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Sun X, LaVoie M, Lefebvre PA, Gallaher SD, Glaesener AG, Strenkert D, Mehta R, Merchant SS, Silflow CD. Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii. bioRxiv 2024:2024.03.22.586359. [PMID: 38586028 PMCID: PMC10996464 DOI: 10.1101/2024.03.22.586359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Oxygen is known to prevent hydrogen production in Chlamydomonas, both by inhibiting the hydrogenase enzyme and by preventing the accumulation of HYDA-encoding transcripts. We developed a screen for mutants showing constitutive accumulation of HYDA1 transcripts in the presence of oxygen. A reporter gene required for ciliary motility, placed under the control of the HYDA1 promoter, conferred motility only in hypoxic conditions. By selecting for mutants able to swim even in the presence of oxygen we obtained strains that express the reporter gene constitutively. One mutant identified a gene encoding an F-box only protein 3 (FBXO3), known to participate in ubiquitylation and proteasomal degradation pathways in other eukaryotes. Transcriptome profiles revealed that the mutation, termed cehc1-1 , leads to constitutive expression of HYDA1 and other genes regulated by hypoxia, and of many genes known to be targets of CRR1, a transcription factor in the nutritional copper signaling pathway. CRR1 was required for the constitutive expression of the HYDA1 reporter gene in cehc1-1 mutants. The CRR1 protein, which is normally degraded in Cu-supplemented cells, was stabilized in cehc1-1 cells, supporting the conclusion that CEHC1 acts to facilitate the degradation of CRR1. Our results reveal a novel negative regulator in the CRR1 pathway and possibly other pathways leading to complex metabolic changes associated with response to hypoxia.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dupuis S, Lingappa UF, Mayali X, Sindermann ES, Chastain JL, Weber PK, Stuart R, Merchant SS. Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction. bioRxiv 2024:2024.01.26.577492. [PMID: 38328118 PMCID: PMC10849638 DOI: 10.1101/2024.01.26.577492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
While the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum , a vitamin B 12 -producing α- proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diel light with single-cell resolution. We found that more 13 C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15 NH 4 assimilation rates and changes in cell size revealed that the carbon transferred was insufficient for balanced growth of M. japonicum cells, which instead underwent reductive division. However, despite this sign of starvation, M. japonicum still supported a B 12 -dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship, demonstrate B 12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.
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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. bioRxiv 2023:2023.10.19.563170. [PMID: 37905083 PMCID: PMC10614975 DOI: 10.1101/2023.10.19.563170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Successful acclimation to copper (Cu) deficiency involves a fine balance between Cu import and export. In the unicellular green alga Chlamydomonas reinhardtii , Cu import is dependent on C opper R esponse R egulator 1 (CRR1), the master regulator of Cu homeostasis. Among CRR1 target genes are two Cu transporters belonging to the CTR/COPT gene family ( CTR1 and CTR2 ) and a related soluble cysteine-rich 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 , recapitulate the poor growth of crr1 in Cu-deficient medium, consistent with a dominant role for CTR1 in high affinity Cu(I) uptake. Notably, the over-accumulation of Cu(I) in Zinc (Zn)-deficiency (20 times the quota) 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 is consistent with the lower substrate affinity of CTR2.
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Dupuis S, Merchant SS. Chlamydomonas reinhardtii: a model for photosynthesis and so much more. Nat Methods 2023; 20:1441-1442. [PMID: 37803226 DOI: 10.1038/s41592-023-02023-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Affiliation(s)
- Sunnyjoy Dupuis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Davidi L, Gallaher SD, Ben-David E, Purvine SO, Fillmore TL, Nicora CD, Craig RJ, Schmollinger S, Roje S, Blaby-Haas CE, Auber RP, Wisecaver JH, Merchant SS. Pumping iron: A multi-omics analysis of two extremophilic algae reveals iron economy management. Proc Natl Acad Sci U S A 2023; 120:e2305495120. [PMID: 37459532 PMCID: PMC10372677 DOI: 10.1073/pnas.2305495120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Marine algae are responsible for half of the world's primary productivity, but this critical carbon sink is often constrained by insufficient iron. One species of marine algae, Dunaliella tertiolecta, is remarkable for its ability to maintain photosynthesis and thrive in low-iron environments. A related species, Dunaliella salina Bardawil, shares this attribute but is an extremophile found in hypersaline environments. To elucidate how algae manage their iron requirements, we produced high-quality genome assemblies and transcriptomes for both species to serve as a foundation for a comparative multiomics analysis. We identified a host of iron-uptake proteins in both species, including a massive expansion of transferrins and a unique family of siderophore-iron-uptake proteins. Complementing these multiple iron-uptake routes, ferredoxin functions as a large iron reservoir that can be released by induction of flavodoxin. Proteomic analysis revealed reduced investment in the photosynthetic apparatus coupled with remodeling of antenna proteins by dramatic iron-deficiency induction of TIDI1, which is closely related but identifiably distinct from the chlorophyll binding protein, LHCA3. These combinatorial iron scavenging and sparing strategies make Dunaliella unique among photosynthetic organisms.
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Affiliation(s)
- Lital Davidi
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Eyal Ben-David
- Department of Human Genetics, University of California, Los Angeles, CA 90095
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Rory J Craig
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163
| | - Crysten E Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert P Auber
- Department of Biochemistry, Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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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:mfad043. [PMID: 37422438 PMCID: PMC10357957 DOI: 10.1093/mtomcs/mfad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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 Laboratory Berkeley CA USA
| | | | - 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 Laboratory Berkeley CA USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley CA USA
| | - 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 Laboratory Berkeley CA USA
- 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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Long H, Fang J, Ye L, Zhang B, Hui C, Deng X, Merchant SS, Huang K. Structural and functional regulation of Chlamydomonas lysosome-related organelles during environmental changes. Plant Physiol 2023; 192:927-944. [PMID: 36946208 PMCID: PMC10231462 DOI: 10.1093/plphys/kiad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 06/01/2023]
Abstract
Lysosome-related organelles (LROs) are a class of heterogeneous organelles conserved in eukaryotes that primarily play a role in storage and secretion. An important function of LROs is to mediate metal homeostasis. Chlamydomonas reinhardtii is a model organism for studying metal ion metabolism; however, structural and functional analyses of LROs in C. reinhardtii are insufficient. Here, we optimized a method for purifying these organelles from 2 populations of cells: stationary phase or overloaded with iron. The morphology, elemental content, and lysosomal activities differed between the 2 preparations, even though both have phosphorus and metal ion storage functions. LROs in stationary phase cells had multiple non-membrane-bound polyphosphate granules to store phosphorus. Those in iron-overloaded cells were similar to acidocalcisomes (ACs), which have a boundary membrane and contain 1 or 2 large polyphosphate granules to store more phosphorus. We established a method for quantifying the capacity of LROs to sequester individual trace metals. Based on a comparative proteomic analysis of these 2 types of LROs, we present a comprehensive AC proteome and identified 113 putative AC proteins. The methods and protein inventories provide a framework for studying the biogenesis and modification of LROs and the mechanisms by which they participate in regulating metal ion metabolism.
