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Tulin F, Clark-Cotton MR, Onishi M. Chlamydomonas. Curr Biol 2024; 34:R611-R612. [PMID: 38981421 DOI: 10.1016/j.cub.2024.05.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Tulin et al. introduce Chlamydomonas, a unicellular green alga commonly used as a microbial reference system for plants and animals.
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Affiliation(s)
- Frej Tulin
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - Manuella R Clark-Cotton
- Department of Biology, Duke University, 124 Science Drive, French Family Science Center 3105, Durham, NC 27708, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, 124 Science Drive, French Family Science Center 3105, Durham, NC 27708, USA.
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2
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Hufft-Martinez BM, Wang HH, Saadi I, Tran PV. Actin cytoskeletal regulation of ciliogenesis in development and disease. Dev Dyn 2024. [PMID: 38958410 DOI: 10.1002/dvdy.724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/29/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024] Open
Abstract
Primary cilia are antenna-like sensory organelles that are evolutionarily conserved in nearly all modern eukaryotes, from the single-celled green alga, Chlamydomonas reinhardtii, to vertebrates and mammals. Cilia are microtubule-based cellular projections that have adapted to perform a broad range of species-specific functions, from cell motility to detection of light and the transduction of extracellular mechanical and chemical signals. These functions render cilia essential for organismal development and survival. The high conservation of cilia has allowed for discoveries in C. reinhardtii to inform our understanding of the basic biology of mammalian primary cilia, and to provide insight into the genetic etiology of ciliopathies. Over the last two decades, a growing number of studies has revealed that multiple aspects of ciliary homeostasis are regulated by the actin cytoskeleton, including centrosome migration and positioning, vesicle transport to the basal body, ectocytosis, and ciliary-mediated signaling. Here, we review actin regulation of ciliary homeostasis, and highlight conserved and divergent mechanisms in C. reinhardtii and mammalian cells. Further, we compare the disease manifestations of patients with ciliopathies to those with mutations in actin and actin-associated genes, and propose that primary cilia defects caused by genetic alteration of the actin cytoskeleton may underlie certain birth defects.
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Affiliation(s)
- Brittany M Hufft-Martinez
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Henry H Wang
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Irfan Saadi
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
- Institute of Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Pamela V Tran
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas, USA
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3
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Bellido-Pedraza CM, Torres MJ, Llamas A. The Microalgae Chlamydomonas for Bioremediation and Bioproduct Production. Cells 2024; 13:1137. [PMID: 38994989 PMCID: PMC11240456 DOI: 10.3390/cells13131137] [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: 05/31/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
The extensive metabolic diversity of microalgae, coupled with their rapid growth rates and cost-effective production, position these organisms as highly promising resources for a wide range of biotechnological applications. These characteristics allow microalgae to address crucial needs in the agricultural, medical, and industrial sectors. Microalgae are proving to be valuable in various fields, including the remediation of diverse wastewater types, the production of biofuels and biofertilizers, and the extraction of various products from their biomass. For decades, the microalga Chlamydomonas has been widely used as a fundamental research model organism in various areas such as photosynthesis, respiration, sulfur and phosphorus metabolism, nitrogen metabolism, and flagella synthesis, among others. However, in recent years, the potential of Chlamydomonas as a biotechnological tool for bioremediation, biofertilization, biomass, and bioproducts production has been increasingly recognized. Bioremediation of wastewater using Chlamydomonas presents significant potential for sustainable reduction in contaminants and facilitates resource recovery and valorization of microalgal biomass, offering important economic benefits. Chlamydomonas has also established itself as a platform for the production of a wide variety of biotechnologically interesting products, such as different types of biofuels, and high-value-added products. The aim of this review is to achieve a comprehensive understanding of the potential of Chlamydomonas in these aspects, and to explore their interrelationship, which would offer significant environmental and biotechnological advantages.
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Affiliation(s)
- Carmen M Bellido-Pedraza
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), University of Córdoba, Edificio Severo Ochoa, 14071 Córdoba, Spain
| | - Maria J Torres
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), University of Córdoba, Edificio Severo Ochoa, 14071 Córdoba, Spain
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), University of Córdoba, Edificio Severo Ochoa, 14071 Córdoba, Spain
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Lihanova Y, Nagel R, Jakob T, Sasso S. Characterization of activating cis-regulatory elements from the histone genes of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:525-539. [PMID: 38693717 DOI: 10.1111/tpj.16781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Regulation of gene expression in eukaryotes is controlled by cis-regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis-regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii. To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii, and their activity was quantified by flow cytometry. Two tested candidates, Eupstr and Ehist cons, significantly upregulated gene expression and were characterized in detail. Eupstr, which originates from highly expressed genes of C. reinhardtii, is an orientation-independent CRE capable of activating both the RBCS2 and β2-tubulin promoters. Ehist cons, which is a CRM from histone genes of angiosperms, upregulates the β2-tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in Ehist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta, Chlamydomonas schloesseri, and Edaphochlamys debaryana, demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
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Affiliation(s)
- Yuliia Lihanova
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Torsten Jakob
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Severin Sasso
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
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Zhou Y, Fichman Y, Zhang S, Mittler R, Chen SJ. Modeling the reactive oxygen species (ROS) wave in Chlamydomonas reinhardtii colonies. Free Radic Biol Med 2024; 222:165-172. [PMID: 38851517 DOI: 10.1016/j.freeradbiomed.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/10/2024]
Abstract
Reactive oxygen species (ROS) play a crucial role as signaling molecules in both plant and animal cells, enabling rapid responses to various stimuli. Among the many cellular mechanisms used to generate and transduce ROS signals, ROS-induced-ROS release (RIRR) is emerging as an important pathway involved in the responses of various multicellular and unicellular organisms to environmental stresses. In RIRR, one cellular compartment, organelle, or cell generates or releases ROS, triggering an increased ROS production and release by another compartment, organelle, or cell, thereby giving rise to a fast propagating ROS wave. This RIRR-based signal relay has been demonstrated to facilitate mitochondria-to-mitochondria communication in animal cells and long-distance systemic signaling in plants in response to biotic and abiotic stresses. More recently, it has been discovered that different unicellular microorganism communities also exhibit a RIRR cell-to-cell signaling process triggered by a localized stress treatment. However, the precise mechanism underlying the propagation of the ROS signal among cells within these unicellular communities remained elusive. In this study, we employed a reaction-diffusion model incorporating the RIRR mechanism to analyze the propagation of ROS-mediated signals. By effectively balancing production and scavenging processes, our model successfully reproduces the experimental ROS signal velocities observed in unicellular green algae (Chlamydomonas reinhardtii) colonies grown on agar plates, furthering our understanding of intercellular ROS communication.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.
| | - Yosef Fichman
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Sicheng Zhang
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA.
| | - Ron Mittler
- Division of Plant Science and Technology, College of Agriculture, Food and Natural Resources and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA; Department of Surgery, School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St, Columbia, MO, 65211, USA.
