1
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Strenkert D, Schmollinger S, Paruthiyil S, Brown BC, Green S, Shafer CM, Salomé P, Nelson H, Blaby-Haas CE, Moseley JL, Merchant SS. Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization. Metallomics 2024; 16:mfae013. [PMID: 38439674 PMCID: PMC10959442 DOI: 10.1093/mtomcs/mfae013] [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: 10/20/2023] [Accepted: 03/02/2024] [Indexed: 03/06/2024]
Abstract
Successful acclimation to copper (Cu) deficiency involves a fine balance between Cu import and export. In the green alga Chlamydomonas reinhardtii, Cu import is dependent on a transcription factor, Copper Response Regulator 1 (CRR1), responsible for activating genes in Cu-deficient cells. Among CRR1 target genes are two Cu transporters belonging to the CTR/COPT gene family (CTR1 and CTR2) and a related soluble protein (CTR3). The ancestor of these green algal proteins was likely acquired from an ancient chytrid and contained conserved cysteine-rich domains (named the CTR-associated domains, CTRA) that are predicted to be involved in Cu acquisition. We show by reverse genetics that Chlamydomonas CTR1 and CTR2 are canonical Cu importers albeit with distinct affinities, while loss of CTR3 did not result in an observable phenotype under the conditions tested. Mutation of CTR1, but not CTR2, recapitulates the poor growth of crr1 in Cu-deficient medium, consistent with a dominant role for CTR1 in high-affinity Cu(I) uptake. On the other hand, the overaccumulation of Cu(I) (20 times the quota) in zinc (Zn) deficiency depends on CRR1 and both CTR1 and CTR2. CRR1-dependent activation of CTR gene expression needed for Cu over-accumulation can be bypassed by the provision of excess Cu in the growth medium. Over-accumulated Cu is sequestered into the acidocalcisome but can become remobilized by restoring Zn nutrition. This mobilization is also CRR1-dependent, and requires activation of CTR2 expression, again distinguishing CTR2 from CTR1 and consistent with the lower substrate affinity of CTR2. ONE SENTENCE SUMMARY Regulation of Cu uptake and sequestration by members of the CTR family of proteins in Chlamydomonas.
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Affiliation(s)
- Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Srinand Paruthiyil
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Bonnie C Brown
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Sydnee Green
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Catherine M Shafer
- Molecular Toxicology Inter-departmental Ph.D. program, University of California, Los Angeles, CA 90095, USA
| | - Patrice Salomé
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Hosea Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Crysten E Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jeffrey L Moseley
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
- Department of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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2
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Zhang L, Braynen J, Fahey A, Chopra K, Cifani P, Tadesse D, Regulski M, Hu F, van Dam HJJ, Xie M, Ware D, Blaby-Haas CE. Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1237722. [PMID: 37965006 PMCID: PMC10642216 DOI: 10.3389/fpls.2023.1237722] [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: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of AtZNG1, AtMAP1A, AtMAP2A, and AtMAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Janeen Braynen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Audrey Fahey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, United States
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fangle Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Hubertus J. J. van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, United States
| | - Crysten E. Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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3
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Vogelauer M, Cheng C, Karimian A, Iranpour HG, Kurdistani SK. Zinc is Essential for the Copper Reductase Activity of Yeast Nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557765. [PMID: 37745536 PMCID: PMC10515886 DOI: 10.1101/2023.09.14.557765] [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] [Indexed: 09/26/2023]
Abstract
The histone H3-H4 tetramer is a copper reductase enzyme, facilitating the production of cuprous (Cu1+) ions for distribution to copper-dependent enzymes. It was, however, unknown if this enzymatic activity occurred within nucleosomes. To investigate this, we obtained native nucleosomes from Saccharomyces cerevisiae using micrococcal nuclease digestion of chromatin in isolated nuclei and ion-exchange chromatographic purification. The purified nucleosomal fragments robustly reduced Cu2+ to Cu1+ ions, with the optimal activity dependent on the presence of zinc ions. Mutation of the histone H3 histidine 113 (H3H113) residue at the active site substantially reduced the enzymatic activity of nucleosomes, underscoring the catalytic role of histone H3. Consistently, limiting zinc ions reduced intracellular Cu1+ levels and compromised growth, phenotypes that were mitigated by genetically enhancing the copper reductase activity of histone H3. These results indicate that yeast nucleosomes possess copper reductase activity, suggesting that the fundamental unit of eukaryotic chromatin is an enzyme complex.
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Affiliation(s)
- Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ansar Karimian
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Hooman Golshan Iranpour
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Siavash K. Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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4
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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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5
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Strenkert D, Schmollinger S, Hu Y, Hofmann C, Holbrook K, Liu HW, Purvine SO, Nicora CD, Chen S, Lipton MS, Northen TR, Clemens S, Merchant SS. Zn deficiency disrupts Cu and S homeostasis in Chlamydomonas resulting in over accumulation of Cu and Cysteine. Metallomics 2023; 15:mfad043. [PMID: 37422438 PMCID: PMC10357957 DOI: 10.1093/mtomcs/mfad043] [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: 04/12/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. We show that Chlamydomonas controls its Cu quota by balancing Cu import and export, which is disrupted in a Zn deficient cell, thus establishing a mechanistic connection between Cu and Zn homeostasis. Transcriptomics, proteomics and elemental profiling revealed that Zn-limited Chlamydomonas cells up-regulate a subset of genes encoding "first responder" proteins involved in sulfur (S) assimilation and consequently accumulate more intracellular S, which is incorporated into L-cysteine, γ-glutamylcysteine, and homocysteine. Most prominently, in the absence of Zn, free L-cysteine is increased ∼80-fold, corresponding to ∼2.8 × 109 molecules/cell. Interestingly, classic S-containing metal binding ligands like glutathione and phytochelatins do not increase. X-ray fluorescence microscopy showed foci of S accumulation in Zn-limited cells that co-localize with Cu, phosphorus and calcium, consistent with Cu-thiol complexes in the acidocalcisome, the site of Cu(I) accumulation. Notably, cells that have been previously starved for Cu do not accumulate S or Cys, causally connecting cysteine synthesis with Cu accumulation. We suggest that cysteine is an in vivo Cu(I) ligand, perhaps ancestral, that buffers cytosolic Cu.
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Affiliation(s)
- Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Stefan Schmollinger
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yuntao Hu
- Environmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryBerkeley CAUSA
| | | | - Kristen Holbrook
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Helen W Liu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, US Department of Energy, Richland, WA 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, US Department of Energy, Richland, WA 99352, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, US Department of Energy, Richland, WA 99352, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryBerkeley CAUSA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley CAUSA
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Germany
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National LaboratoryBerkeley CAUSA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
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6
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Schmollinger S, Chen S, Merchant SS. Quantitative elemental imaging in eukaryotic algae. Metallomics 2023; 15:mfad025. [PMID: 37186252 PMCID: PMC10209819 DOI: 10.1093/mtomcs/mfad025] [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: 08/30/2022] [Accepted: 03/03/2023] [Indexed: 05/17/2023]
Abstract
All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.
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Affiliation(s)
- Stefan Schmollinger
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Si Chen
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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7
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Strenkert D, Schmollinger S, Hu Y, Hofmann C, Holbrook K, Liu HW, Purvine SO, Nicora CD, Chen S, Lipton MS, Northen TR, Clemens S, Merchant SS. Cysteine: an ancestral Cu binding ligand in green algae? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532757. [PMID: 36993560 PMCID: PMC10055113 DOI: 10.1101/2023.03.15.532757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. We show that Chlamydomonas controls its Cu quota by balancing Cu import and export, which is disrupted in a Zn deficient cell, thus establishing a mechanistic connection between Cu and Zn homeostasis. Transcriptomics, proteomics and elemental profiling revealed that Zn-limited Chlamydomonas cells up-regulate a subset of genes encoding "first responder" proteins involved in sulfur (S) assimilation and consequently accumulate more intracellular S, which is incorporated into L-cysteine, γ-glutamylcysteine and homocysteine. Most prominently, in the absence of Zn, free L-cysteine is increased ~80-fold, corresponding to ~ 2.8 × 10 9 molecules/cell. Interestingly, classic S-containing metal binding ligands like glutathione and phytochelatins do not increase. X-ray fluorescence microscopy showed foci of S accumulation in Zn-limited cells that co-localize with Cu, phosphorus and calcium, consistent with Cu-thiol complexes in the acidocalcisome, the site of Cu(I) accumulation. Notably, cells that have been previously starved for Cu do not accumulate S or Cys, causally connecting cysteine synthesis with Cu accumulation. We suggest that cysteine is an in vivo Cu(I) ligand, perhaps ancestral, that buffers cytosolic Cu.