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Affiliation(s)
- Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinhua Fang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430072, China
| | - Lian Ye
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baolong Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
| | - Colleen Hui
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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 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] [What about the content of this article? (0)] [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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Craig RJ, Gallaher SD, Shu S, Salomé PA, Jenkins JW, Blaby-Haas CE, Purvine SO, O’Donnell S, Barry K, Grimwood J, Strenkert D, Kropat J, Daum C, Yoshinaga Y, Goodstein DM, Vallon O, Schmutz J, Merchant SS. The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory. Plant Cell 2023; 35:644-672. [PMID: 36562730 PMCID: PMC9940879 DOI: 10.1093/plcell/koac347] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 10/12/2022] [Accepted: 12/16/2022] [Indexed: 05/20/2023]
Abstract
Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating-type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.
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Affiliation(s)
- Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean D Gallaher
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Shengqiang Shu
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, 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
| | - Jerry W Jenkins
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Crysten E Blaby-Haas
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Samuel O’Donnell
- Laboratory of Computational and Quantitative Biology, UMR 7238, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris 75005, France
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Chris Daum
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - David M Goodstein
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
| | - Olivier Vallon
- Unité Mixte de Recherche 7141, CNRS, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris 75005, France
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, California 94720, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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12
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Glaesener AG, Merchant SS. Optimizing Fe Nutrition for Algal Growth. Methods Mol Biol 2023; 2665:203-215. [PMID: 37166603 DOI: 10.1007/978-1-0716-3183-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Chlamydomonas is an excellent reference system for dissecting the impact of iron (Fe) nutrition on photosynthetic and other metabolisms. The operational definition of four stages of Fe nutrition is described and a guide to the practical use of these stages is offered, specifically the preparation of media and growth of mixotrophic cultures. A key consideration is the impact of carbon metabolism on the expression of Fe-containing enzymes and hence the Fe quota. The absolute concentration of Fe in the medium is less determinative of gene expression than the Fe available on a per-cell basis. In nature, algal cells may transition from Fe-replete to -deficient to -limited during a bloom.
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Affiliation(s)
- Anne G Glaesener
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA.
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13
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Strenkert D, Yildirim A, Yan J, Yoshinaga Y, Pellegrini M, O'Malley RC, Merchant SS, Umen JG. The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle. Plant J 2022; 112:352-368. [PMID: 35986497 PMCID: PMC9588799 DOI: 10.1111/tpj.15948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/09/2022] [Accepted: 08/14/2022] [Indexed: 05/29/2023]
Abstract
Chromatin modifications are epigenetic regulatory features with major roles in various cellular events, yet they remain understudied in algae. We interrogated the genome-wide distribution pattern of mono- and trimethylated histone H3 lysine 4 (H3K4) using chromatin-immunoprecipitation followed by deep-sequencing (ChIP-seq) during key phases of the Chlamydomonas cell cycle: early G1 phase, Zeitgeber Time 1 (ZT1), when cells initiate biomass accumulation, S/M phase (ZT13) when cells are replicating DNA and undergoing mitosis, and late G0 phase (ZT23) when they are quiescent. Tri-methylated H3K4 was predominantly enriched at transcription start sites of the majority of protein coding genes (85%). The likelihood of a gene being marked by H3K4me3 correlated with it being transcribed at some point during the life cycle but not necessarily by continuous active transcription, as exemplified by early zygotic genes, which may remain transcriptionally dormant for thousands of generations between sexual cycles. The exceptions to this rule were around 120 loci, some of which encode non-poly-adenylated transcripts, such as small nuclear RNAs and replication-dependent histones that had H3K4me3 peaks only when they were being transcribed. Mono-methylated H3K4 was the default state for the vast majority of histones that were bound outside of transcription start sites and terminator regions of genes. A small fraction of the genome that was depleted of any H3 lysine 4 methylation was enriched for DNA cytosine methylation and the genes within these DNA methylation islands were poorly expressed. Besides marking protein coding genes, H3K4me3 ChIP-seq data served also as a annotation tool for validation of hundreds of long non-coding RNA genes.
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Affiliation(s)
- Daniela Strenkert
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Asli Yildirim
- Institute of Quantitative and Computational Biosciences, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 520 Boyer Hall, Los Angeles, CA, 90095, USA
| | - Juying Yan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matteo Pellegrini
- Institute of Quantitative and Computational Biosciences, University of California, Los Angeles, CA, 90095, USA
- Department of Molecular, Cell and Developmental Biology Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Ronan C O'Malley
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sabeeha S Merchant
- 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
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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14
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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. Plant J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Goldberg RB, Larkins BA, Quatrano RS, Jorgensen RA, Martin C, Merchant SS, Meyers BC, Eckardt NA. Thank you and best wishes to Annette Kessler, Peer Review Manager for The Plant Cell. Plant Cell 2022; 34:2568-2569. [PMCID: PMC9252482 DOI: 10.1093/plcell/koac129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Robert B Goldberg
- Founding Editor (1987–1991), The Plant Cell, American Society of Plant Biologists, USA
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095, USA
| | - Brian A Larkins
- Founding Associate Editor and Editor (1992–1998), The Plant Cell, American Society of Plant Biologists, USA
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85745, USA
| | - Ralph S Quatrano
- Founding Associate Editor and Editor (1999–2003), The Plant Cell, American Society of Plant Biologists, USA
- Emeritus Dean and Professor, Department of Biology, Washington University, St. Louis, Missouri, 63130, USA
| | - Richard A Jorgensen
- Editor-in-Chief (2004–2008), The Plant Cell, American Society of Plant Biologists, USA
- Emeritus Professor, School of Plant Sciences, University of Arizona, Arizona 85721, USA
| | - Cathie Martin
- Editor-in-Chief (2009–2014), The Plant Cell, American Society of Plant Biologists, USA
- Department of Metabolic Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sabeeha S Merchant
- Editor-in-Chief (2014–2019), The Plant Cell, American Society of Plant Biologists, USA
- Department of Plant and Microbial Biology and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Blake C Meyers
- Editor-in-Chief (2020–2024), The Plant Cell, American Society of Plant Biologists, USA
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
- The Division of Plant Science and Technology, University of Missouri–Columbia, Columbia, Missouri 65211, USA
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16
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Strenkert D, Mingay M, Schmollinger S, Chen C, O'Malley RC, Merchant SS. An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis. Plant Direct 2022; 6:e392. [PMID: 35382117 PMCID: PMC8961045 DOI: 10.1002/pld3.392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The eukaryotic green alga Chromochloris zofingiensis is a reference organism for studying carbon partitioning and a promising candidate for the production of biofuel precursors. Recent transcriptome profiling transformed our understanding of its biology and generally algal biology, but epigenetic regulation remains understudied and represents a fundamental gap in our understanding of algal gene expression. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a powerful tool for the discovery of such mechanisms, by identifying genome-wide histone modification patterns and transcription factor-binding sites alike. Here, we established a ChIP-Seq framework for Chr. zofingiensis yielding over 20 million high-quality reads per sample. The most critical steps in a ChIP experiment were optimized, including DNA shearing to obtain an average DNA fragment size of 250 bp and assessment of the recommended formaldehyde concentration for optimal DNA-protein cross-linking. We used this ChIP-Seq framework to generate a genome-wide map of the H3K4me3 distribution pattern and to integrate these data with matching RNA-Seq data. In line with observations from other organisms, H3K4me3 marks predominantly transcription start sites of genes. Our H3K4me3 ChIP-Seq data will pave the way for improved genome structural annotation in the emerging reference alga Chr. zofingiensis.
