36
|
Nag Dasgupta C, Nayaka S, Toppo K, Singh AK, Deshpande U, Mohapatra A. Draft genome sequence and detailed characterization of biofuel production by oleaginous microalga Scenedesmus quadricauda LWG002611. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:308. [PMID: 30455737 PMCID: PMC6225629 DOI: 10.1186/s13068-018-1308-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/30/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND Due to scarcity of fossil fuel, the importance of alternative energy sources is ever increasing. The oleaginous microalgae have demonstrated their potential as an alternative source of energy, but have not achieved commercialization owing to some biological and technical inefficiency. Modern methods of recombinant strain development for improved efficacy are suffering due to inadequate knowledge of genome and limited molecular tools available for their manipulation. RESULTS In the present study, microalga Scenedesmus quadricauda LWG002611 was selected as the preferred organism for lipid production as it contained high biomass (0.37 g L-1 day-1) and lipid (102 mg L-1 day-1), compared to other oleaginous algae examined in the present study as well as earlier reports. It possessed suitable biodiesel properties as per the range defined by the European biodiesel standard EN14214 and petro-diesel standard EN590:2013. To investigate the potential of S. quadricauda LWG002611 in details, the genome of the organism was assembled and annotated. This was the first genome sequencing and assembly of S. quadricauda, which predicted a genome size of 65.35 Mb with 13,514 genes identified by de novo and 16,739 genes identified by reference guided annotation. Comparative genomics revealed that it belongs to class Chlorophyceae and order Sphaeropleales. Further, small subunit ribosomal RNA gene (18S rRNA) sequencing was carried out to confirm its molecular identification. S. quadricauda LWG002611 exhibited higher number of genes related to major activities compared to other potential algae reported earlier with a total of 283 genes identified in lipid metabolism. Metabolic pathways were reconstructed and multiple gene homologs responsible for carbon fixation and triacylglycerol (TAG) biosynthesis pathway were identified to further improve this potential algal strain for biofuel production by metabolic engineering approaches. CONCLUSION Here we present the first draft genome sequence, genetic characterization and comparative evaluation of S. quadricauda LWG002611 which exhibit high biomass as well as high lipid productivity. The knowledge of genome sequence, reconstructed metabolic pathways and identification of rate-limiting steps in TAG biosynthesis pathway will strengthen the development of molecular tools towards further improving this potentially one of the major algal strains for biofuel production.
Collapse
Affiliation(s)
- Chitralekha Nag Dasgupta
- Algology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226 001 India
| | - Sanjeeva Nayaka
- Algology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226 001 India
| | - Kiran Toppo
- Algology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226 001 India
| | - Atul Kumar Singh
- Algology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, Uttar Pradesh 226 001 India
| | - Uday Deshpande
- Bioserve|A CGI Company, 3-1-135/1A, CNR Complex, Mallapur, Hyderabad, Telangana 500 076 India
| | - Amitabikram Mohapatra
- Bioserve|A CGI Company, 3-1-135/1A, CNR Complex, Mallapur, Hyderabad, Telangana 500 076 India
| |
Collapse
|
37
|
Sánchez Roque Y, Pérez-Luna YDC, Moreira Acosta J, Farrera Vázquez N, Berrones Hernández R, Saldaña Trinidad S, Pathiyamattom JS. Evaluation of the population dynamics of microalgae isolated from the state of Chiapas, Mexico with respect to the nutritional quality of water. Biodivers Data J 2018:e28496. [PMID: 30294208 PMCID: PMC6170526 DOI: 10.3897/bdj.6.e28496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/05/2018] [Indexed: 12/18/2022] Open
Abstract
As Chiapas state, México, counts on an extensive hydrography with diverse nutrimental and climatic characteristics, it therefore allows isolating and identifying microalgae with bioenergetics potential. For this purpose, samples from 8 locations were collected, corresponding to 6 rivers, a wastewater and a springwater. The isolation of microalgae was developed for 4 weeks with 12:12 light/dark cycles. We demonstrated that the most efficient means for the isolation of microalgae of the hydrographic areas evaluated was the medium BG11 with 80.53% effectiveness. Of the microalgal consortium identified, 90% are composed of microalgae belonging to the class Chlorophycear. It was shown that another factor favouring the richness of morphotypes identified in the Santo Domingo River is associated with adequate concentrations of macroelements such as nitrates, nitrites, ammonium, phosphorus, sodium, potassium, magnesium and calcium at concentrations of 0.03 mg/l, 0.0006 mg/l, 0.08 mg/l, 0.03 mg/l, 62.93 mg/l, 5.46 mg/l, 34.52 mg/l and 48.78 mg/l respectively and microelements such as copper, zinc, iron, andmanganese at concentrations less than 0.2 mg/l in all microelements. The identified morphotypes, according to literature, have lipid contents ranging from 2 to 90%; this is of biotechnological importance for the production of biodiesel.