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8
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Hui C, Schmollinger S, Strenkert D, Holbrook K, Montgomery HR, Chen S, Nelson HM, Weber PK, Merchant SS. Simple steps to enable reproducibility: culture conditions affecting Chlamydomonas growth and elemental composition. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:995-1014. [PMID: 35699388 DOI: 10.1111/tpj.15867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 05/26/2023]
Abstract
Even subtle modifications in growth conditions elicit acclimation responses affecting the molecular and elemental makeup of organisms, both in the laboratory and in natural habitats. We systematically explored the effect of temperature, pH, nutrient availability, culture density, and access to CO2 and O2 in laboratory-grown algal cultures on growth rate, the ionome, and the ability to accumulate Fe. We found algal cells accumulate Fe in alkaline conditions, even more so when excess Fe is present, coinciding with a reduced growth rate. Using a combination of Fe-specific dyes, X-ray fluorescence microscopy, and NanoSIMS, we show that the alkaline-accumulated Fe was intracellularly sequestered into acidocalcisomes, which are localized towards the periphery of the cells. At high photon flux densities, Zn and Ca specifically over-accumulate, while Zn alone accumulates at low temperatures. The impact of aeration was probed by reducing shaking speeds and changing vessel fill levels; the former increased the Cu quota of cultures, the latter resulted in a reduction in P, Ca, and Mn at low fill levels. Trace element quotas were also affected in the stationary phase, where specifically Fe, Cu, and Zn accumulate. Cu accumulation here depends inversely on the Fe concentration of the medium. Individual laboratory strains accumulate Ca, P, and Cu to different levels. All together, we identified a set of specific changes to growth rate, elemental composition, and the capacity to store Fe in response to subtle differences in culturing conditions of Chlamydomonas, affecting experimental reproducibility. Accordingly, we recommend that these variables be recorded and reported as associated metadata.
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Affiliation(s)
- Colleen Hui
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
| | - Kristen Holbrook
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Hosea M Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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9
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Kochoni E, Doose C, Gonzalez P, Fortin C. Role of iron in gene expression and in the modulation of copper uptake in a freshwater alga: Insights on Cu and Fe assimilation pathways. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119311. [PMID: 35439593 DOI: 10.1016/j.envpol.2022.119311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/21/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Metal uptake and toxicity can generally be related to its aqueous speciation and to the presence of competitive ions as described by the biotic ligand model. Beyond these simple chemical interactions at the surface of aquatic organisms, several internal biological feedback mechanisms can also modulate metal uptake. This is particularly important for essential elements for which specific transport systems were developed over the course of evolution. Based on the results of short-term Cu2+ uptake experiments and on the analysis of the expression of certain genes involved in Cu and Fe homeostasis, we studied the effects of Fe3+ on Cu2+ uptake by the freshwater green alga Chlamydomonas reinhardtii. We observed a significant increase in Cu2+ uptake rate in algal cells acclimated to a low Fe3+ medium up to 4.7 times greater compared to non-acclimated algal cells. The overexpression of the ferroxidase FOX1 and permease FTR1 genes suggests an activation of the high affinity Fe3+ assimilation system, which could constitute a plausible explanation for the increase in Cu2+ uptake rate in acclimatized algae. We show that Fe availability can have a significant impact on Cu uptake. Our observations reinforce the importance of considering physiological factors to better predict metal bioavailability.
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Affiliation(s)
- Emeric Kochoni
- EcotoQ, Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC, G1K 9A9, Canada
| | - Caroline Doose
- Laboratoire de Biologie des Organismes et des écosystèmes Aquatiques, Muséum National d'Histoire Naturelle, Station Marine Concarneau, 29900, Concarneau, France
| | - Patrice Gonzalez
- Université de Bordeaux, CNRS, EPOC, EPHE, UMR 5805, 33600, Pessac, France
| | - Claude Fortin
- EcotoQ, Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC, G1K 9A9, Canada.
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10
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Pasquini M, Grosjean N, Hixson KK, Nicora CD, Yee EF, Lipton M, Blaby IK, Haley JD, Blaby-Haas CE. Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase. Cell Rep 2022; 39:110834. [PMID: 35584675 DOI: 10.1016/j.celrep.2022.110834] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/28/2022] [Accepted: 04/27/2022] [Indexed: 12/12/2022] Open
Abstract
The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. In vitro, Zng1p can transfer Zn2+ or Co2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon because of loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.
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Affiliation(s)
- Miriam Pasquini
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kim K Hixson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mary Lipton
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ian K Blaby
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - John D Haley
- Department of Pathology and Biological Mass Spectrometry Facility, Stony Brook University, Stony Brook, NY 11794, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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11
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Pham KLJ, Schmollinger S, Merchant SS, Strenkert D. Chlamydomonas ATX1 is essential for Cu distribution to multiple cupro-enzymes and maintenance of biomass in conditions demanding cupro-enzyme-dependent metabolic pathways. PLANT DIRECT 2022; 6:e383. [PMID: 35141461 PMCID: PMC8814560 DOI: 10.1002/pld3.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/13/2021] [Accepted: 01/10/2022] [Indexed: 06/01/2023]
Abstract
Copper (Cu) chaperones, of which yeast ATX1 is a prototype, are small proteins with a Cu(I) binding MxCxxC motif and are responsible for directing intracellular Cu toward specific client protein targets that use Cu as a cofactor. The Chlamydomonas reinhardtii ATX1 (CrATX1) was identified by its high sequence similarity with yeast ATX1. Like the yeast homologue, CrATX1 accumulates in iron-deficient cells (but is not impacted by other metal-deficiencies). N- and C-terminally YFP-ATX1 fusion proteins are distributed in the cytoplasm. Reverse genetic analysis using artificial microRNA (amiRNA) to generate lines with reduced CrATX1 abundance and CRISPR/Cpf1 to generate atx1 knockout lines validated a function for ATX1 in iron-poor cells, again reminiscent of yeast ATX1, most likely because of an impact on metalation of the multicopper oxidase FOX1, which is an important component in high-affinity iron uptake. We further identify other candidate ATX1 targets owing to reduced growth of atx1 mutant lines on guanine as a sole nitrogen source, which we attribute to loss of function of UOX1, encoding a urate oxidase, a cupro-enzyme involved in guanine assimilation. An impact of ATX1 on Cu distribution in atx1 mutants is strikingly evident by a reduced amount of intracellular Cu in all conditions probed in this work.
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Affiliation(s)
- Keegan L. J. Pham
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Stefan Schmollinger
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Molecular & Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Daniela Strenkert
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
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12
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Abinandan S, Venkateswarlu K, Megharaj M. Phenotypic changes in microalgae at acidic pH mediate their tolerance to higher concentrations of transition metals. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 2:100081. [PMID: 35028626 PMCID: PMC8714768 DOI: 10.1016/j.crmicr.2021.100081] [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: 08/10/2021] [Revised: 10/22/2021] [Accepted: 11/06/2021] [Indexed: 11/25/2022] Open
Abstract
Acid-tolerant microalgae were grown at pH 3.5 and 6.7 in presence of heavy metals (HMs). HMs-induced phenotypic changes in microalgae were evaluated by ATR-FTIR spectroscopy. Higher HMs bioavailability affected microalgae more at pH 6.7 than pH 3.5. Acclimation of microalgal strains to acidic pH significantly alleviates HMs toxicity.
Acclimatory phenotypic response is a common phenomenon in microalgae, particularly during heavy metal stress. It is not clear so far whether acclimating to one abiotic stressor can alleviate the stress imposed by another abiotic factor. The intent of the present study was to demonstrate the implication of acidic pH in effecting phenotypic changes that facilitate microalgal tolerance to biologically excess concentrations of heavy metals. Two microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, were exposed to biologically excess concentrations of Cu (0.50 and 1.0 mg L‒1), Fe (5 and 10 mg L‒1), Mn (5 and 10 mg L‒1) and Zn (2, 5 and 10 mg L‒1) supplemented to the culture medium at pH 3.5 and 6.7. Chlorophyll autofluorescence and biochemical fingerprinting using FTIR-spectroscopy were used to assess the microalgal strains for phenotypic changes that mediate tolerance to metals. Both the strains responded to acidic pH by effecting differential changes in biochemicals such as carbohydrates, proteins, and lipids. Both the microalgal strains, when acclimated to low pH of 3.5, exhibited an increase in protein (< 2-fold) and lipid (> 1.5-fold). Strain MAS1 grown at pH 3.5 showed a reduction (1.5-fold) in carbohydrates while strain MAS3 exhibited a 17-fold increase in carbohydrates as compared to their growth at pH 6.7. However, lower levels of biologically excess concentrations of the selected transition metals at pH 6.7 unveiled positive or no effect on physiology and biochemistry in microalgal strains, whereas growth with higher metal concentrations at this pH resulted in decreased chlorophyll content. Although the bioavailability of free-metal ions is higher at pH 3.5, as revealed by Visual MINTEQ model, no adverse effect was observed on chlorophyll content in cells grown at pH 3.5 than at pH 6.7. Furthermore, increasing concentrations of Fe, Mn and Zn significantly upregulated the carbohydrate metabolism, but not protein and lipid synthesis, in both strains at pH 3.5 as compared to their growth at pH 6.7. Overall, the impact of pH 3.5 on growth response suggested that acclimation of microalgal strains to acidic pH alleviates metal toxicity by triggering physiological and biochemical changes in microalgae for their survival.