| | - Shi-Jie Chen
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, 65211, USA; Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
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Carrasco Flores D, Hotter V, Vuong T, Hou Y, Bando Y, Scherlach K, Burgunter-Delamare B, Hermenau R, Komor AJ, Aiyar P, Rose M, Sasso S, Arndt HD, Hertweck C, Mittag M. A mutualistic bacterium rescues a green alga from an antagonist. Proc Natl Acad Sci U S A 2024; 121:e2401632121. [PMID: 38568970 PMCID: PMC11009677 DOI: 10.1073/pnas.2401632121] [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: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Photosynthetic protists, known as microalgae, are key contributors to primary production on Earth. Since early in evolution, they coexist with bacteria in nature, and their mode of interaction shapes ecosystems. We have recently shown that the bacterium Pseudomonas protegens acts algicidal on the microalga Chlamydomonas reinhardtii. It secretes a cyclic lipopeptide and a polyyne that deflagellate, blind, and lyse the algae [P. Aiyar et al., Nat. Commun. 8, 1756 (2017) and V. Hotter et al., Proc. Natl. Acad. Sci. U.S.A. 118, e2107695118 (2021)]. Here, we report about the bacterium Mycetocola lacteus, which establishes a mutualistic relationship with C. reinhardtii and acts as a helper. While M. lacteus enhances algal growth, it receives methionine as needed organic sulfur and the vitamins B1, B3, and B5 from the algae. In tripartite cultures with the alga and the antagonistic bacterium P. protegens, M. lacteus aids the algae in surviving the bacterial attack. By combining synthetic natural product chemistry with high-resolution mass spectrometry and an algal Ca2+ reporter line, we found that M. lacteus rescues the alga from the antagonistic bacterium by cleaving the ester bond of the cyclic lipopeptide involved. The resulting linearized seco acid does not trigger a cytosolic Ca2+ homeostasis imbalance that leads to algal deflagellation. Thus, the algae remain motile, can swim away from the antagonistic bacteria and survive the attack. All three involved genera cooccur in nature. Remarkably, related species of Pseudomonas and Mycetocola also act antagonistically against C. reinhardtii or as helper bacteria in tripartite cultures.
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Affiliation(s)
- David Carrasco Flores
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Vivien Hotter
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Yu Hou
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Yuko Bando
- Institute for Organic Chemistry and Macromolecular Chemistry, Organic Chemistry, Friedrich Schiller University Jena, Jena07743, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Ron Hermenau
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Anna J. Komor
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Prasad Aiyar
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Magdalena Rose
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Institute of Biology, Plant Physiology, Leipzig University, Leipzig04103, Germany
| | - Severin Sasso
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Institute of Biology, Plant Physiology, Leipzig University, Leipzig04103, Germany
| | - Hans-Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry, Organic Chemistry, Friedrich Schiller University Jena, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena07743, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
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Brückner DB, Broedersz CP. Learning dynamical models of single and collective cell migration: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:056601. [PMID: 38518358 DOI: 10.1088/1361-6633/ad36d2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 03/22/2024] [Indexed: 03/24/2024]
Abstract
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description.
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Affiliation(s)
- David B Brückner
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Chase P Broedersz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilian-University Munich, Theresienstr. 37, D-80333 Munich, Germany
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Burgunter-Delamare B, Shetty P, Vuong T, Mittag M. Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships. PLANTS (BASEL, SWITZERLAND) 2024; 13:829. [PMID: 38592793 PMCID: PMC10974524 DOI: 10.3390/plants13060829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as mutualism or antagonism. These interactions are shaped through exchanges of primary and secondary metabolites provided by one of the partners. Metabolites, such as N-sources or vitamins, can be beneficial to the partner and they may be assimilated through chemotaxis towards the partner producing these metabolites. Other metabolites, especially many natural products synthesized by bacteria, can act as toxins and damage or kill the partner. For instance, the green microalga Chlamydomonas reinhardtii establishes a mutualistic partnership with a Methylobacterium, in stark contrast to its antagonistic relationship with the toxin producing Pseudomonas protegens. In other cases, as with a coccolithophore haptophyte alga and a Phaeobacter bacterium, the same alga and bacterium can even be subject to both processes, depending on the secreted bacterial and algal metabolites. Some bacteria also influence algal morphology by producing specific metabolites and micronutrients, as is observed in some macroalgae. This review focuses on algal-bacterial interactions with micro- and macroalgal models from marine, freshwater, and terrestrial environments and summarizes the advances in the field. It also highlights the effects of temperature on these interactions as it is presently known.
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Affiliation(s)
- Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Prateek Shetty
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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Sridhara S. Multiple structural flavors of RNase P in precursor tRNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1835. [PMID: 38479802 DOI: 10.1002/wrna.1835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/06/2024]
Abstract
The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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Zhang N, Venn B, Bailey CE, Xia M, Mattoon EM, Mühlhaus T, Zhang R. Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:979-1003. [PMID: 37877811 DOI: 10.1093/jxb/erad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 10/21/2023] [Indexed: 10/26/2023]
Abstract
High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.
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Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Benedikt Venn
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Erin M Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Timo Mühlhaus
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Prieto Maradona M, Querol A, Sijtsma L, Suarez JE, Sundh I, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 19: Suitability of taxonomic units notified to EFSA until September 2023. EFSA J 2024; 22:e8517. [PMID: 38213415 PMCID: PMC10782250 DOI: 10.2903/j.efsa.2024.8517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
The qualified presumption of safety (QPS) process was developed to provide a safety assessment approach for microorganisms intended for use in food or feed chains. The QPS approach is based on an assessment of published data for each taxonomic unit (TU), with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a TU are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 71 microorganisms notified to EFSA between April and September 2023 (30 as feed additives, 22 as food enzymes or additives, 7 as novel foods and 12 from plant protection products [PPP]), 61 were not evaluated because: 26 were filamentous fungi, 1 was Enterococcus faecium, 5 were Escherichia coli, 1 was a bacteriophage (all excluded from the QPS evaluation) and 28 were TUs that already have a QPS status. The other 10 notifications belonged to 9 TUs which were evaluated for a possible QPS status: Ensifer adhaerens and Heyndrickxia faecalis did not get the QPS recommendation due to the limited body of knowledge about their occurrence in the food and/or feed chains and Burkholderia ubonensis also due to its ability to generate biologically active compounds with antimicrobial activity; Klebsiella pneumoniae, Serratia marcescens and Pseudomonas putida due to safety concerns. K. pneumoniae is excluded from future QPS evaluations. Chlamydomonas reinhardtii is recommended for QPS status with the qualification 'for production purposes only'; Clostridium tyrobutyricum is recommended for QPS status with the qualification 'absence of genetic determinants for toxigenic activity'; Candida oleophila has been added as a synonym of Yarrowia lipolytica. The Panel clarifies the extension of the QPS status for genetically modified strains.
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12
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Knoshaug EP, Sun P, Nag A, Nguyen H, Mattoon EM, Zhang N, Liu J, Chen C, Cheng J, Zhang R, St. John P, Umen J. Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis. PLANT DIRECT 2023; 7:e527. [PMID: 38044962 PMCID: PMC10690477 DOI: 10.1002/pld3.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 12/05/2023]
Abstract
The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome-wide protein-coding gene annotation. A substantial fraction of protein-coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): Arabidopsis thaliana (eudicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high-value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.
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Affiliation(s)
- Eric P. Knoshaug
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Peipei Sun
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Ambarish Nag
- Computational Sciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Huong Nguyen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil ScienceTexas Tech UniversityLubbockTexasUSA
| | - Erin M. Mattoon
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical SciencesWashington University in Saint LouisSt. LouisMissouriUSA
| | | | - Jian Liu
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Chen Chen
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Ru Zhang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Peter St. John
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - James Umen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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13
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de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
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Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
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14
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Esteves SM, Jadoul A, Iacono F, Schloesser M, Bosman B, Carnol M, Druet T, Cardol P, Hanikenne M. Natural variation of nutrient homeostasis among laboratory and field strains of Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5198-5217. [PMID: 37235689 DOI: 10.1093/jxb/erad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/24/2023] [Indexed: 05/28/2023]
Abstract
Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macronutrients have a wide range of functions in photosynthetic organisms, and mineral nutrition thus plays a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, 24 Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared with autotrophy and nine deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, and -S) and micronutrients (-Cu, -Fe, -Mn, and -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.