Collapse
Affiliation(s)
- Yazmin Sánchez Roque
- Universidad Politécnica de Chiapas, Suchiapa, Mexico Universidad Politécnica de Chiapas Suchiapa Mexico
| | | | - Joel Moreira Acosta
- Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico Universidad de Ciencias y Artes de Chiapas Tuxtla Gutiérrez Mexico
| | - Neín Farrera Vázquez
- Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico Universidad de Ciencias y Artes de Chiapas Tuxtla Gutiérrez Mexico
| | | | - Sergio Saldaña Trinidad
- Universidad Politécnica de Chiapas, Suchiapa, Mexico Universidad Politécnica de Chiapas Suchiapa Mexico
| | | |
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Baier T, Wichmann J, Kruse O, Lauersen KJ. Intron-containing algal transgenes mediate efficient recombinant gene expression in the green microalga Chlamydomonas reinhardtii. Nucleic Acids Res 2018; 46:6909-6919. [PMID: 30053227 PMCID: PMC6061784 DOI: 10.1093/nar/gky532] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/16/2018] [Accepted: 06/08/2018] [Indexed: 12/27/2022] Open
Abstract
Among green freshwater microalgae, Chlamydomonas reinhardtii has the most comprehensive and developed molecular toolkit, however, advanced genetic and metabolic engineering driven from the nuclear genome is generally hindered by inherently low transgene expression levels. Progressive strain development and synthetic promoters have improved the capacity of transgene expression; however, the responsible regulatory mechanisms are still not fully understood. Here, we elucidate the sequence specific dynamics of native regulatory element insertion into nuclear transgenes. Systematic insertions of the first intron of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit 2 (rbcS2i1) throughout codon-optimized coding sequences (CDS) generates optimized algal transgenes which express reliably in C. reinhardtii. The optimal rbcS2i1 insertion site for efficient splicing was systematically determined and improved gene expression rates were shown using a codon-optimized sesquiterpene synthase CDS. Sequential insertions of rbcS2i1 were found to have a step-wise additive effect on all levels of transgene expression, which is likely correlated to a synergy of transcriptional machinery recruitment and mimicking the short average exon lengths natively found in the C. reinhardtii genome. We further demonstrate the value of this optimization with five representative transgene examples and provide guidelines for the design of any desired sequence with this strategy.
Collapse
MESH Headings
- Abies/enzymology
- Abies/genetics
- Chlamydomonas reinhardtii/genetics
- Codon/genetics
- DNA, Plant/genetics
- DNA, Recombinant/genetics
- Gene Expression Regulation, Plant
- Genes, Plant
- Genes, Synthetic
- Introns
- Isomerases/biosynthesis
- Isomerases/genetics
- Mutagenesis, Insertional
- Plant Proteins/biosynthesis
- Plant Proteins/genetics
- Pogostemon/enzymology
- Pogostemon/genetics
- Protein Engineering
- RNA Splicing
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombinant Proteins/biosynthesis
- Ribulose-Bisphosphate Carboxylase/genetics
- Transgenes
Collapse
Affiliation(s)
- Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Julian Wichmann
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Kyle J Lauersen
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| |
Collapse
|
40
|
Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an insight into genome evolution and environmental adaptations in the Sphaeropleales. Sci Rep 2018; 8:8058. [PMID: 29795299 PMCID: PMC5966456 DOI: 10.1038/s41598-018-26331-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 05/08/2018] [Indexed: 11/08/2022] Open
Abstract
The Sphaeropleales are a dominant group of green algae, which contain species important to freshwater ecosystems and those that have potential applied usages. In particular, Raphidocelis subcapitata is widely used worldwide for bioassays in toxicological risk assessments. However, there are few comparative genome analyses of the Sphaeropleales. To reveal genome evolution in the Sphaeropleales based on well-resolved phylogenetic relationships, nuclear, mitochondrial, and plastid genomes were sequenced in this study. The plastid genome provides insights into the phylogenetic relationships of R. subcapitata, which is located in the most basal lineage of the four species in the family Selenastraceae. The mitochondrial genome shows dynamic evolutionary histories with intron expansion in the Selenastraceae. The 51.2 Mbp nuclear genome of R. subcapitata, encoding 13,383 protein-coding genes, is more compact than the genome of its closely related oil-rich species, Monoraphidium neglectum (Selenastraceae), Tetradesmus obliquus (Scenedesmaceae), and Chromochloris zofingiensis (Chromochloridaceae); however, the four species share most of their genes. The Sphaeropleales possess a large number of genes for glycerolipid metabolism and sugar assimilation, which suggests that this order is capable of both heterotrophic and mixotrophic lifestyles in nature. Comparison of transporter genes suggests that the Sphaeropleales can adapt to different natural environmental conditions, such as salinity and low metal concentrations.