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Affiliation(s)
- Sudharsanam Abinandan
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW 2308, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, 515003, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, Callaghan, NSW 2308, Australia
- Corresponding author at: Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW 2308, Australia.
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13
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Wang X, Wang WX. Intracellular Biotransformation of Cu(II)/Cu(I) Explained High Cu Toxicity to Phytoplankton Chlamydomonas reinhardtii. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14772-14781. [PMID: 34647741 DOI: 10.1021/acs.est.1c05408] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The toxicity of Cu is related to its redox species, but the differential toxicity of Cu(II) and Cu(I) remains unknown. In the present study, we developed a novel protocol to simultaneously detect the biologically produced extracellular Cu(I) and internalized Cu(II) in a freshwater phytoplankton Chlamydomonas reinhardtii. The intracellular Cu(I) was further imaged using a fluorometric probe. Combining these pieces of evidence, we demonstrated that Cu(I) dominated the Cu toxicity in algal cells under Fe-deficient conditions. Our results showed that the labile Cu(I) content increased significantly in the low Fe quota cells. Intracellular biotransformation from Cu(II) to Cu(I) rather than the direct uptake of Cu(I) was responsible for the high Cu toxicity. The abnormal biotransformation from Cu(II) to Cu(I) under Fe deficiency was not resulted from the increase of overall Cu bioaccumulation but was likely due to the change of Cu(II) metabolism. High contents of Cu(II) were accumulated in the normal cells and the low Zn quota cells upon Cu exposure but did not induce cell death, further suggesting that Cu(I) dominated the Cu toxicity to the algae. This is the first study to simultaneously consider the effect of Cu(I) and Cu(II) during Cu exposure in phytoplankton. The results uncovered the underlying mechanisms of high Cu toxicity under Fe deficiency and highlighted the critical role of modulation of Cu metabolism in phytoplankton.
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Affiliation(s)
- Xiangrui Wang
- School of Energy and Environment and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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Liedschulte V, Duncan Battey JN, Laparra H, Kleinhans S, Bovet L, Goepfert S. Zinc uptake and HMA4 activity are required for micro- and macroelement balance in tobacco (Nicotiana tabacum). PHYTOCHEMISTRY 2021; 191:112911. [PMID: 34418773 DOI: 10.1016/j.phytochem.2021.112911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
The pleiotropic effects of zinc deficiency on ion homeostasis have already been described in several plants. Tobacco (Nicotiana tabacum) heavy metal ATPases HMA4.1 and HMA4.2 are involved in zinc and cadmium root-to-shoot translocation. In previous research, we have shown that N. tabacum HMA4 RNAi plants and HMA4 double-nonsense mutants exhibit strongly reduced zinc and cadmium levels in leaves as well as stunted growth. In this study, the ionome and transcriptome of these lines were investigated to better characterize the effect of reduced zinc levels and to understand the impaired growth phenotype. We found that, under standard greenhouse fertilization rates, these lines accumulated up to 4- to 6-fold more phosphorus, iron, manganese, and copper than their respective controls. Under field conditions, HMA4 double-mutant plants also exhibited similar accumulation phenotypes, albeit to a lower extent. In both HMA4 RNAi plants and HMA4 mutants, transcription analysis showed a local zinc-deficiency response in leaves as well as an FIT1-mediated iron-deficiency response in roots, likely contributing to iron and manganese uptake at the root level. A phosphate-starvation response involving HHO2 was also observed in HMA4-impaired plant leaves. The high level of phosphorus observed in HMA4-impaired plants is correlated with leaf swelling and necrosis. The upregulation of aquaporin genes is in line with cellular water influx and the observed leaf swelling phenotype. These results highlight the involvement of HMA4 in zinc homeostasis and related regulatory processes that balance the micro- and macroelements in above-ground organs.
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Affiliation(s)
- Verena Liedschulte
- Philip Morris International, Philip Morris Products SA, Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | | | - Hélène Laparra
- Philip Morris International, Philip Morris Products SA, Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Samuel Kleinhans
- Philip Morris International, Philip Morris Products SA, Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Lucien Bovet
- Philip Morris International, Philip Morris Products SA, Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland.
| | - Simon Goepfert
- Philip Morris International, Philip Morris Products SA, Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
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15
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Zhu Q, Zhang M, Bao J, Liu J. Physiological, metabolomic, and transcriptomic analyses reveal the dynamic redox homeostasis upon extended exposure of Dunaliella salina GY-H13 cells to Cd. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112593. [PMID: 34358929 DOI: 10.1016/j.ecoenv.2021.112593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/27/2021] [Accepted: 07/31/2021] [Indexed: 06/13/2023]
Abstract
The study was done to elucidate the molecular mechanisms underlying the steady maintenance of the green microalga Dunaliella salina GY-H13 in successive subcultures in F/2 medium supplemented with the high cadmium (Cd) concentration (5 mg L-1) for 3 months or 84 days using physiological, metabolomic, and transcriptomic methodologies. Physiological analysis indicated that Cd suppressed growth rate, photosynthetic efficiency, and pigment contents and promoted Cd accumulation, reactive oxygen species (ROS) generation and lipid peroxidation. UPLC-MS/MS-based metabolic analysis identified the top most upregulated and downregulated metabolites, the 5'-dehydroxyadenosine and thiamine acetic acid that were associated with the formation and removal of H2O2. RNA-seq-based transcriptomic analysis showed the overrepresentation of low-CO2-inducible genes in the most downregulated gene set. Metabolomic and transcriptomic analyses further showed that the decreased GSSG/GSH-based redox potential, increased oxidative-phosphorylation gene expression, and reduced activity of TCA cycle in cells after extended exposure to Cd. Taken together, our results imply that cellular defense to Cd in D. salina is achieved by upregulation of ROS-scavenging activities including depletion of thiamine acetic acid. Dynamic redox homeostasis is maintained in cells with extended exposure to Cd by production of both oxidants and antioxidants through multiple pathways.
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Affiliation(s)
- Qingling Zhu
- Systems Biology, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Mengmeng Zhang
- Systems Biology, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Jingjing Bao
- Zhejiang Marine Development Research Institute, Zhoushan, Zhejiang 316000, China
| | - Jianhua Liu
- Systems Biology, School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China; National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
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16
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Ma F, Salomé PA, Merchant SS, Pellegrini M. Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. THE PLANT CELL 2021; 33:1042-1057. [PMID: 33585940 PMCID: PMC8226295 DOI: 10.1093/plcell/koab025] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/13/2021] [Indexed: 05/02/2023]
Abstract
The photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of its ease of culture in the laboratory. Genomic and systems biology approaches have previously described transcriptome responses to environmental changes using bulk data, thus representing the average behavior from pools of cells. Here, we apply single-cell RNA sequencing (scRNA-seq) to probe the heterogeneity of Chlamydomonas cell populations under three environments and in two genotypes differing by the presence of a cell wall. First, we determined that RNA can be extracted from single algal cells with or without a cell wall, offering the possibility to sample natural algal communities. Second, scRNA-seq successfully separated single cells into nonoverlapping cell clusters according to their growth conditions. Cells exposed to iron or nitrogen deficiency were easily distinguished despite a shared tendency to arrest photosynthesis and cell division to economize resources. Notably, these groups of cells not only recapitulated known patterns observed with bulk RNA-seq but also revealed their inherent heterogeneity. A substantial source of variation between cells originated from their endogenous diurnal phase, although cultures were grown in constant light. We exploited this result to show that circadian iron responses may be conserved from algae to land plants. We document experimentally that bulk RNA-seq data represent an average of typically hidden heterogeneity in the population.
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Affiliation(s)
- Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095, USA
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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17
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Salomé PA, Merchant SS. Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery. THE PLANT CELL 2021; 33:1058-1082. [PMID: 33793846 PMCID: PMC8226298 DOI: 10.1093/plcell/koab042] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/25/2021] [Indexed: 05/18/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.