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Affiliation(s)
- Daniela Strenkert
- California Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyCAUSA
| | - Matthew Mingay
- DOE Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Stefan Schmollinger
- California Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyCAUSA
| | - Cindy Chen
- DOE Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Ronan C. O'Malley
- DOE Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCAUSA
- Department of Molecular & Cell BiologyUniversity of California, BerkeleyBerkeleyCAUSA
- Division of Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Campos OA, Attar N, Cheng C, Vogelauer M, Mallipeddi NV, Schmollinger S, Matulionis N, Christofk HR, Merchant SS, Kurdistani SK. A pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich's ataxia. Sci Adv 2021; 7:eabj9889. [PMID: 34919435 PMCID: PMC8682991 DOI: 10.1126/sciadv.abj9889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Disruptions to iron-sulfur (Fe-S) clusters, essential cofactors for a broad range of proteins, cause widespread cellular defects resulting in human disease. A source of damage to Fe-S clusters is cuprous (Cu1+) ions. Since histone H3 enzymatically produces Cu1+ for copper-dependent functions, we asked whether this activity could become detrimental to Fe-S clusters. Here, we report that histone H3–mediated Cu1+ toxicity is a major determinant of cellular functional pool of Fe-S clusters. Inadequate Fe-S cluster supply, due to diminished assembly as occurs in Friedreich’s ataxia or defective distribution, causes severe metabolic and growth defects in Saccharomyces cerevisiae. Decreasing Cu1+ abundance, through attenuation of histone cupric reductase activity or depletion of total cellular copper, restored Fe-S cluster–dependent metabolism and growth. Our findings reveal an interplay between chromatin and mitochondria in Fe-S cluster homeostasis and a potential pathogenic role for histone enzyme activity and Cu1+ in diseases with Fe-S cluster dysfunction.
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Affiliation(s)
- Oscar A. Campos
- Department of Biological Chemistry, 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
| | - Narsis Attar
- Department of Biological Chemistry, 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
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan V. Mallipeddi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Nedas Matulionis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, 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
| | - Sabeeha S. Merchant
- QB3-Berkeley, University of California, Berkeley, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Siavash K. Kurdistani
- Department of Biological Chemistry, 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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19
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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. 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Salomé PA, Merchant SS. Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery. 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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Attar N, Campos OA, Vogelauer M, Cheng C, Xue Y, Schmollinger S, Salwinski L, Mallipeddi NV, Boone BA, Yen L, Yang S, Zikovich S, Dardine J, Carey MF, Merchant SS, Kurdistani SK. The histone H3-H4 tetramer is a copper reductase enzyme. Science 2020; 369:59-64. [PMID: 32631887 DOI: 10.1126/science.aba8740] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022]
Abstract
Eukaryotic histone H3-H4 tetramers contain a putative copper (Cu2+) binding site at the H3-H3' dimerization interface with unknown function. The coincident emergence of eukaryotes with global oxygenation, which challenged cellular copper utilization, raised the possibility that histones may function in cellular copper homeostasis. We report that the recombinant Xenopus laevis H3-H4 tetramer is an oxidoreductase enzyme that binds Cu2+ and catalyzes its reduction to Cu1+ in vitro. Loss- and gain-of-function mutations of the putative active site residues correspondingly altered copper binding and the enzymatic activity, as well as intracellular Cu1+ abundance and copper-dependent mitochondrial respiration and Sod1 function in the yeast Saccharomyces cerevisiae The histone H3-H4 tetramer, therefore, has a role other than chromatin compaction or epigenetic regulation and generates biousable Cu1+ ions in eukaryotes.
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Affiliation(s)
- Narsis Attar
- Department of Biological Chemistry, 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
| | - Oscar A Campos
- Department of Biological Chemistry, 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
| | - 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
| | - Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Stefan Schmollinger
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lukasz Salwinski
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.,UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan V Mallipeddi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon A Boone
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Linda Yen
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sichen Yang
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Shannon Zikovich
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jade Dardine
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, 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
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, 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. .,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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22
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Amstutz CL, Fristedt R, Schultink A, Merchant SS, Niyogi KK, Malnoë A. An atypical short-chain dehydrogenase-reductase functions in the relaxation of photoprotective qH in Arabidopsis. Nat Plants 2020; 6:154-166. [PMID: 32055052 PMCID: PMC7288749 DOI: 10.1038/s41477-020-0591-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/28/2019] [Indexed: 05/20/2023]
Abstract
Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase-reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.
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Affiliation(s)
- Cynthia L Amstutz
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Rikard Fristedt
- Department of Physics and Astronomy, Vrije University of Amsterdam, Amsterdam, The Netherlands
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Alex Schultink
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Alizée Malnoë
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden.