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Affiliation(s)
- Sara M Esteves
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Alice Jadoul
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Fabrizio Iacono
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Bernard Bosman
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, Belgium
| | - Monique Carnol
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics (GIGA), University of Liège, Belgium
| | - Pierre Cardol
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
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15
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Lv Y, Han F, Liu M, Zhang T, Cui G, Wang J, Yang Y, Yang YG, Yang W. Characteristics of N 6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:756-768. [PMID: 35550876 PMCID: PMC10787120 DOI: 10.1016/j.gpb.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as photosynthesis, sexual reproduction, and life cycle. N6-methyladenosine (m6A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m6A modification during the sexual reproduction of Chlamydomonas remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle. The results show that m6A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in Chlamydomonas mRNAs. Moreover, m6A peaks in Chlamydomonas mRNAs are mainly enriched in the 3' untranslated regions (3'UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m6A levels of genes involved in the microtubule-associated pathway, indicating that m6A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m6A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m6A modification in the process of sexual reproduction in other plant organisms.
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Affiliation(s)
- Ying Lv
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengxia Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Guanshen Cui
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jiaojiao Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqiang Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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16
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Findinier J, Grossman AR. Chlamydomonas: Fast tracking from genomics. JOURNAL OF PHYCOLOGY 2023; 59:644-652. [PMID: 37417760 DOI: 10.1111/jpy.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
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Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| | - Arthur R Grossman
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
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17
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Tejada-Jimenez M, Leon-Miranda E, Llamas A. Chlamydomonas reinhardtii-A Reference Microorganism for Eukaryotic Molybdenum Metabolism. Microorganisms 2023; 11:1671. [PMID: 37512844 PMCID: PMC10385300 DOI: 10.3390/microorganisms11071671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
Molybdenum (Mo) is vital for the activity of a small but essential group of enzymes called molybdoenzymes. So far, specifically five molybdoenzymes have been discovered in eukaryotes: nitrate reductase, sulfite oxidase, xanthine dehydrogenase, aldehyde oxidase, and mARC. In order to become biologically active, Mo must be chelated to a pterin, forming the so-called Mo cofactor (Moco). Deficiency or mutation in any of the genes involved in Moco biosynthesis results in the simultaneous loss of activity of all molybdoenzymes, fully or partially preventing the normal development of the affected organism. To prevent this, the different mechanisms involved in Mo homeostasis must be finely regulated. Chlamydomonas reinhardtii is a unicellular, photosynthetic, eukaryotic microalga that has produced fundamental advances in key steps of Mo homeostasis over the last 30 years, which have been extrapolated to higher organisms, both plants and animals. These advances include the identification of the first two molybdate transporters in eukaryotes (MOT1 and MOT2), the characterization of key genes in Moco biosynthesis, the identification of the first enzyme that protects and transfers Moco (MCP1), the first characterization of mARC in plants, and the discovery of the crucial role of the nitrate reductase-mARC complex in plant nitric oxide production. This review aims to provide a comprehensive summary of the progress achieved in using C. reinhardtii as a model organism in Mo homeostasis and to propose how this microalga can continue improving with the advancements in this field in the future.
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Affiliation(s)
- Manuel Tejada-Jimenez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Esperanza Leon-Miranda
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
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18
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Prabhakara KH, Kuehn S. Algae drive convergent bacterial community assembly at low dilution frequency. iScience 2023; 26:106879. [PMID: 37275519 PMCID: PMC10238937 DOI: 10.1016/j.isci.2023.106879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/22/2022] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Abstract
Microbial community assembly is a complex dynamical process that determines community structure and function. The interdependence of inter-species interactions and nutrient availability presents a challenge for understanding community assembly. We sought to understand how external nutrient supply rate modulated interactions to affect the assembly process. A statistical decomposition of taxonomic structures of bacterial communities assembled with and without algae and at varying dilution frequencies allowed the separation of the effects of biotic (presence of algae) and abiotic (dilution frequency) factors on community assembly. For infrequent dilutions, the algae strongly impact community assembly, driving initially diverse bacterial consortia to converge to a common structure. Analyzing sequencing data revealed that this convergence is largely mediated by a decline in the relative abundance of specific taxa in the presence of algae. This study shows that complex phototroph-heterotroph communities can be powerful model systems for understanding assembly processes relevant to the global ecosystem functioning.
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Affiliation(s)
- Kaumudi H Prabhakara
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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19
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Cornwallis CK, Svensson-Coelho M, Lindh M, Li Q, Stábile F, Hansson LA, Rengefors K. Single-cell adaptations shape evolutionary transitions to multicellularity in green algae. Nat Ecol Evol 2023; 7:889-902. [PMID: 37081145 PMCID: PMC10250200 DOI: 10.1038/s41559-023-02044-6] [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: 11/01/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023]
Abstract
The evolution of multicellular life has played a pivotal role in shaping biological diversity. However, we know surprisingly little about the natural environmental conditions that favour the formation of multicellular groups. Here we experimentally examine how key environmental factors (predation, nitrogen and water turbulence) combine to influence multicellular group formation in 35 wild unicellular green algae strains (19 Chlorophyta species). All environmental factors induced the formation of multicellular groups (more than four cells), but there was no evidence this was adaptive, as multicellularity (% cells in groups) was not related to population growth rate under any condition. Instead, population growth was related to extracellular matrix (ECM) around single cells and palmelloid formation, a unicellular life-cycle stage where two to four cells are retained within a mother-cell wall after mitosis. ECM production increased with nitrogen levels resulting in more cells being in palmelloids and higher rates of multicellular group formation. Examining the distribution of 332 algae species across 478 lakes monitored over 55 years, showed that ECM and nitrogen availability also predicted patterns of obligate multicellularity in nature. Our results highlight that adaptations of unicellular organisms to cope with environmental challenges may be key to understanding evolutionary routes to multicellular life.
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Affiliation(s)
| | | | - Markus Lindh
- Swedish Meteorological and Hydrological Institute, Västra Frölunda, Sweden
| | - Qinyang Li
- Department of Biology, Lund University, Lund, Sweden
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20
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Zhang B, Tang Y, Yu F, Peng Z, Yao S, Deng X, Long H, Wang X, Huang K. Translatomics and physiological analyses of the detoxification mechanism of green alga Chlamydomonas reinhardtii to cadmium toxicity. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130990. [PMID: 36860060 DOI: 10.1016/j.jhazmat.2023.130990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Cadmium (Cd) is one of the most toxic pollutants found in aquatic ecosystems. Although gene expression in algae exposed to Cd has been studied at the transcriptional level, little is known about Cd impacts at the translational level. Ribosome profiling is a novel translatomics method that can directly monitor RNA translation in vivo. Here, we analyzed the translatome of the green alga Chlamydomonas reinhardtii following treatment with Cd to identify the cellular and physiological responses to Cd stress. Interestingly, we found that the cell morphology and cell wall structure were altered, and starch and high-electron-density particles accumulated in the cytoplasm. Several ATP-binding cassette transporters that responded to Cd exposure were identified. Redox homeostasis was adjusted to adapt to Cd toxicity, and GDP-L-galactose phosphorylase (VTC2), glutathione peroxidase (GPX5), and ascorbate were found to play important roles in maintaining reactive oxygen species homeostasis. Moreover, we found that the key enzyme of flavonoid metabolism, i.e., hydroxyisoflavone reductase (IFR1), is also involved in the detoxification of Cd. Thus, in this study, translatome and physiological analyses provided a complete picture of the molecular mechanisms of green algae cell responses to Cd.
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Affiliation(s)
- Baolong Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Yuxin Tang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Fei Yu
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Zhao Peng
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Sheng Yao
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Xun Wang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
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21
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Kong F, Li M, Liu K, Ge Y, Yamasaki T, Beyly-Adriano A, Ohama T, Li-Beisson Y. Efficient approaches for nuclear transgene stacking in the unicellular green microalga Chlamydomonas reinhardtii. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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22
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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: 15] [Impact Index Per Article: 15.0] [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).