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18
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Single-cell visualization and quantification of trace metals in Chlamydomonas lysosome-related organelles. Proc Natl Acad Sci U S A 2021; 118:2026811118. [PMID: 33879572 DOI: 10.1073/pnas.2026811118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The acidocalcisome is an acidic organelle in the cytosol of eukaryotes, defined by its low pH and high calcium and polyphosphate content. It is visualized as an electron-dense object by transmission electron microscopy (TEM) or described with mass spectrometry (MS)-based imaging techniques or multimodal X-ray fluorescence microscopy (XFM) based on its unique elemental composition. Compared with MS-based imaging techniques, XFM offers the additional advantage of absolute quantification of trace metal content, since sectioning of the cell is not required and metabolic states can be preserved rapidly by either vitrification or chemical fixation. We employed XFM in Chlamydomonas reinhardtii to determine single-cell and organelle trace metal quotas within algal cells in situations of trace metal overaccumulation (Fe and Cu). We found up to 70% of the cellular Cu and 80% of Fe sequestered in acidocalcisomes in these conditions and identified two distinct populations of acidocalcisomes, defined by their unique trace elemental makeup. We utilized the vtc1 mutant, defective in polyphosphate synthesis and failing to accumulate Ca, to show that Fe sequestration is not dependent on either. Finally, quantitation of the Fe and Cu contents of individual cells and compartments via XFM, over a range of cellular metal quotas created by nutritional and genetic perturbations, indicated excellent correlation with bulk data from corresponding cell cultures, establishing a framework to distinguish the nutritional status of single cells.
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19
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Villanova V, Singh D, Pagliardini J, Fell D, Le Monnier A, Finazzi G, Poolman M. Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2021; 12:642199. [PMID: 33897733 PMCID: PMC8063856 DOI: 10.3389/fpls.2021.642199] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable, and diverse marine phytoplankton. They are extremely interesting not only for their ecological role but also as potential feedstocks for sustainable biofuels and high-value commodities such as omega fatty acids, because of their capacity to accumulate lipids. However, the cultivation of microalgae on an industrial scale requires higher cell densities and lipid accumulation than those found in nature to make the process economically viable. One of the known ways to induce lipid accumulation in Phaeodactylum tricornutum is nitrogen deprivation, which comes at the expense of growth inhibition and lower cell density. Thus, alternative ways need to be explored to enhance the lipid production as well as biomass density to make them sustainable at industrial scale. In this study, we have used experimental and metabolic modeling approaches to optimize the media composition, in terms of elemental composition, organic and inorganic carbon sources, and light intensity, that boost both biomass quality and quantity of P. tricornutum. Eventually, the optimized conditions were scaled-up to 2 L photobioreactors, where a better system control (temperature, pH, light, aeration/mixing) allowed a further improvement of the biomass capacity of P. tricornutum to 12 g/L.
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Affiliation(s)
- Valeria Villanova
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
- Fermentalg SA, Libourne, France
| | - Dipali Singh
- Microbes in the Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - David Fell
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
| | - Mark Poolman
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
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20
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da Silva VAS, de Lima ALC, Codognoto L, Ferreira TL, dos Santos MC, Cerchiaro G, Valle EMA. Electrochemical and spectroscopy studies of the interaction between the Zn2+ and the diethylditiocarbamate ligand (Et2DTC−). TRANSIT METAL CHEM 2021. [DOI: 10.1007/s11243-020-00445-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Polishchuk OV. Stress-Related Changes in the Expression and Activity of Plant Carbonic Anhydrases. PLANTA 2021; 253:58. [PMID: 33532871 DOI: 10.1007/s00425-020-03553-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/23/2020] [Indexed: 05/17/2023]
Abstract
The data on stress-related changes in the expression and activity of plant carbonic anhydrases (CAs) suggest that they are generally upregulated at moderate stress severity. This indicates probable involvement of CAs in adaptation to drought, high salinity, heat, high light, Ci deficit, and excess bicarbonate. The changes in CA levels under cold stress are less studied and generally represented by the downregulation of CAs excepting βCA2. Excess Cd2+ and deficit of Zn2+ specifically reduce CA activity and reduce its synthesis. Probable roles of βCAs in stress adaptation include stomatal closure, ROS scavenging and partial compensation for decreased mesophyll CO2 conductance. βCAs play contrasting roles in pathogen responses, interacting with phytohormone signaling networks. Their role can be either negative or positive, probably depending on the host-pathogen system, pathogen initial titer, and levels of ·NO and ROS. It is still not clear why CAs are suppressed under severe stress levels. It should be noted, that the role of βCAs in the facilitation of CO2 diffusion and their involvement in redox signaling or ROS detoxication are potentially antagonistic, as they are inactivated by oxidation or nitrosylation. Interestingly, some chloroplastic βCAs may be relocated to the cytoplasm under stress conditions, but the physiological meaning of this effect remains to be studied.
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Affiliation(s)
- O V Polishchuk
- Membranology and Phytochemistry Department, M.G. Kholodny Institute of Botany of NAS of Ukraine, 2 Tereshchenkivska Str, Kyiv, 01004, Ukraine.
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22
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Ecotoxicity and Essential Properties of Fine-Recycled Aggregate. MATERIALS 2021; 14:ma14020463. [PMID: 33477911 PMCID: PMC7833381 DOI: 10.3390/ma14020463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/29/2020] [Accepted: 01/13/2021] [Indexed: 12/03/2022]
Abstract
This article deals with the possibility of utilization of secondary-raw materials as a natural sand replacement in concrete. Four types of waste construction materials were examined—recycled aggregate from four different sources. The natural aggregate was examined as well as used as the reference sample. All the samples were tested to evaluate the water absorption, particle size distribution, and particle density. The basic chemical reactions in the view of ecotoxicology are investigated and measured based on Czech standards. Chemical analysis, Lemna growth inhibition test, freshwater algae, daphnia acute, and mustard germination toxicity test were made and discussed in this paper. Based on the physical and geometrical properties and ecotoxicology of examined waste materials, this work evaluated them as suitable for utilization in concrete as a sand replacement.
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Gauslaa Y, Goward T. Melanic pigments and canopy-specific elemental concentration shape growth rates of the lichen Lobaria pulmonaria in unmanaged mixed forest. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Su L, Xie J, Wen W, Li J, Zhou P, An Y. Interaction of zinc and IAA alleviate aluminum-induced damage on photosystems via promoting proton motive force and reducing proton gradient in alfalfa. BMC PLANT BIOLOGY 2020; 20:433. [PMID: 32948141 PMCID: PMC7501636 DOI: 10.1186/s12870-020-02643-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND In acidic soils, aluminum (Al) competing with Zn results in Zn deficiency in plants. Zn is essential for auxin biosynthesis. Zn-mediated alleviation of Al toxicity has been rarely studied, the mechanism of Zn alleviation on Al-induced photoinhibition in photosystems remains unclear. The objective of this study was to investigate the effects of Zn and IAA on photosystems of Al-stressed alfalfa. Alfalfa seedlings with or without apical buds were exposed to 0 or100 μM AlCl3 combined with 0 or 50 μM ZnCl2, and then foliar spray with water or 6 mg L- 1 IAA. RESULTS Our results showed that Al stress significantly decreased plant growth rate, net photosynthetic rate (Pn), quantum yields and electron transfer rates of PSI and PSII. Exogenous application of Zn and IAA significantly alleviated the Al-induced negative effects on photosynthetic machinery, and an interaction of Zn and IAA played an important role in the alleviative effects. After removing apical buds of Al-stressed alfalfa seedlings, the values of pmf, gH+ and Y(II) under exogenous spraying IAA were significantly higher, and ΔpHpmf was significantly lower in Zn addition than Al treatment alone, but the changes did not occur under none spraying IAA. The interaction of Zn and IAA directly increased Y(I), Y(II), ETRI and ETRII, and decreased O2- content of Al-stressed seedlings. In addition, the transcriptome analysis showed that fourteen functionally noted genes classified into functional category of energy production and conversion were differentially expressed in leaves of alfalfa seedlings with and without apical buds. CONCLUSION Our results suggest that the interaction of zinc and IAA alleviate aluminum-induced damage on photosystems via increasing pmf and decreasing ΔpHpmf between lumen and stroma.
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Affiliation(s)
- Liantai Su
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jianping Xie
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Wuwu Wen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jiaojiao Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Peng Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yuan An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, 201101, China.