Collapse
|
41
|
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.
Collapse
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.
| |
Collapse
|
42
|
Satjarak A, Graham LE. Genome-wide analysis of carbohydrate-active enzymes in Pyramimonas parkeae (Prasinophyceae). JOURNAL OF PHYCOLOGY 2017; 53:1072-1086. [PMID: 28708263 DOI: 10.1111/jpy.12566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The wall-less green flagellate Pyramimonas parkeae is classified in clade I of the prasinophytes, a paraphyletic assemblage representing the last common ancestor of Viridiplantae, a monophyletic group composed of the green algae and land plants. Consequently, P. parkeae and other prasinophytes illuminate early-evolved Viridiplantae traits likely fundamental in the systems biology of green algae and land plants. Cellular structure and organellar genomes of P. parkeae are now well understood, and transcriptomic sequence data are also publically available for one strain of this species, but corresponding nuclear genomic sequence data are lacking. For this reason, we obtained shotgun genomic sequence and assembled a draft nuclear genome for P. parkeaeNIES254 to use along with existing transcriptomic sequence to focus on carbohydrate-active enzymes. We found that the P. parkeae nuclear genome encodes carbohydrate-active protein families similar to those previously observed for other prasinophytes, green algae, and early-diverging embryophytes for which full nuclear genomic sequence is publically available. Sequences homologous to genes related to biosynthesis of starch and cell wall carbohydrates were identified in the P. parkeae genome, indicating molecular traits common to Viridiplantae. For example, the P. parkeae genome includes sequences clustering with bacterial genes that encode cellulose synthases (Bcs), including regions coding for domains common to bacterial and plant cellulose synthases; these new sequences were incorporated into phylogenies aimed at illuminating the evolutionary history of cellulose production by Viridiplantae. Genomic sequences related to biosynthesis of xyloglucans, pectin, and starch likewise shed light on the origin of key Viridiplantae traits.
Collapse
Affiliation(s)
- Anchittha Satjarak
- Department of Botany, Chulalongkorn University, Bangkok, Thailand
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA
| | - Linda E Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA
| |
Collapse
|
43
|
Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O. Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:197. [PMID: 28814974 PMCID: PMC5556983 DOI: 10.1186/s13068-017-0882-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/03/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering. RESULTS An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum. Transcript data were correlated with metabolic data for cellular contents of starch and of different lipid fractions. A pronounced transcriptional down-regulation of photosynthesis became apparent in response to nitrogen starvation, whereas glucose catabolism was found to be up-regulated. An in-depth reconstruction and analysis of the pathways for glycerolipid, central carbon, and starch metabolism revealed that distinct transcriptional changes were generally found only for specific steps within a metabolic pathway. In addition to pathway analyses, the transcript data were also used to refine the current genome annotation. The transcriptome data were integrated into a database and complemented with data for other microalgae which were also subjected to nitrogen starvation. It is available at https://tdbmn.cebitec.uni-bielefeld.de. CONCLUSIONS Based on the transcriptional responses to different stages of nitrogen availability, a model for triacylglycerol and lipid hyperaccumulation is proposed, which involves transcriptional induction of thioesterases, differential regulation of lipases, and a re-routing of the central carbon metabolism. Over-expression of distinct thioesterases was identified to be a potential strategy to increase the oleaginous phenotype of M. neglectum, and furthermore specific lipases were identified as potential targets for future metabolic engineering approaches.