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23
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Eckardt NA, Meyers BC, Merchant SS. The Plant Cell Is Accepting Applications for Assistant Features Editors. Plant Cell 2019; 31:2545. [PMID: 33831150 PMCID: PMC6881125 DOI: 10.1105/tpc.19.00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
| | - Blake C Meyers
- Donald Danforth Plant Science CenterDivision of Plant SciencesUniversity of Missouri-ColumbiaSt. Louis, Missouri
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24
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Tsednee M, Castruita M, Salomé PA, Sharma A, Lewis BE, Schmollinger SR, Strenkert D, Holbrook K, Otegui MS, Khatua K, Das S, Datta A, Chen S, Ramon C, Ralle M, Weber PK, Stemmler TL, Pett-Ridge J, Hoffman BM, Merchant SS. Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in manganese-deficient conditions. J Biol Chem 2019; 294:17626-17641. [PMID: 31527081 DOI: 10.1074/jbc.ra119.009130] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/09/2019] [Indexed: 12/27/2022] Open
Abstract
Exposing cells to excess metal concentrations well beyond the cellular quota is a powerful tool for understanding the molecular mechanisms of metal homeostasis. Such improved understanding may enable bioengineering of organisms with improved nutrition and bioremediation capacity. We report here that Chlamydomonas reinhardtii can accumulate manganese (Mn) in proportion to extracellular supply, up to 30-fold greater than its typical quota and with remarkable tolerance. As visualized by X-ray fluorescence microscopy and nanoscale secondary ion MS (nanoSIMS), Mn largely co-localizes with phosphorus (P) and calcium (Ca), consistent with the Mn-accumulating site being an acidic vacuole, known as the acidocalcisome. Vacuolar Mn stores are accessible reserves that can be mobilized in Mn-deficient conditions to support algal growth. We noted that Mn accumulation depends on cellular polyphosphate (polyP) content, indicated by 1) a consistent failure of C. reinhardtii vtc1 mutant strains, which are deficient in polyphosphate synthesis, to accumulate Mn and 2) a drastic reduction of the Mn storage capacity in P-deficient cells. Rather surprisingly, X-ray absorption spectroscopy, EPR, and electron nuclear double resonance revealed that only little Mn2+ is stably complexed with polyP, indicating that polyP is not the final Mn ligand. We propose that polyPs are a critical component of Mn accumulation in Chlamydomonas by driving Mn relocation from the cytosol to acidocalcisomes. Within these structures, polyP may, in turn, escort vacuolar Mn to a number of storage ligands, including phosphate and phytate, and other, yet unidentified, compounds.
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Affiliation(s)
| | - Madeli Castruita
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Brianne E Lewis
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Stefan R Schmollinger
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Kristen Holbrook
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Marisa S Otegui
- Departments of Botany and Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Kaustav Khatua
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sayani Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ankona Datta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Martina Ralle
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095 .,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
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25
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Salomé PA, Merchant SS. A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism. Plant Cell 2019; 31:1682-1707. [PMID: 31189738 PMCID: PMC6713297 DOI: 10.1105/tpc.18.00952] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/20/2019] [Accepted: 06/08/2019] [Indexed: 05/13/2023]
Abstract
The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.
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Affiliation(s)
- Patrice A Salomé
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
| | - Sabeeha S Merchant
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
- University of California, Berkeley, Departments of Plant and Microbial Biology and Molecular and Cell Biology, Berkeley, CA 94720
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26
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Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 2019; 20:605. [PMID: 31337355 PMCID: PMC6652019 DOI: 10.1186/s12864-019-5629-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. RESULTS A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. CONCLUSIONS The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.
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Affiliation(s)
| | - Olaf Müller
- Department of Biology, Duke University, Durham, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | | | - Ólafur S. Andrésson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Guillaume Blanc
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften & Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
| | - Fred Dietrich
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
| | - Suzanne Joneson
- Department of Biology, Duke University, Durham, USA
- College of General Studies, University of Wisconsin - Milwaukee at Waukesha, Waukesha, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
| | - Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | | | | | - Francis Martin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Susan P. May
- Department of Biology, Duke University, Durham, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, USA
| | - Tami R. McDonald
- Department of Biology, Duke University, Durham, USA
- Department of Biology, St. Catherine University, St. Paul, USA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, USA
| | - Vivian Miao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Morin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California - Santa Barbara, Santa Barbara, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, and DOE Institute for Genomics and Proteomics, University of California, Los Angeles, USA
| | - Nimrod Rubinstein
- National Evolutionary Synthesis Center, Durham, USA
- Calico Life Sciences LLC, South San Francisco, USA
| | | | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Fachbereich Biowissenschaften, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jason C. Slot
- College of Food, Agricultural, and Environmental Sciences, Department of Plant Pathology, The Ohio State University, Columbus, USA
| | - Darren Soanes
- College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Claire Veneault-Fourrey
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
- Université de Lorraine, INRA, Interactions Arbres-Microorganismes, Faculté des Sciences et Technologies, Vandoeuvre les Nancy Cedex, France
| | - Basil B. Xavier
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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27
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Abstract
Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.
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Affiliation(s)
| | - Sabeeha S Merchant
- Departments of Plant and Microbial Biology and Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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28
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Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Foflonker F, Bowen BP, Ataii NN, Song J, Chen JH, Blaby-Haas CE, Larabell C, Auer M, Northen TR, Merchant SS, Niyogi KK. Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis. Plant Cell 2019; 31:579-601. [PMID: 30787178 PMCID: PMC6482638 DOI: 10.1105/tpc.18.00742] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/18/2018] [Accepted: 02/15/2019] [Indexed: 05/04/2023]
Abstract
Light and nutrients are critical regulators of photosynthesis and metabolism in plants and algae. Many algae have the metabolic flexibility to grow photoautotrophically, heterotrophically, or mixotrophically. Here, we describe reversible Glc-dependent repression/activation of oxygenic photosynthesis in the unicellular green alga Chromochloris zofingiensis. We observed rapid and reversible changes in photosynthesis, in the photosynthetic apparatus, in thylakoid ultrastructure, and in energy stores including lipids and starch. Following Glc addition in the light, C. zofingiensis shuts off photosynthesis within days and accumulates large amounts of commercially relevant bioproducts, including triacylglycerols and the high-value nutraceutical ketocarotenoid astaxanthin, while increasing culture biomass. RNA sequencing reveals reversible changes in the transcriptome that form the basis of this metabolic regulation. Functional enrichment analyses show that Glc represses photosynthetic pathways while ketocarotenoid biosynthesis and heterotrophic carbon metabolism are upregulated. Because sugars play fundamental regulatory roles in gene expression, physiology, metabolism, and growth in both plants and animals, we have developed a simple algal model system to investigate conserved eukaryotic sugar responses as well as mechanisms of thylakoid breakdown and biogenesis in chloroplasts. Understanding regulation of photosynthesis and metabolism in algae could enable bioengineering to reroute metabolism toward beneficial bioproducts for energy, food, pharmaceuticals, and human health.