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25
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Ibuot A, Dean AP, Pittman JK. Multi-genomic analysis of the cation diffusion facilitator transporters from algae. Metallomics 2020; 12:617-630. [PMID: 32195517 DOI: 10.1039/d0mt00009d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Metal transport processes are relatively poorly understood in algae in comparison to higher plants and other eukaryotes. A screen of genomes from 33 taxonomically diverse algal species was conducted to identify members of the Cation Diffusion Facilitator (CDF) family of metal ion transporter. All algal genomes contained at least one CDF gene with four species having >10 CDF genes (median of 5 genes per genome), further confirming that this is a ubiquitous gene family. Phylogenetic analysis suggested a CDF gene organisation of five groups, which includes Zn-CDF, Fe/Zn-CDF and Mn-CDF groups, consistent with previous phylogenetic analyses, and two functionally undefined groups. One of these undefined groups was algal specific although excluded chlorophyte and rhodophyte sequences. The majority of sequences (22 out of 26 sequences) from this group had a putative ion binding site motif within transmembrane domain 2 and 5 that was distinct from other CDF proteins, such that alanine or serine replaced the conserved histidine residue. The phylogenetic grouping was supported by sequence cluster analysis. Yeast heterologous expression of CDF proteins from Chlamydomonas reinhardtii indicated Zn2+ and Co2+ transport function by CrMTP1, and Mn2+ transport function by CrMTP2, CrMTP3 and CrMTP4, which validated the phylogenetic prediction. However, the Mn-CDF protein CrMTP3 was also able to provide zinc and cobalt tolerance to the Zn- and Co-sensitive zrc1 cot1 yeast strain. There is wide diversity of CDF transporters within the algae lineage, and some of these genes may be attractive targets for future applications of metal content engineering in plants or microorganisms.
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Affiliation(s)
- Aniefon Ibuot
- Department of Science Technology, Akwa Ibom State Polytechnic, P.M.B. 1200 Ikot Ekpene, Ikot Osurua, Akwa Ibom State, Nigeria
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The metal transporter CrNRAMP1 is involved in zinc and cobalt transports in Chlamydomonas reinhardtii. Biochem Biophys Res Commun 2020; 523:880-886. [DOI: 10.1016/j.bbrc.2019.12.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 12/24/2019] [Indexed: 11/20/2022]
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Ameri M, Baron-Sola A, Khavari-Nejad RA, Soltani N, Najafi F, Bagheri A, Martinez F, Hernández LE. Aluminium triggers oxidative stress and antioxidant response in the microalgae Scenedesmus sp. JOURNAL OF PLANT PHYSIOLOGY 2020; 246-247:153114. [PMID: 31958684 DOI: 10.1016/j.jplph.2020.153114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Aluminium (Al) water pollution is an increasing environmental problem and comprehensive analysis of toxic responses of aquatic primary producer organisms is imperative. We characterized the antioxidant response of Scenedesmus sp. microalga to Al-induced oxidative stress. After 72 h of exposure to Al (0, 10, and 100 μM) in a modified Bold Basal Medium (pH 5.0), we observed cell aggregation and alterations in the subcellular structure, strong lipid peroxidation and oxidative stress induction (detected with the fluorescent probe 2',7'-dichlorodihydrofluorescein diacetate) in parallel with Al accumulation in cells. At the same time, Al toxicity caused depletion of important macronutrients like Ca, which is important for cell-wall structure. Analysis of antioxidant enzymatic activities in Al-treated Scenedesmus cells revealed that catalase, ascorbate peroxidase, as well as different isoforms of superoxide dismutase were inhibited especially at the highest Al dose (100 μM), cells that accumulated the highest concentration of Al. On the other hand, glutathione reductase activity increased at that Al concentration. Immunodetection after Western-blotting confirmed that only ascorbate peroxidase inhibition was apparently due to a decrease in enzyme levels. However, the inhibition of catalase and activation of glutathione reductase activities seemed related with post-translational modifications in protein function as protein expression decreased or increased, respectively under Al stress. Our results may help to understand toxic mechanisms triggered by Al in freshwater microalgae, which in turn could aid to select suitable biomarkers of Al contamination in aquatic ecosystems.
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Affiliation(s)
- Maryam Ameri
- Department of Plant Science, Faculty of Biological Science, Kharazmi University, Tehran, Iran.
| | - Angel Baron-Sola
- Laboratory of Plant Physiology-Department of Biology/Research Centre for Biodiversity and Global Change, Universidad Autónoma Madrid, Darwin 2, ES28049 Madrid, Spain
| | - Ramazan Ali Khavari-Nejad
- Department of Plant Science, Faculty of Biological Science, Kharazmi University, Tehran, Iran; Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Neda Soltani
- Department of Petroleum Microbiology, Research Institute of Applied Science, ACECR, Tehran, Iran
| | - Farzaneh Najafi
- Department of Plant Science, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Abdolreza Bagheri
- Faculty of Agriculture, Ferdowsi University of Mashhad, Khorasan, Iran
| | - Flor Martinez
- Laboratory of Plant Physiology-Department of Biology/Research Centre for Biodiversity and Global Change, Universidad Autónoma Madrid, Darwin 2, ES28049 Madrid, Spain
| | - Luis E Hernández
- Laboratory of Plant Physiology-Department of Biology/Research Centre for Biodiversity and Global Change, Universidad Autónoma Madrid, Darwin 2, ES28049 Madrid, Spain.
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Mandal MK, Saikia P, Chanu NK, Chaurasia N. Modulation of lipid content and lipid profile by supplementation of iron, zinc, and molybdenum in indigenous microalgae. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:20815-20828. [PMID: 31111387 DOI: 10.1007/s11356-019-05065-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/02/2019] [Indexed: 05/06/2023]
Abstract
The effects of iron (Fe), zinc (Zn), and molybdenum (Mo) on the biomass yield, lipid content, lipid yield, and fatty acid composition of Chlorella sp. NC-MKM, Graesiella emersonii NC-M1, Scenedesmus acutus NC-M2, and Chlorophyta sp. NC-M5 were studied. Among them, G. emersonii NC-M1 recorded the highest percentage increase in lipid content (140.3%) and neutral lipid (50.9%) under Zn-supplemented condition compared to the control. Also, it showed a 105% and 41.88% increase in lipid yield and neutral lipid under Fe-supplemented condition compared to the control. However, Chlorella sp. NC-MKM recorded an elevation in lipid yield (70.3% rise) and neutral lipid (24.32% rise) compared to the control in Mo-supplemented condition. The enhanced production of reactive oxygen species (ROS) and antioxidant enzyme (SOD and POD) under Fe-, Zn-, and Mo-supplemented condition supports the lipid accumulation. FAME analysis showed that the overall percentage of SFA and MUFA increased after the addition of Fe, Zn, and Mo in a culture medium compared to the control which is vital for a good-quality biodiesel. Further, biodiesel properties derived from FAMEs such as CN, SV, IV, CFPP, OS, υ, ρ, and HHV were found in accordance with biodiesel standard.
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Affiliation(s)
- Madan Kumar Mandal
- Environmental Biotechnology laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, India
| | - Papori Saikia
- Environmental Biotechnology laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, India
| | - Ng Kunjarani Chanu
- Environmental Biotechnology laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, India
| | - Neha Chaurasia
- Environmental Biotechnology laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, India.
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29
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Andresen E, Peiter E, Küpper H. Trace metal metabolism in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:909-954. [PMID: 29447378 DOI: 10.1093/jxb/erx465] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/04/2017] [Indexed: 05/18/2023]
Abstract
Many trace metals are essential micronutrients, but also potent toxins. Due to natural and anthropogenic causes, vastly different trace metal concentrations occur in various habitats, ranging from deficient to toxic levels. Therefore, one focus of plant research is on the response to trace metals in terms of uptake, transport, sequestration, speciation, physiological use, deficiency, toxicity, and detoxification. In this review, we cover most of these aspects for the essential micronutrients copper, iron, manganese, molybdenum, nickel, and zinc to provide a broader overview than found in other recent reviews, to cross-link aspects of knowledge in this very active research field that are often seen in a separated way. For example, individual processes of metal usage, deficiency, or toxicity often were not mechanistically interconnected. Therefore, this review also aims to stimulate the communication of researchers following different approaches, such as gene expression analysis, biochemistry, or biophysics of metalloproteins. Furthermore, we highlight recent insights, emphasizing data obtained under physiologically and environmentally relevant conditions.
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Affiliation(s)
- Elisa Andresen
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Branišovská, Ceské Budejovice, Czech Republic
| | - Edgar Peiter
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Plant Nutrition Laboratory, Betty-Heimann-Strasse, Halle (Saale), Germany
| | - Hendrik Küpper
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Plant Biophysics and Biochemistry, Branišovská, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, Department of Experimental Plant Biology, Branišovská, České Budějovice, Czech Republic
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30
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Blaby-Haas CE, Page MD, Merchant SS. Using YFP as a Reporter of Gene Expression in the Green Alga Chlamydomonas reinhardtii. Methods Mol Biol 2018; 1755:135-148. [PMID: 29671268 PMCID: PMC6448394 DOI: 10.1007/978-1-4939-7724-6_10] [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] [Indexed: 06/08/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a valuable experimental system in plant biology for studying metal homeostasis. Analyzing transcriptional regulation with promoter-fusion constructs in C. reinhardtii is a powerful method for connecting metal-responsive regulation with cis-regulatory elements, but overcoming expression-level variability between transformants and optimizing experimental conditions can be laborious. Here, we provide detailed protocols for the high-throughput cultivation of C. reinhardtii and assaying Venus fluorescence as a reporter for promoter activity. We also describe procedural considerations for relating metal supply to transcriptional activity.