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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.
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23
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Hou Y, Bando Y, Carrasco Flores D, Hotter V, Das R, Schiweck B, Melzer T, Arndt HD, Mittag M. A cyclic lipopeptide produced by an antagonistic bacterium relies on its tail and transient receptor potential-type Ca 2+ channels to immobilize a green alga. THE NEW PHYTOLOGIST 2023; 237:1620-1635. [PMID: 36464797 DOI: 10.1111/nph.18658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The antagonistic bacterium Pseudomonas protegens secretes the cyclic lipopeptide (CLiP) orfamide A, which triggers a Ca2+ signal causing rapid deflagellation of the microalga Chlamydomonas reinhardtii. We performed chemical synthesis of orfamide A derivatives and used an aequorin reporter line to measure their Ca2+ responses. Immobilization of algae was studied using a modulator and mutants of transient receptor potential (TRP)-type channels. By investigating targeted synthetic orfamide A derivatives, we found that N-terminal amino acids of the linear part and the terminal fatty acid region are important for the specificity of the Ca2+ -signal causing deflagellation. Molecular editing indicates that at least two distinct Ca2+ -signaling pathways are triggered. One is involved in deflagellation (Thr3 change, fatty acid tail shortened by 4C), whereas the other still causes an increase in cytosolic Ca2+ in the algal cells, but does not cause substantial deflagellation (Leu1 change, fatty acid hydroxylation, fatty acid changes by 2C). Using mutants, we define four TRP-type channels that are involved in orfamide A signaling; only one (ADF1) responds additionally to low pH. These results suggest that the linear part of the CLiP plays one major role in Ca2+ signaling, and that orfamide A uses a network of algal TRP-type channels for deflagellation.
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Affiliation(s)
- Yu Hou
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Yuko Bando
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - David Carrasco Flores
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Vivien Hotter
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Ritam Das
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Bastian Schiweck
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Tommy Melzer
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Hans-Dieter Arndt
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743, Jena, Germany
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24
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Pigment Production of Chlamydomonas Strains in Response to Norflurazon and ZnO Nanoparticles. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Numerous species of microalgae have been utilized for pigment production. More and more species are gaining popularity due to their ability to accumulate pigments with varying chemical compositions and the fact that some have distinctive byproducts that can be co-produced. Despite the fact that many of the species have unique by-products and traits, they are not being used economically due to high production costs. Utilizing agricultural and industrial wastewater for algae cultivation is one way to lower manufacturing costs. Herbicide-contaminated wastewater can result from agricultural contamination. Norflurazon is a popular pesticide frequently used for weed control. The presence of norflurazon in water renders that water unusable and requires proper treatment. Nanoparticles of ZnO (ZnO NPs), on the other hand, are utilized in a variety of industrial productions of numerous household goods. Water contaminated with ZnO NPs can present potential risks to human health and the environment. In this study, two field isolates of the green microalga Chlamydomonas reinhardtii, a widely used model organism, were examined for their reaction to these two compounds in order to assess the responses of different natural strains to environmental stresses. Norflurazon at 10 µM had a higher inhibitory effect on growth and pigment production than ZnO NPs at 200 mg L−1. Although both norflurazon and ZnO NPs inhibit cell growth and pigmentation, they do so through distinct processes. Norflurazon induces oxidative stress in cells, resulting in photosystem damage. ZnO nanoparticles, on the other hand, did not cause photosystem damage but rather mechanical cell damage and disintegration. In addition, the physiological responses of the two Chlamydomonas strains were distinct, supporting the utilization of natural algal strains for specific types of environmental pollutants.
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25
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Calatrava V, Tejada-Jimenez M, Sanz-Luque E, Fernandez E, Galvan A, Llamas A. Chlamydomonas reinhardtii, a Reference Organism to Study Algal-Microbial Interactions: Why Can't They Be Friends? PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040788. [PMID: 36840135 PMCID: PMC9965935 DOI: 10.3390/plants12040788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 05/13/2023]
Abstract
The stability and harmony of ecological niches rely on intricate interactions between their members. During evolution, organisms have developed the ability to thrive in different environments, taking advantage of each other. Among these organisms, microalgae are a highly diverse and widely distributed group of major primary producers whose interactions with other organisms play essential roles in their habitats. Understanding the basis of these interactions is crucial to control and exploit these communities for ecological and biotechnological applications. The green microalga Chlamydomonas reinhardtii, a well-established model, is emerging as a model organism for studying a wide variety of microbial interactions with ecological and economic significance. In this review, we unite and discuss current knowledge that points to C. reinhardtii as a model organism for studying microbial interactions.
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Affiliation(s)
- Victoria Calatrava
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama St., Stanford, CA 94305, USA
| | - Manuel Tejada-Jimenez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Emanuel Sanz-Luque
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Emilio Fernandez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Aurora Galvan
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
- Correspondence: ; Tel.: +34-957-218352
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26
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Bafort Q, Prost L, Aydogdu E, Van de Vloet A, Casteleyn G, Van de Peer Y, De Clerck O. Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas. Methods Mol Biol 2023; 2545:351-372. [PMID: 36720822 DOI: 10.1007/978-1-0716-2561-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo- and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.
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Affiliation(s)
- Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Lucas Prost
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Eylem Aydogdu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Antoine Van de Vloet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Griet Casteleyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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27
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Ford SA, Craig RJ, Ness RW. A novel method for identifying Chlamydomonas reinhardtii (Chlorophyta) and closely related species from nature. JOURNAL OF PHYCOLOGY 2023; 59:281-288. [PMID: 36453860 DOI: 10.1111/jpy.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Here, we introduce a new method for efficiently sampling Chlamydomonas reinhardtii and closely related species using a colony PCR-based screen with novel primer sets designed to specifically detect these important model microalgae. To demonstrate the utility of our new method, we collected 130 soil samples from a wide range of habitats in Ontario, Canada and identified 33 candidate algae, which were barcoded by sequencing a region of the rbcL plastid gene. For select isolates, 18S rRNA gene and YPT4 nuclear markers were also sequenced. Based on phylogenetic and haplotype network analyses of these three loci, seven novel isolates were identified as C. reinhardtii, and one additional isolate appeared to be more closely related to C. reinhardtii than any other known species. All seven new C. reinhardtii strains were interfertile with previously collected C. reinhardtii field isolates, validating the effectiveness of our molecular screen.
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Affiliation(s)
- Scott A Ford
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada
| | - Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California, 94720-3220, USA
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
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28
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Yamada R, Yokota M, Matsumoto T, Hankamer B, Ogino H. Promoting cell growth and characterizing partial symbiotic relationships in the co-cultivation of green alga Chlamydomonas reinhardtii and Escherichia coli. Biotechnol J 2023; 18:e2200099. [PMID: 36479591 DOI: 10.1002/biot.202200099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND By co-culturing selected microalgae and heterotrophic microorganisms, the growth rate of microalgae can be improved even under atmospheric conditions with a low CO2 concentration. However, the detailed mechanism of improvement of proliferative capacity by co-culture has not been elucidated. In this study, we investigated changes in the proliferative capacity of the green alga Chlamydomonas reinhardtii by co-culturing with Escherichia coli. MAIN METHODS AND MAJOR RESULTS In the co-culture, the number of C. reinhardtii cells reached 2.22 × 1010 cell/L on day 14 of culture. This was about 1.9 times the number of cells (1.16 × 1010 cell/L) on day 14 compared to C. reinhardtii cells in monoculture. The starch content per cell in the co-culture of C. reinhardtii and E. coli on the 14th day (2.09 × 10-11 g/cell) was 1.3 times higher than that in the C. reinhardtii monoculture (1.59 × 10-11 g/cell), and the starch content per culture medium improved 2.5 times with co-cultivation. By analyzing the gene transcription profiles and key media components, we clarified that E. coli produced CO2 from the organic carbon in the medium and the organic carbon produced by photosynthesis of C. reinhardtii, and this CO2 likely enhanced the growth of C. reinhardtii. CONCLUSIONS Consequently, E. coli plays a key role in promoting the growth of C. reinhardtii as well as the accumulation of starch which is a valuable intermediate for the production of a range of useful chemicals from CO2 .