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Affiliation(s)
- Melissa S Roth
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095-1569
| | - Daniel J Westcott
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Masakazu Iwai
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Katherine B Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Maria Mueller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Andreas Walter
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Fatima Foflonker
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Nassim N Ataii
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Junha Song
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, California 94143
- National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095-1569
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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29
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Merchant SS, Eckardt NA, Winchester N. The Plant Cell Celebrates 30 Years of Publishing the Best Work in Plant Biology . Plant Cell 2019; 31:1. [PMID: 30674688 PMCID: PMC6391700 DOI: 10.1105/tpc.19.00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Sabeeha S Merchant
- Editor-in-Chief, The Plant CellUniversity of California, BerkeleyBerkeley, California 94720
| | - Nancy A Eckardt
- Senior Features Editor, The Plant CellAmerican Society of Plant Biologists
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30
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Li M, van Zee M, Riche CT, Tofig B, Gallaher SD, Merchant SS, Damoiseaux R, Goda K, Di Carlo D. A Gelatin Microdroplet Platform for High-Throughput Sorting of Hyperproducing Single-Cell-Derived Microalgal Clones. Small 2018; 14:e1803315. [PMID: 30369052 DOI: 10.1002/smll.201803315] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/06/2018] [Indexed: 05/08/2023]
Abstract
Microalgae are an attractive feedstock organism for sustainable production of biofuels, chemicals, and biomaterials, but the ability to rationally engineer microalgae to enhance production has been limited. To enable the evolution-based selection of new hyperproducing variants of microalgae, a method is developed that combines phase-transitioning monodisperse gelatin hydrogel droplets with commercial flow cytometric instruments for high-throughput screening and selection of clonal populations of cells with desirable properties, such as high lipid productivity per time traced over multiple cell cycles. It is found that gelatin microgels enable i) the growth and metabolite (e.g., chlorophyll and lipids) production of single microalgal cells within the compartments, ii) infusion of fluorescent reporter molecules into the hydrogel matrices following a sol-gel transition, iii) selection of high-producing clonal populations of cells using flow cytometry, and iv) cell recovery under mild conditions, enabling regrowth after sorting. This user-friendly method is easily integratable into directed cellular evolution pipelines for strain improvement and can be adopted for other applications that require high-throughput processing, e.g., cellular secretion phenotypes and intercellular interactions.
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Affiliation(s)
- Ming Li
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- School of Engineering, Macquarie University, Sydney, NSW, 2122, Australia
| | - Mark van Zee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Carson T Riche
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Bobby Tofig
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Robert Damoiseaux
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Molecular and Medicinal Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo, 113-8655, Japan
- Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
- Department of Electrical Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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31
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Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD, Beck M. In situ architecture of the algal nuclear pore complex. Nat Commun 2018; 9:2361. [PMID: 29915221 PMCID: PMC6006428 DOI: 10.1038/s41467-018-04739-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.
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Affiliation(s)
- Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Center for Structural Systems Biology (CSSB), Notkestrasse 85, 22607, Hamburg, Germany
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Daniela Strenkert
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Patrice A Salomé
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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Fristedt R, Hu C, Wheatley N, Roy LM, Wachter RM, Savage L, Harbinson J, Kramer DM, Merchant SS, Yeates T, Croce R. RAF2 is a RuBisCO assembly factor in Arabidopsis thaliana. Plant J 2018; 94:146-156. [PMID: 29396988 DOI: 10.1111/tpj.13849] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 06/07/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the reaction between gaseous carbon dioxide (CO2 ) and ribulose-1,5-bisphosphate. Although it is one of the most studied enzymes, the assembly mechanisms of the large hexadecameric RuBisCO is still emerging. In bacteria and in the C4 plant Zea mays, a protein with distant homology to pterin-4α-carbinolamine dehydratase (PCD) has recently been shown to be involved in RuBisCO assembly. However, studies of the homologous PCD-like protein (RAF2, RuBisCO assembly factor 2) in the C3 plant Arabidopsis thaliana (A. thaliana) have so far focused on its role in hormone and stress signaling. We investigated whether A. thalianaRAF2 is also involved in RuBisCO assembly. We localized RAF2 to the soluble chloroplast stroma and demonstrated that raf2 A. thaliana mutant plants display a severe pale green phenotype with reduced levels of stromal RuBisCO. We concluded that the RAF2 protein is probably involved in RuBisCO assembly in the C3 plant A. thaliana.
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Affiliation(s)
- Rikard Fristedt
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Chen Hu
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nicole Wheatley
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Laura M Roy
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rebekka M Wachter
- School of Molecular Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ, USA
| | - Linda Savage
- Department of Energy Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Jeremy Harbinson
- Horticulture and Product Physiology Group, Wageningen University, Wageningen, The Netherlands
| | - David M Kramer
- Department of Energy Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Todd Yeates
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Roberta Croce
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
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Gallaher SD, Fitz-Gibbon ST, Strenkert D, Purvine SO, Pellegrini M, Merchant SS. High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates. Plant J 2018; 93:545-565. [PMID: 29172250 PMCID: PMC5775909 DOI: 10.1111/tpj.13788] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 05/18/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal-based platform for producing biofuels and bio-products. Its highly repetitive, ~205-kbp circular chloroplast genome and ~15.8-kbp linear mitochondrial genome were sequenced prior to the advent of high-throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA-Seq was used to quantify their relative abundances across 12 different growth conditions. Forty-six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA-Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine-rich polynucleotide tails were observed at the 3'-end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.
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Affiliation(s)
- Sean D. Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Corresponding author:
| | - Sorel T. Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Nancy A Eckardt
- American Society of Plant BiologistsSenior Features Editor, The Plant Cell
| | - Mary Williams
- American Society of Plant BiologistsFeatures Editor, The Plant Cell
| | - Sabeeha S Merchant
- Department of Chemistry and BiochemistryUniversity of California, Los AngelesEditor in Chief, The Plant Cell
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37
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Blaby-Haas CE, Castruita M, Fitz-Gibbon ST, Kropat J, Merchant SS. Ni induces the CRR1-dependent regulon revealing overlap and distinction between hypoxia and Cu deficiency responses in Chlamydomonas reinhardtii. Metallomics 2017; 8:679-91. [PMID: 27172123 DOI: 10.1039/c6mt00063k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The selectivity of metal sensors for a single metal ion is critical for cellular metal homeostasis. A suite of metal-responsive regulators is required to maintain a prescribed balance of metal ions ensuring that each apo-protein binds the correct metal. However, there are cases when non-essential metals ions disrupt proper metal sensing. An analysis of the Ni-responsive transcriptome of the green alga Chlamydomonas reinhardtii reveals that Ni artificially turns on the CRR1-dependent Cu-response regulon. Since this regulon also responds to hypoxia, a combinatorial transcriptome analysis was leveraged to gain insight into the mechanisms by which Ni interferes with the homeostatic regulation of Cu and oxygen status. Based on parallels with the effect of Ni on the hypoxic response in animals, we propose that a possible link between Cu, oxygen and Ni sensing is an as yet uncharacterized prolyl hydroxylase that regulates a co-activator of CRR1. This analysis also identified transcriptional responses to the pharmacological activation of the Cu-deficiency regulon. Although the Ni-responsive CRR1 regulon is composed of 56 genes (defined as the primary response), 259 transcripts responded to Ni treatment only when a copy of the wild-type CRR1 gene was present. The genome-wide impact of CRR1 target genes on the transcriptome was also evident from the 210 transcripts that were at least 2-fold higher in the crr1 strain, where the abundance of many CRR1 targets was suppressed. Additionally, we identified 120 transcripts that responded to Ni independent of CRR1 function. The putative functions of the proteins encoded by these transcripts suggest that high Ni results in protein damage.