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Affiliation(s)
| | - M Dudley Page
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA
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31
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Blaby-Haas CE, Merchant SS. Regulating cellular trace metal economy in algae. CURRENT OPINION IN PLANT BIOLOGY 2017; 39:88-96. [PMID: 28672168 PMCID: PMC5595633 DOI: 10.1016/j.pbi.2017.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 05/05/2023]
Abstract
As indispensable protein cofactors, Fe, Mn, Cu and Zn are at the center of multifaceted acclimation mechanisms that have evolved to ensure extracellular supply meets intracellular demand. Starting with selective transport at the plasma membrane and ending in protein metalation, metal homeostasis in algae involves regulated trafficking of metal ions across membranes, intracellular compartmentalization by proteins and organelles, and metal-sparing/recycling mechanisms to optimize metal-use efficiency. Overlaid on these processes are additional circuits that respond to the metabolic state as well as to the prior metal status of the cell. In this review, we focus on recent progress made toward understanding the pathways by which the single-celled, green alga Chlamydomonas reinhardtii controls its cellular trace metal economy. We also compare these mechanisms to characterized and putative processes in other algal lineages. Photosynthetic microbes continue to provide insight into cellular regulation and handling of Cu, Fe, Zn and Mn as a function of the nutritional supply and cellular demand for metal cofactors. New experimental tools such as RNA-Seq and subcellular metal imaging are bringing us closer to a molecular understanding of acclimation to supply dynamics in algae and beyond.
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Affiliation(s)
- Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Building 463, Upton, NY 11973, USA.
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, USA; Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, USA
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32
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Metal bioremediation by CrMTP4 over-expressing Chlamydomonas reinhardtii in comparison to natural wastewater-tolerant microalgae strains. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.03.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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33
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Ackerman CM, Lee S, Chang CJ. Analytical Methods for Imaging Metals in Biology: From Transition Metal Metabolism to Transition Metal Signaling. Anal Chem 2017; 89:22-41. [PMID: 27976855 PMCID: PMC5827935 DOI: 10.1021/acs.analchem.6b04631] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cheri M. Ackerman
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Sumin Lee
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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34
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van Lis R, Popek M, Couté Y, Kosta A, Drapier D, Nitschke W, Atteia A. Concerted Up-regulation of Aldehyde/Alcohol Dehydrogenase (ADHE) and Starch in Chlamydomonas reinhardtii Increases Survival under Dark Anoxia. J Biol Chem 2016; 292:2395-2410. [PMID: 28007962 DOI: 10.1074/jbc.m116.766048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/21/2016] [Indexed: 11/06/2022] Open
Abstract
Aldehyde/alcohol dehydrogenases (ADHEs) are bifunctional enzymes that commonly produce ethanol from acetyl-CoA with acetaldehyde as intermediate and play a key role in anaerobic redox balance in many fermenting bacteria. ADHEs are also present in photosynthetic unicellular eukaryotes, where their physiological role and regulation are, however, largely unknown. Herein we provide the first molecular and enzymatic characterization of the ADHE from the photosynthetic microalga Chlamydomonas reinhardtii Purified recombinant ADHE catalyzed the reversible NADH-mediated interconversions of acetyl-CoA, acetaldehyde, and ethanol but seemed to be poised toward the production of ethanol from acetaldehyde. Phylogenetic analysis of the algal fermentative enzyme supports a vertical inheritance from a cyanobacterial-related ancestor. ADHE was located in the chloroplast, where it associated in dimers and higher order oligomers. Electron microscopy analysis of ADHE-enriched stromal fractions revealed fine spiral structures, similar to bacterial ADHE spirosomes. Protein blots showed that ADHE is regulated under oxic conditions. Up-regulation is observed in cells exposed to diverse physiological stresses, including zinc deficiency, nitrogen starvation, and inhibition of carbon concentration/fixation capacity. Analyses of the overall proteome and fermentation profiles revealed that cells with increased ADHE abundance exhibit better survival under dark anoxia. This likely relates to the fact that greater ADHE abundance appeared to coincide with enhanced starch accumulation, which might reflect ADHE-mediated anticipation of anaerobic survival.
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Affiliation(s)
- Robert van Lis
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France.,LBE, INRA, 11100 Narbonne, France
| | - Marion Popek
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France
| | - Yohann Couté
- the Université Grenoble Alpes, BIG-BGE, 38000 Grenoble, France.,the Commissariat à l'Energie Atomique, BIG-BGE, 38000 Grenoble, France.,INSERM, BGE, 38000 Grenoble, France
| | - Artemis Kosta
- the Microscopy Core Facility, FR3479 Institut de Microbiologie de la Méditerranée, 13402 Marseille cedex 20, France, and
| | - Dominique Drapier
- the Institut de Biologie Physico-Chimique, UMR7141 CNRS-UPMC, 75005 Paris, France
| | - Wolfgang Nitschke
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France
| | - Ariane Atteia
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France,
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35
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Zuliani L, Frison N, Jelic A, Fatone F, Bolzonella D, Ballottari M. Microalgae Cultivation on Anaerobic Digestate of Municipal Wastewater, Sewage Sludge and Agro-Waste. Int J Mol Sci 2016; 17:ijms17101692. [PMID: 27735859 PMCID: PMC5085724 DOI: 10.3390/ijms17101692] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/16/2016] [Accepted: 09/29/2016] [Indexed: 02/08/2023] Open
Abstract
Microalgae are fast-growing photosynthetic organisms which have the potential to be exploited as an alternative source of liquid fuels to meet growing global energy demand. The cultivation of microalgae, however, still needs to be improved in order to reduce the cost of the biomass produced. Among the major costs encountered for algal cultivation are the costs for nutrients such as CO2, nitrogen and phosphorous. In this work, therefore, different microalgal strains were cultivated using as nutrient sources three different anaerobic digestates deriving from municipal wastewater, sewage sludge or agro-waste treatment plants. In particular, anaerobic digestates deriving from agro-waste or sewage sludge treatment induced a more than 300% increase in lipid production per volume in Chlorella vulgaris cultures grown in a closed photobioreactor, and a strong increase in carotenoid accumulation in different microalgae species. Conversely, a digestate originating from a pilot scale anaerobic upflow sludge blanket (UASB) was used to increase biomass production when added to an artificial nutrient-supplemented medium. The results herein demonstrate the possibility of improving biomass accumulation or lipid production using different anaerobic digestates.
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Affiliation(s)
- Luca Zuliani
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Nicola Frison
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Aleksandra Jelic
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Francesco Fatone
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - David Bolzonella
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy.
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36
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Ramanan R, Kim BH, Cho DH, Oh HM, Kim HS. Algae-bacteria interactions: Evolution, ecology and emerging applications. Biotechnol Adv 2016; 34:14-29. [PMID: 26657897 DOI: 10.1016/j.biotechadv.2015.12.003] [Citation(s) in RCA: 523] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 11/28/2022]
Abstract
Algae and bacteria have coexisted ever since the early stages of evolution. This coevolution has revolutionized life on earth in many aspects. Algae and bacteria together influence ecosystems as varied as deep seas to lichens and represent all conceivable modes of interactions - from mutualism to parasitism. Several studies have shown that algae and bacteria synergistically affect each other's physiology and metabolism, a classic case being algae-roseobacter interaction. These interactions are ubiquitous and define the primary productivity in most ecosystems. In recent years, algae have received much attention for industrial exploitation but their interaction with bacteria is often considered a contamination during commercialization. A few recent studies have shown that bacteria not only enhance algal growth but also help in flocculation, both essential processes in algal biotechnology. Hence, there is a need to understand these interactions from an evolutionary and ecological standpoint, and integrate this understanding for industrial use. Here we reflect on the diversity of such relationships and their associated mechanisms, as well as the habitats that they mutually influence. This review also outlines the role of these interactions in key evolutionary events such as endosymbiosis, besides their ecological role in biogeochemical cycles. Finally, we focus on extending such studies on algal-bacterial interactions to various environmental and bio-technological applications.