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Affiliation(s)
- Ryosuke Yamada
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Moe Yokota
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
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29
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Masi A, Leonelli F, Scognamiglio V, Gasperuzzo G, Antonacci A, Terzidis MA. Chlamydomonas reinhardtii: A Factory of Nutraceutical and Food Supplements for Human Health. Molecules 2023; 28:molecules28031185. [PMID: 36770853 PMCID: PMC9921279 DOI: 10.3390/molecules28031185] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Chlamydomonas reinhardtii (C. reinhardtii) is one of the most well-studied microalgae organisms that revealed important information for the photosynthetic and metabolic processes of plants and eukaryotes. Numerous extensive studies have also underpinned its great potential as a biochemical factory, capable of producing various highly desired molecules with a direct impact on human health and longevity. Polysaccharides, lipids, functional proteins, pigments, hormones, vaccines, and antibodies are among the valuable biomolecules that are produced spontaneously or under well-defined conditions by C. reinhardtii and can be directly linked to human nutrition and diet. The aim of this review is to highlight the recent advances in the field focusing on the most relevant applications related to the production of important biomolecules for human health that are also linked with human nutrition and diet. The limitations and challenges are critically discussed along with the potential future applications of C. reinhardtii biomass and processed products in the field of nutraceuticals and food supplements. The increasing need for high-value and low-cost biomolecules produced in an environmentally and economy sustainable manner also underline the important role of C. reinhardtii.
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Affiliation(s)
- Annalisa Masi
- Institute of Crystallography, National Research Council, 00010 Montelibretti, Italy
| | - Francesca Leonelli
- Department of Chemistry, University of Rome “Sapienza”, 00185 Rome, Italy
| | - Viviana Scognamiglio
- Institute of Crystallography, National Research Council, 00010 Montelibretti, Italy
| | - Giulia Gasperuzzo
- Institute of Crystallography, National Research Council, 00010 Montelibretti, Italy
| | - Amina Antonacci
- Institute of Crystallography, National Research Council, 00010 Montelibretti, Italy
- Correspondence: (A.A.); (M.A.T.); Tel.: +39-0690675597 (A.A.); +30-2310013224 (M.A.T.)
| | - Michael A. Terzidis
- Department of Nutritional Sciences and Dietetics, International Hellenic University, Sindos Campus, 57400 Thessaloniki, Greece
- Correspondence: (A.A.); (M.A.T.); Tel.: +39-0690675597 (A.A.); +30-2310013224 (M.A.T.)
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30
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Salarvan F, Meydan H, Aksoy M. Transcription level and phylogeny analyses of Chlamydomonas reinhardtii arylsulfatases. J Eukaryot Microbiol 2023; 70:e12943. [PMID: 36018447 DOI: 10.1111/jeu.12943] [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: 07/22/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 01/13/2023]
Abstract
Sulfur is a required macroelement for all organisms, and sulfate deficiency causes growth and developmental defects. Arylsulfatases (ARS) hydrolyze sulfate from sulfate esters and make sulfate bioavailable for plant uptake. These enzymes are found in microorganisms and animals; however, plant genomes do not encode any ARS gene. Our database searches found nineteen ARS genes in the genome of Chlamydomonas reinhardtii. Among these, ARS1 and ARS2 were studied in the literature; however, the remaining seventeen gene models were not studied. Our results show that putative polypeptide sequences of the ARS gene models all have the sulfatase domain and sulfatase motifs found in known ARSs. Phylogenetic analyses show that C. reinhardtii proteins are in close branches with Volvox carterii proteins while they were clustered in a separate group from Homo sapiens and bacterial species (Pseudomonas aeruginosa and Rhodopirellula baltica SH1), except human Sulf1, Sulf2, and GNS are clustered with algal ARSs. RT-PCR analyses showed that transcription of ARS6, ARS7, ARS11, ARS12, ARS13, ARS17, and ARS19 increased under sulfate deficiency. However, this increase was not as high as the increase seen in ARS2. Since plant genomes do not encode any ARS gene, our results highlight the importance of microbial ARS genes.
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Affiliation(s)
- Fatma Salarvan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Hasan Meydan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Münevver Aksoy
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
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31
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Production of Recombinant Biopharmaceuticals in Chlamydomonas reinhardtii. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb14010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
This review aimed to present Chlamydomonas reinhardtii as an alternative for heterologous protein production, especially for biopharmaceuticals, and its general characteristics when compared with other expression systems. The need to produce heterologous proteins for industrial interest, therapeutic ends, and diagnostic kits has led to the development of recombinant microalgal technology. This technology presents some interesting features, such as rapid growth and low transgene dispersion compared to plants, the ability to fold complex proteins compared to bacteria, and low production costs compared to other expression systems, such as yeast and mammalian cells. Overall, C. reinhardtii heterologous protein expression is coming of age with several research groups focused on developing an optimal producer strain.
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32
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Jebali A, Sanchez MR, Hanschen ER, Starkenburg SR, Corcoran AA. Trait drift in microalgae and applications for strain improvement. Biotechnol Adv 2022; 60:108034. [PMID: 36089253 DOI: 10.1016/j.biotechadv.2022.108034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/06/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Microalgae are increasingly used to generate a wide range of commercial products, and there is growing evidence that microalgae-based products can be produced sustainably. However, industrial production of microalgal biomass is not as developed as other biomanufacturing platform technologies. In addition, results of bench-scale research often fail to translate to large-scale or mass production systems. This disconnect may result from trait drift and evolution occurring, through time, in response to unique drivers in each environment, such as cultivation regimes, weather, and pests. Moreover, outdoor and indoor cultivation of microalgae has the potential to impose negative selection pressures, which makes the maintenance of desired traits a challenge. In this context, this review sheds the light on our current understanding of trait drift and evolution in microalgae. We delineate the basics of phenotype plasticity and evolution, with a focus on how microalgae respond under various conditions. In addition, we review techniques that exploit phenotypic plasticity and evolution for strain improvement in view of industrial commercial applications, highlighting associated advantages and shortcomings. Finally, we suggest future research directions and recommendations to overcome unwanted trait drift and evolution in microalgae cultivation.