Collapse
Affiliation(s)
- Daniel Jaeger
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Jan H. Mussgnug
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, 35392 Gießen, Germany
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 27, 33615 Bielefeld, Germany
| |
Collapse
|
44
|
Proteomic approaches in microalgae: perspectives and applications. 3 Biotech 2017; 7:197. [PMID: 28667637 DOI: 10.1007/s13205-017-0831-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022] Open
Abstract
Biofuels are the promising sources which are produced by various microalgae or in the form of metabolic by-products from organic or food waste products. Microalgae have been widely reported for the production of biofuels since these have a high storage of lipids as triacylglycerides, which can mainly be converted into biofuels. Recently, products such as biodiesel, bioethanol and biogas have renewed the interest toward the microalgae. The proteomics alone will not pave the way toward finding an ideal alga which will fulfill the current energy demands, but a combined approach of proteomics, genomics and bioinformatics can be pivotal for a sustainable solution. The present review emphasizes various technologies currently involved in algal proteomics for the efficient production of biofuels.
Collapse
|
45
|
Jaeger D, Hübner W, Huser T, Mussgnug JH, Kruse O. Nuclear transformation and functional gene expression in the oleaginous microalga Monoraphidium neglectum. J Biotechnol 2017; 249:10-15. [DOI: 10.1016/j.jbiotec.2017.03.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/07/2017] [Accepted: 03/11/2017] [Indexed: 01/22/2023]
|
46
|
Řezanka T, Nedbalová L, Lukavský J, Střížek A, Sigler K. Pilot cultivation of the green alga Monoraphidium sp. producing a high content of polyunsaturated fatty acids in a low-temperature environment. ALGAL RES 2017. [DOI: 10.1016/j.algal.2016.12.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
47
|
Che R, Huang L, Xu JW, Zhao P, Li T, Ma H, Yu X. Effect of fulvic acid induction on the physiology, metabolism, and lipid biosynthesis-related gene transcription of Monoraphidium sp. FXY-10. BIORESOURCE TECHNOLOGY 2017; 227:324-334. [PMID: 28042988 DOI: 10.1016/j.biortech.2016.12.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/02/2016] [Accepted: 12/03/2016] [Indexed: 05/03/2023]
Abstract
Fulvic acid (FA) triggers lipid accumulation in Monoraphidium sp. FXY-10, which can produce biofuels. Therefore, the metabolism shift and gene expression changes influenced by fulvic acid should be investigated. In this study, lipid and protein contents increased rapidly from 44.6% to 54.3% and from 31.4% to 39.7% under FA treatment, respectively. By contrast, carbohydrate content sharply declined from 49.5% to 32.5%. The correlation between lipid content and gene expression was also analyzed. Results revealed that accD, ME, and GPAT genes were significantly correlated with lipid accumulation. These genes could likely influence lipid accumulation and could be selected as modification candidates. These results demonstrated that FA significantly increased microalgal lipid accumulation by changing the intracellular reactive oxygen species, gene expression, and enzyme activities of acetyl-CoA carboxylase, malic enzyme, and phosphoenolpyruvate carboxylase.
Collapse
Affiliation(s)
- Raoqiong Che
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li Huang
- Institute of Chemical Industry, Kunming Metallurgy College, Kunming, China
| | - Jun-Wei Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Peng Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Tao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Huixian Ma
- School of Foreign Languages, Kunming University, Kunming 650200, China
| | - Xuya Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.
| |
Collapse
|
48
|
Macaisne N, Liu F, Scornet D, Peters AF, Lipinska A, Perrineau MM, Henry A, Strittmatter M, Coelho SM, Cock JM. The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Development 2017; 144:409-418. [PMID: 28049657 DOI: 10.1242/dev.141523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/12/2016] [Indexed: 01/09/2023]
Abstract
The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared with the majority of brown algae. The first cell division is symmetrical and the apical-basal axis is established late in development. In the immediate upright (imm) mutant, the initial cell undergoes an asymmetric division to immediately establish the apical-basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function that contains a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus EsV-1. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles, suggesting that the expansion of this family might have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.