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Affiliation(s)
- Rishiram Ramanan
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Byung-Hyuk Kim
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Dae-Hyun Cho
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hee-Mock Oh
- Bioenergy and Biochemical Research Center, KRIBB, Yuseong-gu, Daejeon 305-806, Republic of Korea; Green Chemistry and Environmental Biotechnology, University of Science & Technology, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hee-Sik Kim
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 305-806, Republic of Korea; Green Chemistry and Environmental Biotechnology, University of Science & Technology, Yuseong-gu, Daejeon 305-806, Republic of Korea.
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37
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Blaby IK, Blaby-Haas CE, Pérez-Pérez ME, Schmollinger S, Fitz-Gibbon S, Lemaire SD, Merchant SS. Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:974-988. [PMID: 26473430 PMCID: PMC4715741 DOI: 10.1111/tpj.13053] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/07/2015] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) are produced by and have the potential to be damaging to all aerobic organisms. In photosynthetic organisms, they are an unavoidable byproduct of electron transfer in both the chloroplast and mitochondrion. Here, we employ the reference unicellular green alga Chlamydomonas reinhardtii to identify the effect of H2O2 on gene expression by monitoring the changes in the transcriptome in a time-course experiment. Comparison of transcriptomes from cells sampled immediately prior to the addition of H2O2 and 0.5 and 1 h subsequently revealed 1278 differentially abundant transcripts. Of those transcripts that increase in abundance, many encode proteins involved in ROS detoxification, protein degradation and stress responses, whereas among those that decrease are transcripts encoding proteins involved in photosynthesis and central carbon metabolism. In addition to these transcriptomic adjustments, we observe that addition of H2O2 is followed by an accumulation and oxidation of the total intracellular glutathione pool, and a decrease in photosynthetic O2 output. Additionally, we analyze our transcriptomes in the context of changes in transcript abundance in response to singlet O2 (O2*), and relate our H2O2 -induced transcripts to a diurnal transcriptome, where we demonstrate enrichments of H2O2 -induced transcripts early in the light phase, late in the light phase and 2 h prior to light. On this basis several genes that are highlighted in this work may be involved in previously undiscovered stress remediation pathways or acclimation responses.
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Affiliation(s)
- Ian K Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Crysten E Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - María Esther Pérez-Pérez
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Sorel Fitz-Gibbon
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Stéphane D Lemaire
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095
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Zones JM, Blaby IK, Merchant SS, Umen JG. High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation. THE PLANT CELL 2015; 27:2743-69. [PMID: 26432862 PMCID: PMC4682324 DOI: 10.1105/tpc.15.00498] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/27/2015] [Accepted: 09/14/2015] [Indexed: 05/18/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a useful model organism for investigating diverse biological processes, such as photosynthesis and chloroplast biogenesis, flagella and basal body structure/function, cell growth and division, and many others. We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide diurnal gene expression in Chlamydomonas. Over 80% of the measured transcriptome was expressed with strong periodicity, forming 18 major clusters. Genes associated with complex structures and processes, including cell cycle control, flagella and basal bodies, ribosome biogenesis, and energy metabolism, all had distinct signatures of coexpression with strong predictive value for assigning and temporally ordering function. Importantly, the frequent sampling regime allowed us to discern meaningful fine-scale phase differences between and within subgroups of genes and enabled the identification of a transiently expressed cluster of light stress genes. Coexpression was further used both as a data-mining tool to classify and/or validate genes from other data sets related to the cell cycle and to flagella and basal bodies and to assign isoforms of duplicated enzymes to their cognate pathways of central carbon metabolism. Our diurnal coexpression data capture functional relationships established by dozens of prior studies and are a valuable new resource for investigating a variety of biological processes in Chlamydomonas and other eukaryotes.
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Affiliation(s)
- James Matt Zones
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132 Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Ian K Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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Cellular sensing and transport of metal ions: implications in micronutrient homeostasis. J Nutr Biochem 2015; 26:1103-15. [PMID: 26342943 DOI: 10.1016/j.jnutbio.2015.08.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/23/2015] [Accepted: 08/04/2015] [Indexed: 12/15/2022]
Abstract
Micronutrients include the transition metal ions zinc, copper and iron. These metals are essential for life as they serve as cofactors for many different proteins. On the other hand, they can also be toxic to cell growth when in excess. As a consequence, all organisms require mechanisms to tightly regulate the levels of these metal ions. In eukaryotes, one of the primary ways in which metal levels are regulated is through changes in expression of genes required for metal uptake, compartmentalization, storage and export. By tightly regulating the expression of these genes, each organism is able to balance metal levels despite fluctuations in the diet or extracellular environment. The goal of this review is to provide an overview of how gene expression can be controlled at a transcriptional, posttranscriptional and posttranslational level in response to metal ions in lower and higher eukaryotes. Specifically, I review what is known about how these metalloregulatory factors sense fluctuations in metal ion levels and how changes in gene expression maintain nutrient homeostasis.
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40
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Activation of Autophagy by Metals in Chlamydomonas reinhardtii. EUKARYOTIC CELL 2015; 14:964-73. [PMID: 26163317 DOI: 10.1128/ec.00081-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 07/05/2015] [Indexed: 12/31/2022]
Abstract
Autophagy is an intracellular self-degradation pathway by which eukaryotic cells recycle their own material in response to specific stress conditions. Exposure to high concentrations of metals causes cell damage, although the effect of metal stress on autophagy has not been explored in photosynthetic organisms. In this study, we investigated the effect of metal excess on autophagy in the model unicellular green alga Chlamydomonas reinhardtii. We show in cells treated with nickel an upregulation of ATG8 that is independent of CRR1, a global regulator of copper signaling in Chlamydomonas. A similar effect on ATG8 was observed with copper and cobalt but not with cadmium or mercury ions. Transcriptome sequencing data revealed an increase in the abundance of the protein degradation machinery, including that responsible for autophagy, and a substantial overlap of that increased abundance with the hydrogen peroxide response in cells treated with nickel ions. Thus, our results indicate that metal stress triggers autophagy in Chlamydomonas and suggest that excess nickel may cause oxidative damage, which in turn activates degradative pathways, including autophagy, to clear impaired components and recover cellular homeostasis.
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41
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Wang Y, Stessman DJ, Spalding MH. The CO2 concentrating mechanism and photosynthetic carbon assimilation in limiting CO2 : how Chlamydomonas works against the gradient. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:429-448. [PMID: 25765072 DOI: 10.1111/tpj.12829] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/08/2015] [Accepted: 03/11/2015] [Indexed: 05/04/2023]
Abstract
The CO2 concentrating mechanism (CCM) represents an effective strategy for carbon acquisition that enables microalgae to survive and proliferate when the CO2 concentration limits photosynthesis. The CCM improves photosynthetic performance by raising the CO2 concentration at the site of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), simultaneously enhancing carbon fixation and suppressing photorespiration. Active inorganic carbon (Ci) uptake, Rubisco sequestration and interconversion between different Ci species catalyzed by carbonic anhydrases (CAs) are key components in the CCM, and an array of molecular regulatory elements is present to facilitate the sensing of CO2 availability, to regulate the expression of the CCM and to coordinate interplay between photosynthetic carbon metabolism and other metabolic processes in response to limiting CO2 conditions. This review intends to integrate our current understanding of the eukaryotic algal CCM and its interaction with carbon assimilation, based largely on Chlamydomonas as a model, and to illustrate how Chlamydomonas acclimates to limiting CO2 conditions and how its CCM is regulated.
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Affiliation(s)
- Yingjun Wang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Dan J Stessman
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Martin H Spalding
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
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42
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Guo J, Green BR, Maldonado MT. Sequence Analysis and Gene Expression of Potential Components of Copper Transport and Homeostasis in Thalassiosira pseudonana. Protist 2015; 166:58-77. [DOI: 10.1016/j.protis.2014.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 11/03/2014] [Accepted: 11/29/2014] [Indexed: 10/24/2022]
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Huertas MJ, López-Maury L, Giner-Lamia J, Sánchez-Riego AM, Florencio FJ. Metals in cyanobacteria: analysis of the copper, nickel, cobalt and arsenic homeostasis mechanisms. Life (Basel) 2014; 4:865-86. [PMID: 25501581 PMCID: PMC4284471 DOI: 10.3390/life4040865] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/27/2014] [Accepted: 12/04/2014] [Indexed: 11/16/2022] Open
Abstract
Traces of metal are required for fundamental biochemical processes, such as photosynthesis and respiration. Cyanobacteria metal homeostasis acquires an important role because the photosynthetic machinery imposes a high demand for metals, making them a limiting factor for cyanobacteria, especially in the open oceans. On the other hand, in the last two centuries, the metal concentrations in marine environments and lake sediments have increased as a result of several industrial activities. In all cases, cells have to tightly regulate uptake to maintain their intracellular concentrations below toxic levels. Mechanisms to obtain metal under limiting conditions and to protect cells from an excess of metals are present in cyanobacteria. Understanding metal homeostasis in cyanobacteria and the proteins involved will help to evaluate the use of these microorganisms in metal bioremediation. Furthermore, it will also help to understand how metal availability impacts primary production in the oceans. In this review, we will focus on copper, nickel, cobalt and arsenic (a toxic metalloid) metabolism, which has been mainly analyzed in model cyanobacterium Synechocystis sp. PCC 6803.