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Affiliation(s)
- Ahlem Jebali
- New Mexico Consortium, 4200 W. Jemez Road, Los Alamos, NM 87544, USA.
| | - Monica R Sanchez
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA
| | - Erik R Hanschen
- Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM 87545, USA
| | | | - Alina A Corcoran
- New Mexico Consortium, 4200 W. Jemez Road, Los Alamos, NM 87544, USA
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33
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Moniruzzaman M, Erazo-Garcia MP, Aylward FO. Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii. Virus Evol 2022; 8:veac102. [PMID: 36447475 PMCID: PMC9693826 DOI: 10.1093/ve/veac102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/05/2022] [Accepted: 10/20/2022] [Indexed: 11/14/2023] Open
Abstract
Chlamydomonas reinhardtii is a unicellular eukaryotic alga that has been studied as a model organism for decades. Despite an extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of C. reinhardtii field isolates, and in six we discovered sequences belonging to endogenous giant viruses that reach up to several 100 kb in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta, the closest sequenced relative of C. reinhardtii. Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and interstrain genomic variability of C. reinhardtii. Our findings suggest that the endogenization of giant viruses may have important implications for structuring the population dynamics and ecology of protists in the environment.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Maria P Erazo-Garcia
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, 981 Kraft Dr, Room 2036, Blacksburg, VA 24060, USA
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34
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Petersen J, Rredhi A, Szyttenholm J, Mittag M. Evolution of circadian clocks along the green lineage. PLANT PHYSIOLOGY 2022; 190:924-937. [PMID: 35325228 PMCID: PMC9516769 DOI: 10.1093/plphys/kiac141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/04/2022] [Indexed: 05/10/2023]
Abstract
Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
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35
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Schuman IJ, Meier HS, Layden TJ, Fey SB. The relationship between thermal spatial variability and mean temperature alters movement and population dynamics. Ecosphere 2022. [DOI: 10.1002/ecs2.4254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | | | | | - Samuel B. Fey
- Department of Biology Reed College Portland Oregon USA
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36
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Nitrous Oxide Emissions from Nitrite Are Highly Dependent on Nitrate Reductase in the Microalga Chlamydomonas reinhardtii. Int J Mol Sci 2022; 23:ijms23169412. [PMID: 36012676 PMCID: PMC9409008 DOI: 10.3390/ijms23169412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 12/11/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and an ozone-depleting compound whose synthesis and release have traditionally been ascribed to bacteria and fungi. Although plants and microalgae have been proposed as N2O producers in recent decades, the proteins involved in this process have been only recently unveiled. In the green microalga Chlamydomonas reinhardtii, flavodiiron proteins (FLVs) and cytochrome P450 (CYP55) are two nitric oxide (NO) reductases responsible for N2O synthesis in the chloroplast and mitochondria, respectively. However, the molecular mechanisms feeding these NO reductases are unknown. In this work, we use cavity ring-down spectroscopy to monitor N2O and CO2 in cultures of nitrite reductase mutants, which cannot grow on nitrate or nitrite and exhibit enhanced N2O emissions. We show that these mutants constitute a very useful tool to study the rates and kinetics of N2O release under different conditions and the metabolism of this greenhouse gas. Our results indicate that N2O production, which was higher in the light than in the dark, requires nitrate reductase as the major provider of NO as substrate. Finally, we show that the presence of nitrate reductase impacts CO2 emissions in both light and dark conditions, and we discuss the role of NO in the balance between CO2 fixation and release.
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37
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Hwang OJ, Back K. Functional Characterization of Arylalkylamine N-Acetyltransferase, a Pivotal Gene in Antioxidant Melatonin Biosynthesis from Chlamydomonas reinhardtii. Antioxidants (Basel) 2022; 11:antiox11081531. [PMID: 36009250 PMCID: PMC9405056 DOI: 10.3390/antiox11081531] [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: 07/13/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022] Open
Abstract
Arylalkylamine N-acetyltransferase (AANAT) is a pivotal enzyme in melatonin biosynthesis that catalyzes the conversion of serotonin to N-acetylserotonin. Homologs of animal AANAT genes are present in animals, but not in plants. An AANAT homolog was found in Chlamydomonas reinhardtii, but not other green algae. The characteristics of C. reinhardtii AANAT (CrAANAT) are unclear. Here, full-length CrAANAT was chemically synthesized and expressed in Escherichia coli. Recombinant CrAANAT exhibited AANAT activity with a Km of 247 μM and Vmax of 325 pmol/min/mg protein with serotonin as the substrate. CrAANAT was localized to the cytoplasm in tobacco leaf cells. Transgenic rice plants overexpressing CrAANAT (CrAANAT-OE) exhibited increased melatonin production. CrAANAT-OE plants showed a longer seed length and larger second leaf angle than wild-type plants, indicative of the involvement of brassinosteroids (BRs). As expected, BR biosynthesis- and signaling-related genes such as D2, DWARF4, DWARF11, and BZR1 were upregulated in CrAANAT-OE plants. Therefore, an increased endogenous melatonin level by ectopic overexpression of CrAANAT seems to be closely associated with BR biosynthesis, thereby influencing seed size.
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Regulated processing and secretion of a peptide precursor in cilia. Proc Natl Acad Sci U S A 2022; 119:e2206098119. [PMID: 35878031 PMCID: PMC9351486 DOI: 10.1073/pnas.2206098119] [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] [Indexed: 01/27/2023] Open
Abstract
Cilia are sensory and secretory organelles that both receive information from the environment and transmit signals. Cilia-derived vesicles (ectosomes), formed by outward budding of the ciliary membrane, carry enzymes and other bioactive products; this process represents an ancient mode of regulated secretion. Peptidergic intercellular communication controls a wide range of physiological and behavioral responses and occurs throughout eukaryotes. The Chlamydomonas reinhardtii genome encodes what appear to be numerous prepropeptides and enzymes homologous to those used to convert metazoan prepropeptides into bioactive peptide products. Since C. reinhardtii, a green alga, lack the dense core vesicles in which metazoan peptides are processed and stored, we explored the hypothesis that propeptide processing and secretion occur through the regulated release of ciliary ectosomes. A synthetic peptide (GATI-amide) that could be generated from a 91-kDa peptide precursor (proGATI) serves as a chemotactic modulator, attracting minus gametes while repelling plus gametes. Here we dissect the processing pathway that leads to formation of an amidated peptidergic sexual signal specifically on the ciliary ectosomes of plus gametes. Unlike metazoan propeptides, modeling studies identified stable domains in proGATI. Mass spectrometric analysis of a potential prohormone convertase and the amidated proGATI-derived products found in cilia and mating ectosomes link endoproteolytic cleavage to ectosome entry. Extensive posttranslational modification of proGATI confers stability to its amidated product. Analysis of this pathway affords insight into the evolution of peptidergic signaling; this will facilitate studies of the secretory functions of metazoan cilia.
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Saha M, Fink P. Algal volatiles - the overlooked chemical language of aquatic primary producers. Biol Rev Camb Philos Soc 2022; 97:2162-2173. [PMID: 35912802 DOI: 10.1111/brv.12887] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Abstract
Volatiles are important 'infochemicals' that play a crucial role in structuring life on our planet, fulfilling diverse functions in natural and artificial systems. Algae contribute significant quantities to the global budget of volatiles, but the ecological roles of aquatic volatiles are not well understood. In this review, we discuss the current knowledge of volatile compounds from freshwater and marine microalgae and marine macroalgae, with a focus on their ecological roles. We highlight the multiple reported functions of biogenic volatiles, ranging from intraspecific communication for reproduction, intra-bloom signalling and antioxidant functions, to various interspecific signal exchanges that may allow herbivores to locate them and function in defence against competitors and predators. Beyond reviewing our current understanding, we specifically highlight major knowledge gaps and emerging questions for algal volatile research. These novel perspectives have the potential to improve our understanding of aquatic ecosystems and thus need to be addressed in future research. Filling these gaps and addressing these questions will facilitate humanity's efforts to exploit aquatic volatiles in various applications.
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Affiliation(s)
- Mahasweta Saha
- Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Patrick Fink
- Department River Ecology, Helmholtz Centre of Environmental Research - UFZ, Brückstrasse 3a, 39114, Magdeburg, Germany.,Department Aquatic Ecosystem Analysis and Management, Helmholtz Centre of Environmental Research - UFZ, Brückstrasse 3a, 39114, Magdeburg, Germany
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Bunbury F, Deery E, Sayer AP, Bhardwaj V, Harrison EL, Warren MJ, Smith AG. Exploring the onset of B 12 -based mutualisms using a recently evolved Chlamydomonas auxotroph and B 12 -producing bacteria. Environ Microbiol 2022; 24:3134-3147. [PMID: 35593514 PMCID: PMC9545926 DOI: 10.1111/1462-2920.16035] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 12/01/2022]
Abstract
Cobalamin (vitamin B12 ) is a cofactor for essential metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonize the algal phycosphere, forming stable communities that gain preferential access to photosynthate and in return provide compounds such as B12 . Extended coexistence can then drive gene loss, leading to greater algal-bacterial interdependence. In this study, we investigate how a recently evolved B12 -dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B12 producers, its growth in co-culture was slower than the B12 -independent wild-type, suggesting that high bacterial B12 provision may be necessary to favour B12 auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B12 makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B12 release provided an advantage in co-cultures. We hypothesize that, given the right conditions, bacteria that release more B12 may be selected for, particularly if they form close interactions with B12 -dependent algae.