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Affiliation(s)
- Crysten E Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA.
| | - Madeli Castruita
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA.
| | - Sorel T Fitz-Gibbon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA. and Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA.
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA. and Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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38
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Wittkopp TM, Schmollinger S, Saroussi S, Hu W, Zhang W, Fan Q, Gallaher SD, Leonard MT, Soubeyrand E, Basset GJ, Merchant SS, Grossman AR, Duanmu D, Lagarias JC. Bilin-Dependent Photoacclimation in Chlamydomonas reinhardtii. Plant Cell 2017; 29:2711-2726. [PMID: 29084873 PMCID: PMC5728120 DOI: 10.1105/tpc.17.00149] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/26/2017] [Accepted: 10/27/2017] [Indexed: 05/18/2023]
Abstract
In land plants, linear tetrapyrrole (bilin)-based phytochrome photosensors optimize photosynthetic light capture by mediating massive reprogramming of gene expression. But, surprisingly, many green algal genomes lack phytochrome genes. Studies of the heme oxygenase mutant (hmox1) of the green alga Chlamydomonas reinhardtii suggest that bilin biosynthesis in plastids is essential for proper regulation of a nuclear gene network implicated in oxygen detoxification during dark-to-light transitions. hmox1 cannot grow photoautotrophically and photoacclimates poorly to increased illumination. We show that these phenotypes are due to reduced accumulation of photosystem I (PSI) reaction centers, the PSI electron acceptors 5'-monohydroxyphylloquinone and phylloquinone, and the loss of PSI and photosystem II antennae complexes during photoacclimation. The hmox1 mutant resembles chlorophyll biosynthesis mutants phenotypically, but can be rescued by exogenous biliverdin IXα, the bilin produced by HMOX1. This rescue is independent of photosynthesis and is strongly dependent on blue light. RNA-seq comparisons of hmox1, genetically complemented hmox1, and chemically rescued hmox1 reveal that tetrapyrrole biosynthesis and known photoreceptor and photosynthesis-related genes are not impacted in the hmox1 mutant at the transcript level. We propose that a bilin-based, blue-light-sensing system within plastids evolved together with a bilin-based retrograde signaling pathway to ensure that a robust photosynthetic apparatus is sustained in light-grown Chlamydomonas.
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Affiliation(s)
- Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Department of Biology, Stanford University, Stanford, California 94305
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Wei Hu
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Weiqing Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuling Fan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Michael T Leonard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Eric Soubeyrand
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Gilles J Basset
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Deqiang Duanmu
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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Blaby-Haas CE, Merchant SS. Regulating cellular trace metal economy in algae. Curr Opin Plant Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Eckardt NA, Merchant SS. Journal Impact: Brave New World. Plant Cell 2017; 29:2071-2074. [PMID: 28842535 PMCID: PMC5635977 DOI: 10.1105/tpc.17.00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Nancy A Eckardt
- American Society of Plant Biologists Senior Features Editor, The Plant Cell
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry University of California, Los Angeles Editor in Chief, The Plant Cell
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41
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Xue Y, Schmollinger S, Attar N, Campos OA, Vogelauer M, Carey MF, Merchant SS, Kurdistani SK. Endoplasmic reticulum-mitochondria junction is required for iron homeostasis. J Biol Chem 2017. [PMID: 28637866 DOI: 10.1074/jbc.m117.784249] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) is a protein complex that physically tethers the two organelles to each other and creates the physical basis for communication between them. ERMES functions in lipid exchange between the ER and mitochondria, protein import into mitochondria, and maintenance of mitochondrial morphology and genome. Here, we report that ERMES is also required for iron homeostasis. Loss of ERMES components activates an Aft1-dependent iron deficiency response even in iron-replete conditions, leading to accumulation of excess iron inside the cell. This function is independent of known ERMES roles in calcium regulation, phospholipid biosynthesis, or effects on mitochondrial morphology. A mutation in the vacuolar protein sorting 13 (VPS13) gene that rescues the glycolytic phenotype of ERMES mutants suppresses the iron deficiency response and iron accumulation. Our findings reveal that proper communication between the ER and mitochondria is required for appropriate maintenance of cellular iron levels.
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Affiliation(s)
- Yong Xue
- From the Department of Biological Chemistry.,Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Stefan Schmollinger
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095 and
| | - Narsis Attar
- From the Department of Biological Chemistry.,Molecular Biology Institute, and
| | - Oscar A Campos
- From the Department of Biological Chemistry.,Molecular Biology Institute, and
| | | | - Michael F Carey
- From the Department of Biological Chemistry.,Molecular Biology Institute, and
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095 and
| | - Siavash K Kurdistani
- From the Department of Biological Chemistry, .,Molecular Biology Institute, and.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, and
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42
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Kumar D, Strenkert D, Patel-King RS, Leonard MT, Merchant SS, Mains RE, King SM, Eipper BA. A bioactive peptide amidating enzyme is required for ciliogenesis. eLife 2017; 6. [PMID: 28513435 PMCID: PMC5461114 DOI: 10.7554/elife.25728] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/15/2017] [Indexed: 02/06/2023] Open
Abstract
The pathways controlling cilium biogenesis in different cell types have not been fully elucidated. We recently identified peptidylglycine α-amidating monooxygenase (PAM), an enzyme required for generating amidated bioactive signaling peptides, in Chlamydomonas and mammalian cilia. Here, we show that PAM is required for the normal assembly of motile and primary cilia in Chlamydomonas, planaria and mice. Chlamydomonas PAM knockdown lines failed to assemble cilia beyond the transition zone, had abnormal Golgi architecture and altered levels of cilia assembly components. Decreased PAM gene expression reduced motile ciliary density on the ventral surface of planaria and resulted in the appearance of cytosolic axonemes lacking a ciliary membrane. The architecture of primary cilia on neuroepithelial cells in Pam-/- mouse embryos was also aberrant. Our data suggest that PAM activity and alterations in post-Golgi trafficking contribute to the observed ciliogenesis defects and provide an unanticipated, highly conserved link between PAM, amidation and ciliary assembly.