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Affiliation(s)
- María José Huertas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
| | - Luis López-Maury
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
| | - Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, IBB-CBME, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Ana María Sánchez-Riego
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
| | - Francisco Javier Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, E-41092 Sevilla, Spain.
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Hong-Hermesdorf A, Miethke M, Gallaher SD, Kropat J, Dodani SC, Chan J, Barupala D, Domaille DW, Shirasaki DI, Loo JA, Weber PK, Pett-Ridge J, Stemmler TL, Chang CJ, Merchant SS. Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas. Nat Chem Biol 2014; 10:1034-42. [PMID: 25344811 PMCID: PMC4232477 DOI: 10.1038/nchembio.1662] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/05/2014] [Indexed: 12/03/2022]
Abstract
We identified a Cu-accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulates Cu, a process dependent on the nutritional Cu sensor CRR1, but it is functionally Cu deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. Nano-secondary ion MS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy was consistent with Cu(+) accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu(+) became bioavailable for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mismetallation during Zn deficiency and enabling efficient cuproprotein metallation or remetallation upon Zn resupply.
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Affiliation(s)
- Anne Hong-Hermesdorf
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Marcus Miethke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Sheel C Dodani
- Department of Chemistry and Howard Hughes Medical Institute, University of California, Berkeley, USA
| | - Jefferson Chan
- Department of Chemistry and Howard Hughes Medical Institute, University of California, Berkeley, USA
| | - Dulmini Barupala
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, USA
| | - Dylan W Domaille
- Department of Chemistry and Howard Hughes Medical Institute, University of California, Berkeley, USA
| | - Dyna I Shirasaki
- Department of Biological Chemistry, University of California, Los Angeles, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.Institute for Genomics and Proteomics, University of California, Los Angeles, USA.Department of Biological Chemistry, University of California, Los Angeles, USA
| | - Peter K Weber
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Jennifer Pett-Ridge
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, USA
| | - Christopher J Chang
- Department of Chemistry and Howard Hughes Medical Institute, University of California, Berkeley, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.Institute for Genomics and Proteomics, University of California, Los Angeles, USA
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46
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Abstract
Metal ion assimilation is essential for all forms of life. However, organisms must properly control the availability of these nutrients within the cell to avoid inactivating proteins by mismetallation. To safeguard against an imbalance between supply and demand in eukaryotes, intracellular compartments contain metal transporters that load and unload metals. Although the vacuoles of Saccharomyces cerevisiae and Arabidopsis thaliana are well established locales for the storage of copper, zinc, iron, and manganese, related compartments are emerging as important mediators of metal homeostasis. Here we describe these compartments and review their metal transporter complement.
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Affiliation(s)
| | - Sabeeha S Merchant
- From the Department of Chemistry and Biochemistry and the Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
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47
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Choi S, Bird AJ. Zinc'ing sensibly: controlling zinc homeostasis at the transcriptional level. Metallomics 2014; 6:1198-215. [PMID: 24722954 DOI: 10.1039/c4mt00064a] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Zinc-responsive transcription factors are found in all kingdoms of life and include the transcriptional activators ZntR, SczA, Zap1, bZip19, bZip23, and MTF-1, and transcriptional repressors Zur, AdcR, Loz1, and SmtB. These factors have two defining features; their activity is regulated by zinc and they all play a central role in zinc homeostasis by controlling the expression of genes that directly affect zinc levels or its availability. This review summarizes what is known about the mechanisms by which each of these factors sense changes in intracellular zinc levels and how they control zinc homeostasis through target gene regulation. Other factors that influence zinc ion sensing are also discussed.
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Affiliation(s)
- Sangyong Choi
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
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48
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Barnett JP, Scanlan DJ, Blindauer CA. Identification of major zinc-binding proteins from a marine cyanobacterium: insight into metal uptake in oligotrophic environments. Metallomics 2014; 6:1254-68. [DOI: 10.1039/c4mt00048j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The open ocean cyanobacteriumSynechococcussp. WH8102 thrives at extremely low zinc concentrations. Metalloproteomics experiments have identified an outer-membrane bound porin with zinc-binding ability that is upregulated at low zinc levels, suggesting a role for porins in highly efficient zinc uptake.
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49
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Blaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS. Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. THE PLANT CELL 2013; 25:4305-23. [PMID: 24280389 PMCID: PMC3875720 DOI: 10.1105/tpc.113.117580] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 10/08/2013] [Accepted: 10/31/2013] [Indexed: 05/17/2023]
Abstract
To understand the molecular basis underlying increased triacylglycerol (TAG) accumulation in starchless (sta) Chlamydomonas reinhardtii mutants, we undertook comparative time-course transcriptomics of strains CC-4348 (sta6 mutant), CC-4349, a cell wall-deficient (cw) strain purported to represent the parental STA6 strain, and three independent STA6 strains generated by complementation of sta6 (CC-4565/STA6-C2, CC-4566/STA6-C4, and CC-4567/STA6-C6) in the context of N deprivation. Despite N starvation-induced dramatic remodeling of the transcriptome, there were relatively few differences (5 × 10(2)) observed between sta6 and STA6, the most dramatic of which were increased abundance of transcripts encoding key regulated or rate-limiting steps in central carbon metabolism, specifically isocitrate lyase, malate synthase, transaldolase, fructose bisphosphatase and phosphoenolpyruvate carboxykinase (encoded by ICL1, MAS1, TAL1, FBP1, and PCK1 respectively), suggestive of increased carbon movement toward hexose-phosphate in sta6 by upregulation of the glyoxylate pathway and gluconeogenesis. Enzyme assays validated the increase in isocitrate lyase and malate synthase activities. Targeted metabolite analysis indicated increased succinate, malate, and Glc-6-P and decreased Fru-1,6-bisphosphate, illustrating the effect of these changes. Comparisons of independent data sets in multiple strains allowed the delineation of a sequence of events in the global N starvation response in C. reinhardtii, starting within minutes with the upregulation of alternative N assimilation routes and carbohydrate synthesis and subsequently a more gradual upregulation of genes encoding enzymes of TAG synthesis. Finally, genome resequencing analysis indicated that (1) the deletion in sta6 extends into the neighboring gene encoding respiratory burst oxidase, and (2) a commonly used STA6 strain (CC-4349) as well as the sequenced reference (CC-503) are not congenic with respect to sta6 (CC-4348), underscoring the importance of using complemented strains for more rigorous assignment of phenotype to genotype.
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Affiliation(s)
- Ian K. Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Anne G. Glaesener
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Tabea Mettler
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany 14476
| | - Sorel T. Fitz-Gibbon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Sean D. Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Bensheng Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Nanette R. Boyle
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany 14476
| | - Shannon Johnson
- Genome Science, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - David Casero
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
- Address correspondence to
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50
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Glaesener AG, Merchant SS, Blaby-Haas CE. Iron economy in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2013; 4:337. [PMID: 24032036 PMCID: PMC3759009 DOI: 10.3389/fpls.2013.00337] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/09/2013] [Indexed: 05/05/2023]
Abstract
While research on iron nutrition in plants has largely focused on iron-uptake pathways, photosynthetic microbes such as the unicellular green alga Chlamydomonas reinhardtii provide excellent experimental systems for understanding iron metabolism at the subcellular level. Several paradigms in iron homeostasis have been established in this alga, including photosystem remodeling in the chloroplast and preferential retention of some pathways and key iron-dependent proteins in response to suboptimal iron supply. This review presents our current understanding of iron homeostasis in Chlamydomonas, with specific attention on characterized responses to changes in iron supply, like iron-deficiency. An overview of frequently used methods for the investigation of iron-responsive gene expression, physiology and metabolism is also provided, including preparation of media, the effect of cell size, cell density and strain choice on quantitative measurements and methods for the determination of metal content and assessing the effect of iron supply on photosynthetic performance.
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Affiliation(s)
- Anne G. Glaesener
- Department of Chemistry and Biochemistry, University of California, Los AngelesLos Angeles, CA, USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los AngelesLos Angeles, CA, USA
- Institute of Genomics and Proteomics, David Geffen School of Medicine at the University of CaliforniaLos Angeles, CA, USA
| | - Crysten E. Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los AngelesLos Angeles, CA, USA
- *Correspondence: Crysten E. Blaby-Haas, Department of Chemistry and Biochemistry, University of California, Box 951569, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA e-mail:
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