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Affiliation(s)
- Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Andrew P Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Vaibhav Bhardwaj
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ellen L Harrison
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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Algicidal Effects of Green Synthesized Silver Nanoparticles using Tinospora cordifolia on Chlamydomonas reinhardtii. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eco-friendly anti-algal agents are in demand for preventing the growth of unwanted algae. Green synthesized nanoparticles exhibit antimicrobial properties and have been used as a better alternative against chemical and physical processes. In the present study, treatment of silver nitrate with leaf extracts (5% w/v) of Tinospora cordifolia, a plant with proven antimicrobial effects, exhibited UV-visible absorption maxima between 440-460 nm after 1h indicating bioreduction of silver to nanoparticles. The green synthesised silver nanoparticles (5 mgl-1) exhibited inhibition zones against Chlamydomonas reinhardtii in in vitro agar assays. Treatment with green synthesised silver nanoparticles during exponential phase of algal growth resulted in significant reduction in algal population, carbohydrate, protein and chlorophyll contents confirming the anti-algal potential. This is the first report on the growth inhibitory potential of green synthesised silver nanoparticles against green algae.
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Melero-Jiménez IJ, Bañares-España E, García-Sánchez MJ, Flores-Moya A. Changes in the growth rate of Chlamydomonas reinhardtii under long-term selection by temperature and salinity: Acclimation vs. evolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153467. [PMID: 35093356 DOI: 10.1016/j.scitotenv.2022.153467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
We investigated the roles of acclimation and different components involved in evolution (adaptation, chance and history) on the changes in the growth rate of the model freshwater microalga Chlamydomonas reinhardtii P. A. Dang. exposed to selective temperature and salinity. Three C. reinhardtii strains previously grown during one year in freshwater medium and 20 °C were exposed to 5 °C temperature increase and a salinity of 5 g L-1 NaCl. Cultures under each selective scenario and in combination (increase of salinity and temperature), were propagated until growth rate achieved an invariant mean value for 6 months (100-350 generations, varying as a function of scenario and strain). The changes of the growth rate under increased temperature were due to both adaptation and acclimation, as well as history. However, acclimation was the only mechanism detected under salinity increase as well as in the selective scenario of both temperature and salinity, suggesting that genetic variability would not allow survival at salinity higher than that to which experimental populations were exposed. Therefore, it could be hypothesized that under a global change scenario an increase in salinity would be a greater challenge than warming for some freshwater phytoplankton.
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Affiliation(s)
- Ignacio J Melero-Jiménez
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain.
| | - Elena Bañares-España
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - María J García-Sánchez
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Antonio Flores-Moya
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
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Saint-Sorny M, Brzezowski P, Arrivault S, Alric J, Johnson X. Interactions Between Carbon Metabolism and Photosynthetic Electron Transport in a Chlamydomonas reinhardtii Mutant Without CO 2 Fixation by RuBisCO. FRONTIERS IN PLANT SCIENCE 2022; 13:876439. [PMID: 35574084 PMCID: PMC9096841 DOI: 10.3389/fpls.2022.876439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
A Chlamydomonas reinhardtii RuBisCO-less mutant, ΔrbcL, was used to study carbohydrate metabolism without fixation of atmospheric carbon. The regulatory mechanism(s) that control linear electron flow, known as "photosynthetic control," are amplified in ΔrbcL at the onset of illumination. With the aim to understand the metabolites that control this regulatory response, we have correlated the kinetics of primary carbon metabolites to chlorophyll fluorescence induction curves. We identify that ΔrbcL in the absence of acetate generates adenosine triphosphate (ATP) via photosynthetic electron transfer reactions. Also, metabolites of the Calvin Benson Bassham (CBB) cycle are responsive to the light. Indeed, ribulose 1,5-bisphosphate (RuBP), the last intermediate before carboxylation by Ribulose-1,5-bisphosphate carboxylase-oxygenase, accumulates significantly with time, and CBB cycle intermediates for RuBP regeneration, dihydroxyacetone phosphate (DHAP), pentose phosphates and ribose-5-phosphate (R5P) are rapidly accumulated in the first seconds of illumination, then consumed, showing that although the CBB is blocked, these enzymes are still transiently active. In opposition, in the presence of acetate, consumption of CBB cycle intermediates is strongly diminished, suggesting that the link between light and primary carbon metabolism is almost lost. Phosphorylated hexoses and starch accumulate significantly. We show that acetate uptake results in heterotrophic metabolism dominating phototrophic metabolism, with glyoxylate and tricarboxylic acid (TCA) cycle intermediates being the most highly represented metabolites, specifically succinate and malate. These findings allow us to hypothesize which metabolites and metabolic pathways are relevant to the upregulation of processes like cyclic electron flow that are implicated in photosynthetic control mechanisms.
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Affiliation(s)
- Maureen Saint-Sorny
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Pawel Brzezowski
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | | | - Jean Alric
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Xenie Johnson
- CEA, CNRS, UMR 7265, BIAM, CEA Cadarache, Aix-Marseille Université, Saint-Paul-lez-Durance, France
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Sakato-Antoku M, King SM. Developmental Changes in Ciliary Composition during Gametogenesis in Chlamydomonas. Mol Biol Cell 2022; 33:br10. [PMID: 35389765 PMCID: PMC9561859 DOI: 10.1091/mbc.e22-02-0033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chlamydomonas reinhardtii transitions from mitotically dividing vegetative cells to sexually competent gametes of two distinct mating types following nutrient deprivation. Gametes of opposite mating type interact via their cilia, initiating an intraciliary signaling cascade and ultimately fuse forming diploid zygotes. The process of gametogenesis is genetically encode, and a previous study revealed numerous significant changes in mRNA abundance during this life-cycle transition. Here we describe a proteomic analysis of cilia derived from vegetative and gametic cells of both mating types in an effort to assess the global changes that occur within the organelle during this process. We identify numerous membrane- and/or matrix-associated proteins in gametic cilia that were not detected in cilia from vegetative cells. This includes the pro-protein from which the GATI-amide gametic chemotactic modulator derives, as well as receptors, a dynamin-related protein, ammonium transporters, two proteins potentially involved in the intraciliary signaling cascade-driven increase in cAMP, and multiple proteins with a variety of interaction domains. These changes in ciliary composition likely directly affect the functional properties of this organelle as the cell transitions between life-cycle stages.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
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King SJ, Jerkovic A, Brown LJ, Petroll K, Willows RD. Synthetic biology for improved hydrogen production in Chlamydomonas reinhardtii. Microb Biotechnol 2022; 15:1946-1965. [PMID: 35338590 PMCID: PMC9249334 DOI: 10.1111/1751-7915.14024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
Hydrogen is a clean alternative to fossil fuels. It has applications for electricity generation and transportation and is used for the manufacturing of ammonia and steel. However, today, H2 is almost exclusively produced from coal and natural gas. As such, methods to produce H2 that do not use fossil fuels need to be developed and adopted. The biological manufacturing of H2 may be one promising solution as this process is clean and renewable. Hydrogen is produced biologically via enzymes called hydrogenases. There are three classes of hydrogenases namely [FeFe], [NiFe] and [Fe] hydrogenases. The [FeFe] hydrogenase HydA1 from the model unicellular algae Chlamydomonas reinhardtii has been studied extensively and belongs to the A1 subclass of [FeFe] hydrogenases that have the highest turnover frequencies amongst hydrogenases (21,000 ± 12,000 H2 s−1 for CaHydA from Clostridium acetobutyliticum). Yet to date, limitations in C. reinhardtii H2 production pathways have hampered commercial scale implementation, in part due to O2 sensitivity of hydrogenases and competing metabolic pathways, resulting in low H2 production efficiency. Here, we describe key processes in the biogenesis of HydA1 and H2 production pathways in C. reinhardtii. We also summarize recent advancements of algal H2 production using synthetic biology and describe valuable tools such as high‐throughput screening (HTS) assays to accelerate the process of engineering algae for commercial biological H2 production.