Collapse
Affiliation(s)
- Nicolas Macaisne
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Fuli Liu
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | | | - Agnieszka Lipinska
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Marie-Mathilde Perrineau
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Antoine Henry
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Martina Strittmatter
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| |
Collapse
|
49
|
Kurotani A, Yamada Y, Sakurai T. Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PLANT & CELL PHYSIOLOGY 2017; 58:e6. [PMID: 28069893 PMCID: PMC5444574 DOI: 10.1093/pcp/pcw212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/24/2016] [Indexed: 06/06/2023]
Abstract
Algae are smaller organisms than land plants and offer clear advantages in research over terrestrial species in terms of rapid production, short generation time and varied commercial applications. Thus, studies investigating the practical development of effective algal production are important and will improve our understanding of both aquatic and terrestrial plants. In this study we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algal and three plant species. Algal species were broadly selected from green and red algae, glaucophytes, oomycetes, diatoms and other microalgal groups. The results were deposited in the Algal Protein Annotation Suite database (Alga-PrAS; http://alga-pras.riken.jp/), which can be freely accessed online.
Collapse
Affiliation(s)
- Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Yutaka Yamada
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Interdisciplinary Science Unit, Multidisciplinary Science Cluster, Research and Education Faculty, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| |
Collapse
|
50
|
Klassen V, Blifernez-Klassen O, Wibberg D, Winkler A, Kalinowski J, Posten C, Kruse O. Highly efficient methane generation from untreated microalgae biomass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:186. [PMID: 28725266 PMCID: PMC5513056 DOI: 10.1186/s13068-017-0871-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/10/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND The fact that microalgae perform very efficiently photosynthetic conversion of sunlight into chemical energy has moved them into the focus of regenerative fuel research. Especially, biogas generation via anaerobic digestion is economically attractive due to the comparably simple apparative process technology and the theoretical possibility of converting the entire algal biomass to biogas/methane. In the last 60 years, intensive research on biogas production from microalgae biomass has revealed the microalgae as a rather challenging substrate for anaerobic digestion due to its high cell wall recalcitrance and unfavorable protein content, which requires additional pretreatment and co-fermentation strategies for sufficient fermentation. However, sustainable fuel generation requires the avoidance of cost/energy intensive biomass pretreatments to achieve positive net-energy process balance. RESULTS Cultivation of microalgae in replete and limited nitrogen culture media conditions has led to the formation of protein-rich and low protein biomass, respectively, with the last being especially optimal for continuous fermentation. Anaerobic digestion of nitrogen limited biomass (low-N BM) was characterized by a stable process with low levels of inhibitory substances and resulted in extraordinary high biogas, and subsequently methane productivity [750 ± 15 and 462 ± 9 mLN g-1 volatile solids (VS) day-1, respectively], thus corresponding to biomass-to-methane energy conversion efficiency of up to 84%. The microbial community structure within this highly efficient digester revealed a clear predominance of the phyla Bacteroidetes and the family Methanosaetaceae among the Bacteria and Archaea, respectively. The fermentation of replete nitrogen biomass (replete-N BM), on the contrary, was demonstrated to be less productive (131 ± 33 mLN CH4 g-1VS day-1) and failed completely due to acidosis, caused through high ammonia/ammonium concentrations. The organization of the microbial community of the failed (replete-N) digester differed greatly compared to the stable low-N digester, presenting a clear shift to the phyla Firmicutes and Thermotogae, and the archaeal population shifted from acetoclastic to hydrogenotrophic methanogenesis. CONCLUSIONS The present study underlines the importance of cultivation conditions and shows the practicability of microalgae biomass usage as mono-substrate for highly efficient continuous fermentation to methane without any pretreatment with almost maximum practically achievable energy conversion efficiency (biomass to methane).Graphical abstractGrowth condition dependence of anaerobic conversion efficiency of microalgae biomass to methane.
Collapse
Affiliation(s)
- Viktor Klassen
- Department of Biology/Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Olga Blifernez-Klassen
- Department of Biology/Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Department of Biology/Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Anika Winkler
- Department of Biology/Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Department of Biology/Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Clemens Posten
- Institute of Life Science Engineering (KIT), Bioprocess Engineering, University of Karlsruhe, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Olaf Kruse
- Department of Biology/Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| |
Collapse
|