1
|
Green DH, Rad-Menéndez C, Campbell C, Kilias ES. The genome sequence of Pycnococcus provasolii (CCAP190/2) (Guillard, 1991). Wellcome Open Res 2023; 8:520. [PMID: 38808318 PMCID: PMC11130579 DOI: 10.12688/wellcomeopenres.20345.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 05/30/2024] Open
Abstract
We present a genome assembly from cultured Pycnococcus provasolii (a marine green alga; Chlorophyta; None; Pseudoscourfieldiales; Pycnococcaceae). The genome sequence is 32.2 megabases in span. Most of the assembly is scaffolded into 44 chromosomal pseudomolecules (99.67%). The mitochondrial and plastid genomes have also been assembled, and the length of the mitochondrial scaffold is 24.3 kilobases and of the plastid genome has been assembled and is 80.2 kilobases in length.
Collapse
Affiliation(s)
- David H. Green
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
| | - Cecilia Rad-Menéndez
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
| | - Christine Campbell
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
| | | | | | | | | | - Darwin Tree of Life Barcoding collective
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
- Department of Biology, University of Oxford, Oxford, England, UK
| | | | | | - Tree of Life Core Informatics collective
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
- Department of Biology, University of Oxford, Oxford, England, UK
| | | |
Collapse
|
2
|
Suzuki S, Ota S, Yamagishi T, Tuji A, Yamaguchi H, Kawachi M. Rapid transcriptomic and physiological changes in the freshwater pennate diatom Mayamaea pseudoterrestris in response to copper exposure. DNA Res 2022; 29:6748870. [PMID: 36197113 PMCID: PMC9724779 DOI: 10.1093/dnares/dsac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 12/12/2022] Open
Abstract
Diatoms function as major primary producers, accumulating large amounts of biomass in most aquatic environments. Given their rapid responses to changes in environmental conditions, diatoms are used for the biological monitoring of water quality and for performing ecotoxicological tests in aquatic ecosystems. However, the molecular basis for their toxicity to chemical compounds remains largely unknown. Here, we sequenced the genome of a freshwater diatom, Mayamaea pseudoterrestris NIES-4280, which has been proposed as an alternative strain of Navicula pelliculosa UTEX 664 for performing the Organisation for Economic Co-operation and Development ecotoxicological test. This study shows that M. pseudoterrestris has a small genome and carries the lowest number of genes among freshwater diatoms. The gene content of M. pseudoterrestris is similar to that of the model marine diatom, Phaeodactylum tricornutum. Genes related to cell motility, polysaccharide metabolism, oxidative stress alleviation, intracellular calcium signalling, and reactive compound detoxification showed rapid changes in their expression patterns in response to copper exposure. Active gliding motility was observed in response to copper addition, and copper exposure decreased intracellular calcium concentration. These findings enhance our understanding of the environmental adaptation of diatoms, and elucidate the molecular basis of toxicity of chemical compounds in algae.
Collapse
Affiliation(s)
| | - Shuhei Ota
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Takahiro Yamagishi
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Akihiro Tuji
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| |
Collapse
|
3
|
Bachy C, Wittmers F, Muschiol J, Hamilton M, Henrissat B, Worden AZ. The Land-Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:585-616. [PMID: 35259927 DOI: 10.1146/annurev-arplant-071921-100530] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems-the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.
Collapse
Affiliation(s)
- Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jan Muschiol
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Maria Hamilton
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille Université (AMU), Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Biological Laboratories, Woods Hole, Massachusetts, USA
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| |
Collapse
|
4
|
Shankar U, Lenka SK, Leigh Ackland M, Callahan DL. Review of the structures and functions of algal photoreceptors to optimize bioproduct production with novel bioreactor designs for strain improvement. Biotechnol Bioeng 2022; 119:2031-2045. [PMID: 35441370 DOI: 10.1002/bit.28116] [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: 11/19/2021] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 11/11/2022]
Abstract
Microalgae are important renewable feedstock to produce biodiesel and high-value chemicals. Different wavelengths of light influence the growth and metabolic activities of algae. Recent research has identified the light-sensing proteins called photoreceptors that respond to blue or red light. Structural elucidations of algal photoreceptors have gained momentum over recent years. These include channelrhodopsins, PHOT proteins, animal-like cryptochromes, blue-light sensors utilizing flavin-adenine dinucleotide (BLUF) proteins. Pulsing light has also been investigated as a means to optimize energy inputs into bioreactors. This review summarizes the current structural and functional basis of photoreceptor modulation to optimize the growth, production of carotenoids and other high-value metabolites from microalgae. The review also encompasses novel photobioreactor designs that implement different light regimes including light wavelengths and time to optimize algal growth and desired metabolite profiles for high-value products. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Uttara Shankar
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, 122001, India.,Deakin University, Geelong, Australia. School of Life and Environmental Sciences, (Burwood Campus), Centre for Cellular and Molecular biology. 221 Burwood Highway, Burwood, VIC, 3125, Australia
| | - Sangram K Lenka
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana, 122001, India.,Gujarat Biotechnology University, Gandhinagar, Gujarat, 382355, India
| | - M Leigh Ackland
- Deakin University, Geelong, Australia. School of Life and Environmental Sciences, (Burwood Campus), Centre for Cellular and Molecular biology. 221 Burwood Highway, Burwood, VIC, 3125, Australia
| | - Damien L Callahan
- Deakin University, Geelong, Australia. School of Life and Environmental Sciences, (Burwood Campus), Centre for Cellular and Molecular biology. 221 Burwood Highway, Burwood, VIC, 3125, Australia
| |
Collapse
|
5
|
Petersen J, Rredhi A, Szyttenholm J, Oldemeyer S, Kottke T, Mittag M. The World of Algae Reveals a Broad Variety of Cryptochrome Properties and Functions. FRONTIERS IN PLANT SCIENCE 2021; 12:766509. [PMID: 34790217 PMCID: PMC8591175 DOI: 10.3389/fpls.2021.766509] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/11/2021] [Indexed: 05/25/2023]
Abstract
Algae are photosynthetic eukaryotic (micro-)organisms, lacking roots, leaves, and other organs that are typical for land plants. They live in freshwater, marine, or terrestrial habitats. Together with the cyanobacteria they contribute to about half of global carbon fixation. As primary producers, they are at the basis of many food webs and they are involved in biogeochemical processes. Algae are evolutionarily distinct and are derived either by primary (e.g., green and red algae) or secondary endosymbiosis (e.g., diatoms, dinoflagellates, and brown algae). Light is a key abiotic factor needed to maintain the fitness of algae as it delivers energy for photosynthesis, regulates algal cell- and life cycles, and entrains their biological clocks. However, excess light can also be harmful, especially in the ultraviolet range. Among the variety of receptors perceiving light information, the cryptochromes originally evolved as UV-A and blue-light receptors and have been found in all studied algal genomes so far. Yet, the classification, biophysical properties, wavelength range of absorbance, and biological functions of cryptochromes are remarkably diverse among algal species, especially when compared to cryptochromes from land plants or animals.
Collapse
Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Sabine Oldemeyer
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
- Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| |
Collapse
|