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Affiliation(s)
- Samuel J King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ante Jerkovic
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Robert D Willows
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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van den Berg TE, Croce R. The Loroxanthin Cycle: A New Type of Xanthophyll Cycle in Green Algae (Chlorophyta). FRONTIERS IN PLANT SCIENCE 2022; 13:797294. [PMID: 35251077 PMCID: PMC8891138 DOI: 10.3389/fpls.2022.797294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Xanthophyll cycles (XC) have proven to be major contributors to photoacclimation for many organisms. This work describes a light-driven XC operating in the chlorophyte Chlamydomonas reinhardtii and involving the xanthophylls Lutein (L) and Loroxanthin (Lo). Pigments were quantified during a switch from high to low light (LL) and at different time points from cells grown in Day/Night cycle. Trimeric LHCII was purified from cells acclimated to high or LL and their pigment content and spectroscopic properties were characterized. The Lo/(L + Lo) ratio in the cells varies by a factor of 10 between cells grown in low or high light (HL) leading to a change in the Lo/(L + Lo) ratio in trimeric LHCII from .5 in low light to .07 in HL. Trimeric LhcbMs binding Loroxanthin have 5 ± 1% higher excitation energy (EE) transfer (EET) from carotenoid to Chlorophyll as well as higher thermo- and photostability than trimeric LhcbMs that only bind Lutein. The Loroxanthin cycle operates on long time scales (hours to days) and likely evolved as a shade adaptation. It has many similarities with the Lutein-epoxide - Lutein cycle (LLx) of plants.
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Radin I, Haswell ES. Looking at mechanobiology through an evolutionary lens. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102112. [PMID: 34628340 DOI: 10.1016/j.pbi.2021.102112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Mechanical forces were arguably among the first stimuli to be perceived by cells, and they continue to shape the evolution of all organisms. Great strides have been made in recent years in the field of plant cell and molecular mechanobiology, in part owing to focused efforts on key model systems. Here, we propose to enrich such work through evolutionary mechanobiology, or 'evo-mechano', and describe three major themes that could drive research in this area. We use plastid evo-mechano as a case study, describing how plastids from different lineages perceive their mechanical environments, how their mechanical properties vary across lineages, and their distinct roles in graviperception. Finally, we argue that future research into the biomechanical properties and mechanobiological signaling mechanisms that have been elaborated by green species over the past 1.5 billion years will help us understand both the universal and the unique adaptations of plants to their physical environment.
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Affiliation(s)
- Ivan Radin
- Department of Biology, MSC 1137-154-314, Washington University, 1 Brookings Drive, St. Louis, MO, 63130-489, United States; NSF Center for Engineering Mechanobiology, United States
| | - Elizabeth S Haswell
- Department of Biology, MSC 1137-154-314, Washington University, 1 Brookings Drive, St. Louis, MO, 63130-489, United States; NSF Center for Engineering Mechanobiology, United States.
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Microalgae-Based Fluorimetric Bioassays for Studying Interferences on Photosynthesis Induced by Environmentally Relevant Concentrations of the Herbicide Diuron. BIOSENSORS 2022; 12:bios12020067. [PMID: 35200329 PMCID: PMC8869104 DOI: 10.3390/bios12020067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 11/28/2022]
Abstract
The widespread agricultural use of the phenylurea herbicide Diuron (DCMU) requires the investigation of ecotoxicological risk in freshwater and soil ecosystems in light of potential effects on non-target primary producers and a heavier effect on higher trophic levels. We used microalgae-based fluorimetric bioassays for studying the interferences on the photosynthesis of a freshwater and soil model green microalga (Chlamydomonas reinhardtii) induced by environmentally relevant concentrations of the herbicide DCMU. Measurements of steady-state chlorophyll a (Chl-a) fluorescence emission spectra were performed; as well, the kinetics of the Chl-a fluorescence transient were recorded. Percentage indexes of interference on photosynthesis were calculated after comparison of steady-state and kinetic Chl-a fluorescence measurements of DCMU-exposed and control C. reinhardtii cell suspensions. The results obtained after 30 min exposure to the herbicide DCMU confirmed a significant inhibitory effect of DCMU 2 μg/L, and no significant differences between %ι values for DCMU 0.2 μg/L and 0.02 μg/L exposures. Positive %ε values from kinetic measurements of the Chl-a fluorescence transient confirmed the same interfering effect of 2 μg/L DCMU on PSII photochemistry in the exposed C. reinhardtii cell suspensions. Negative values of %ε observed for 0.2 and 0.02 μg/L DCMU exposures could be attributable to a presumptive ‘stimulatory-like’ effect in the photochemistry of photosynthesis. Short-term exposure to sub-μg/L DCMU concentration (≤0.2 μg/L) affects the photosynthetic process of the model microalga C. reinhardtii. Similar environmental exposures could affect natural communities of unicellular autotrophs, with hardly predictable cascading secondary effects on higher trophic levels.
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Durán P, Flores-Uribe J, Wippel K, Zhang P, Guan R, Melkonian B, Melkonian M, Garrido-Oter R. Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota. Nat Commun 2022; 13:406. [PMID: 35058457 PMCID: PMC8776852 DOI: 10.1038/s41467-022-28055-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Microscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Using synthetic communities derived from C. reinhardtii and Arabidopsis thaliana, we show that phycosphere and root bacteria assemble into taxonomically similar communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggest the existence of shared ecological principles driving the assembly of the A. thaliana root and C. reinhardtii phycosphere microbiota, despite the vast evolutionary distance between these two photosynthetic organisms.
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Affiliation(s)
- Paloma Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences, 40225, Düsseldorf, Germany
| | - José Flores-Uribe
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Kathrin Wippel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Rui Guan
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Barbara Melkonian
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Michael Melkonian
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, 40225, Düsseldorf, Germany.
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50
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Pinello JF, Clark TG. HAP2-Mediated Gamete Fusion: Lessons From the World of Unicellular Eukaryotes. Front Cell Dev Biol 2022; 9:807313. [PMID: 35071241 PMCID: PMC8777248 DOI: 10.3389/fcell.2021.807313] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 01/29/2023] Open
Abstract
Most, if not all the cellular requirements for fertilization and sexual reproduction arose early in evolution and are retained in extant lineages of single-celled organisms including a number of important model organism species. In recent years, work in two such species, the green alga, Chlamydomonas reinhardtii, and the free-living ciliate, Tetrahymena thermophila, have lent important new insights into the role of HAP2/GCS1 as a catalyst for gamete fusion in organisms ranging from protists to flowering plants and insects. Here we summarize the current state of knowledge around how mating types from these algal and ciliate systems recognize, adhere and fuse to one another, current gaps in our understanding of HAP2-mediated gamete fusion, and opportunities for applying what we know in practical terms, especially for the control of protozoan parasites.
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Affiliation(s)
- Jennifer F. Pinello
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Theodore G. Clark
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
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