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Affiliation(s)
- Dhivya Kumar
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, United States
| | - Ramila S Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States
| | - Michael T Leonard
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, United States
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, United States.,Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, United States
| | - Richard E Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, United States
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States
| | - Betty A Eipper
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, United States.,Department of Neuroscience, University of Connecticut Health Center, Farmington, United States
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Wells ML, Potin P, Craigie JS, Raven JA, Merchant SS, Helliwell KE, Smith AG, Camire ME, Brawley SH. Algae as nutritional and functional food sources: revisiting our understanding. J Appl Phycol 2016; 29:949-982. [PMID: 28458464 PMCID: PMC5387034 DOI: 10.1007/s10811-016-0974-5] [Citation(s) in RCA: 521] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 05/21/2023]
Abstract
Global demand for macroalgal and microalgal foods is growing, and algae are increasingly being consumed for functional benefits beyond the traditional considerations of nutrition and health. There is substantial evidence for the health benefits of algal-derived food products, but there remain considerable challenges in quantifying these benefits, as well as possible adverse effects. First, there is a limited understanding of nutritional composition across algal species, geographical regions, and seasons, all of which can substantially affect their dietary value. The second issue is quantifying which fractions of algal foods are bioavailable to humans, and which factors influence how food constituents are released, ranging from food preparation through genetic differentiation in the gut microbiome. Third is understanding how algal nutritional and functional constituents interact in human metabolism. Superimposed considerations are the effects of harvesting, storage, and food processing techniques that can dramatically influence the potential nutritive value of algal-derived foods. We highlight this rapidly advancing area of algal science with a particular focus on the key research required to assess better the health benefits of an alga or algal product. There are rich opportunities for phycologists in this emerging field, requiring exciting new experimental and collaborative approaches.
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Affiliation(s)
- Mark L. Wells
- School of Marine Sciences, University of Maine, Orono, ME 04469 USA
| | - Philippe Potin
- Integrative Biology of Marine Models, Station Biologique Roscoff, CNRS-Université Pierre et Marie Curie, Place Georges Teissier, 29680 Roscoff, France
| | - James S. Craigie
- National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - John A. Raven
- Division of Plant Sciences, University of Dundee (James Hutton Inst), Invergowrie, Dundee, DD2 5DA Scotland UK
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007 Australia
| | - Sabeeha S. Merchant
- Department of Chemistry & Biochemistry, University of California-Los Angeles, 607 Charles E. Young Dr., East, Los Angeles, CA 90095-1569 USA
| | - Katherine E. Helliwell
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA UK
- Marine Biological Association of the UK, Citadel Hill, Plymouth, PL1 2PB UK
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA UK
| | - Mary Ellen Camire
- School of Food and Agriculture, University of Maine, Orono, ME 04469 USA
| | - Susan H. Brawley
- School of Marine Sciences, University of Maine, Orono, ME 04469 USA
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Strenkert D, Limso CA, Fatihi A, Schmollinger S, Basset GJ, Merchant SS. Genetically Programmed Changes in Photosynthetic Cofactor Metabolism in Copper-deficient Chlamydomonas. J Biol Chem 2016; 291:19118-31. [PMID: 27440043 DOI: 10.1074/jbc.m116.717413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 01/08/2023] Open
Abstract
Genetic and genomic studies indicate that copper deficiency triggers changes in the expression of genes encoding key enzymes in various chloroplast-localized lipid/pigment biosynthetic pathways. Among these are CGL78 involved in chlorophyll biosynthesis and HPPD1, encoding 4-hydroxyphenylpyruvate dioxygenase catalyzing the committed step of plastoquinone and tocopherol biosyntheses. Copper deficiency in wild-type cells does not change the chlorophyll content, but a survey of chlorophyll protein accumulation in this situation revealed increased accumulation of LHCSR3, which is blocked at the level of mRNA accumulation when either CGL78 expression is reduced or in the crd1 mutant, which has a copper-nutrition conditional defect at the same step in chlorophyll biosynthesis. Again, like copper-deficient crd1 strains, cgl78 knock-down lines also have reduced chlorophyll content concomitant with loss of PSI-LHCI super-complexes and reduced abundance of a chlorophyll binding subunit of PSI, PSAK, which connects LHCI to PSI. For HPPD1, increased mRNA results in increased abundance of the corresponding protein in copper-deficient cells concomitant with CRR1-dependent increased accumulation of γ-tocopherols, but not plastoquinone-9 nor total tocopherols. In crr1 mutants, where increased HPPD1 expression is blocked, plastochromanol-8, derived from plastoquinone-9 and purported to also have an antioxidant function, is found instead. Although not previously found in algae, this metabolite may occur only in stress conditions.
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Affiliation(s)
- Daniela Strenkert
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Clariss Ann Limso
- the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Abdelhak Fatihi
- the Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, 78026 Versailles Cedex, France, and
| | - Stefan Schmollinger
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Gilles J Basset
- the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Sabeeha S Merchant
- From the Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, the Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095,
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Reyes VC, Spitzmiller MR, Hong-Hermesdorf A, Kropat J, Damoiseaux RD, Merchant SS, Mahendra S. Copper status of exposed microorganisms influences susceptibility to metallic nanoparticles. Environ Toxicol Chem 2016; 35:1148-1158. [PMID: 26387648 PMCID: PMC5439594 DOI: 10.1002/etc.3254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 01/06/2015] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Although interactions of metallic nanoparticles (NPs) with various microorganisms have been previously explored, few studies have examined how metal sensitivity impacts NP toxicity. The present study investigated the effects of copper NPs (Cu-NP) exposure on the model alga Chlamydomonas reinhardtii in the presence and absence of the essential micronutrient copper. The toxic ranges for Cu-NPs and the ionic control, CuCl2 , were determined using a high-throughput adenosine triphosphate (ATP)-based fluorescence assay. The Cu-NPs caused similar mortality in copper-replete and copper-deplete cells (median inhibitory concentration [IC50]: 14-16 mg/L) but were less toxic than the ionic control, CuCl2 (IC50: 7 mg/L). Using this concentration range, the Cu-NP impacts on cell morphology, copper accumulation, chlorophyll content, and expression of stress genes under both copper supply states were assessed. Osmotic swelling, membrane damage, and chloroplast and organelle disintegration were observed by transmission electron microscopy at both conditions. Despite these similarities, copper-deplete cells showed greater accumulation of loosely bound and tightly bound copper after exposure to Cu-NPs. Furthermore, copper-replete cells experienced greater loss of chlorophyll content, 19% for Cu-NPs, compared with only an 11% net decrease in copper-deplete cells. The tightly bound copper was bioavailable as assessed by reverse-transcriptase quantitative polymerase chain reaction analysis of CYC6, a biomarker for Cu deficiency. The increased resistance of copper-deplete cells to Cu-NPs suggests that these cells potentially metabolize excess Cu-NPs or better manage sudden influxes of ions. The results suggest that toxicity assessments must account for the nutritional status of impacted organisms and use toxicity models based on estimations of the bioavailable fractions.
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Affiliation(s)
- Vincent C. Reyes
- Department of Civil and Environmental Engineering, University of California, Los Angeles, California, 90095, USA
| | - Melissa R. Spitzmiller
- Department of Civil and Environmental Engineering, University of California, Los Angeles, California, 90095, USA
| | - Anne Hong-Hermesdorf
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, USA
| | - Robert D. Damoiseaux
- Molecular Screening Shared Resource, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, 90095, USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, USA
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, California, 90095, USA
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Kumar D, Blaby-Haas CE, Merchant SS, Mains RE, King SM, Eipper BA. Early eukaryotic origins for cilia-associated bioactive peptide-amidating activity. J Cell Sci 2016; 129:943-56. [PMID: 26787743 DOI: 10.1242/jcs.177410] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 01/13/2016] [Indexed: 01/15/2023] Open
Abstract
Ciliary axonemes and basal bodies were present in the last eukaryotic common ancestor and play crucial roles in sensing and responding to environmental cues. Peptidergic signaling, generally considered a metazoan innovation, is essential for organismal development and homeostasis. Peptidylglycine α-amidating monooxygenase (PAM) is crucial for the last step of bioactive peptide biosynthesis. However, identification of a complete PAM-like gene in green algal genomes suggests ancient evolutionary roots for bioactive peptide signaling. We demonstrate that the Chlamydomonas reinhardtii PAM gene encodes an active peptide-amidating enzyme (CrPAM) that shares key structural and functional features with the mammalian enzyme, indicating that components of the peptide biosynthetic pathway predate multicellularity. In addition to its secretory pathway localization, CrPAM localizes to cilia and tightly associates with the axonemal superstructure, revealing a new axonemal enzyme activity. This localization pattern is conserved in mammals, with PAM present in both motile and immotile sensory cilia. The conserved ciliary localization of PAM adds to the known signaling capabilities of the eukaryotic cilium and provides a potential mechanistic link between peptidergic signaling and endocrine abnormalities commonly observed in ciliopathies.
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Affiliation(s)
- Dhivya Kumar
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3401, USA
| | - Crysten E Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569, USA Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095-1569, USA
| | - Richard E Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030-3401, USA
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3401, USA
| | - Betty A Eipper
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3401, USA Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030-3401, USA
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Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels 2016; 9:258. [PMID: 27933100 PMCID: PMC5124317 DOI: 10.1186/s13068-016-0670-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches. CONCLUSIONS Functional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.
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Affiliation(s)
- Jesse C. Traller
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Shawn J. Cokus
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - David A. Lopez
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Olga Gaidarenko
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Sarah R. Smith
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - John P. McCrow
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sean D. Gallaher
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Michael Thompson
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Orna Cook
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Marco Morselli
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Artur Jaroszewicz
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Eric E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
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Anderson A, Laohavisit A, Blaby IK, Bombelli P, Howe CJ, Merchant SS, Davies JM, Smith AG. Exploiting algal NADPH oxidase for biophotovoltaic energy. Plant Biotechnol J 2016; 14:22-8. [PMID: 25641364 PMCID: PMC5016757 DOI: 10.1111/pbi.12332] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/14/2014] [Accepted: 12/12/2014] [Indexed: 05/21/2023]
Abstract
Photosynthetic microbes exhibit light-dependent electron export across the cell membrane, which can generate electricity in biological photovoltaic (BPV) devices. How electrons are exported remains to be determined; the identification of mechanisms would help selection or generation of photosynthetic microbes capable of enhanced electrical output. We show that plasma membrane NADPH oxidase activity is a significant component of light-dependent generation of electricity by the unicellular green alga Chlamydomonas reinhardtii. NADPH oxidases export electrons across the plasma membrane to form superoxide anion from oxygen. The C. reinhardtii mutant lacking the NADPH oxidase encoded by RBO1 is impaired in both extracellular superoxide anion production and current generation in a BPV device. Complementation with the wild-type gene restores both capacities, demonstrating the role of the enzyme in electron export. Monitoring light-dependent extracellular superoxide production with a colorimetric assay is shown to be an effective way of screening for electrogenic potential of candidate algal strains. The results show that algal NADPH oxidases are important for superoxide anion production and open avenues for optimizing the biological component of these devices.
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Affiliation(s)
| | | | - Ian K Blaby
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Julia M Davies
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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49
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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. Plant J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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50
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Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M. Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. Plant Physiol 2015; 169:2730-43. [PMID: 26450704 PMCID: PMC4677889 DOI: 10.1104/pp.15.00861] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/07/2015] [Indexed: 05/02/2023]
Abstract
The green alga Chlamydomonas reinhardtii undergoes gametogenesis and mating upon nitrogen starvation. While the steps involved in its sexual reproductive cycle have been extensively characterized, the genome-wide transcriptional and epigenetic changes underlying different life cycle stages have yet to be fully described. Here, we performed transcriptome and methylome sequencing to quantify expression and DNA methylation from vegetative and gametic cells of each mating type and from zygotes. We identified 361 gametic genes with mating type-specific expression patterns and 627 genes that are specifically induced in zygotes; furthermore, these sex-related gene sets were enriched for secretory pathway and alga-specific genes. We also examined the C. reinhardtii nuclear methylation map with base-level resolution at different life cycle stages. Despite having low global levels of nuclear methylation, we detected 23 hypermethylated loci in gene-poor, repeat-rich regions. We observed mating type-specific differences in chloroplast DNA methylation levels in plus versus minus mating type gametes followed by chloroplast DNA hypermethylation in zygotes. Lastly, we examined the expression of candidate DNA methyltransferases and found three, DMT1a, DMT1b, and DMT4, that are differentially expressed during the life cycle and are candidate DNA methylases. The expression and methylation data we present provide insight into cell type-specific transcriptional and epigenetic programs during key stages of the C. reinhardtii life cycle.
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Affiliation(s)
- David Lopez
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Takashi Hamaji
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Janette Kropat
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Peter De Hoff
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Marco Morselli
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Liudmilla Rubbi
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sorel Fitz-Gibbon
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sean D Gallaher
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Sabeeha S Merchant
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - James Umen
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
| | - Matteo Pellegrini
- Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.)
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