1
|
Croce R, Carmo-Silva E, Cho YB, Ermakova M, Harbinson J, Lawson T, McCormick AJ, Niyogi KK, Ort DR, Patel-Tupper D, Pesaresi P, Raines C, Weber APM, Zhu XG. Perspectives on improving photosynthesis to increase crop yield. Plant Cell 2024:koae132. [PMID: 38701340 DOI: 10.1093/plcell/koae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024]
Abstract
Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin-Benson-Bassham (CBB) cycle. Additionally, we explore methods to increase CO2 concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.
Collapse
Affiliation(s)
- Roberta Croce
- Vrije Universiteit Amsterdam, Amsterdam, Netherlands 1081 HV, Netherlands
| | - Elizabete Carmo-Silva
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 3SX, United Kingdom
| | - Young B Cho
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Maria Ermakova
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Jeremy Harbinson
- Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tracy Lawson
- University of Essex, School of Life Sciences, Colchester, Essex CO4 3SQ, United Kingdom
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF, United Kingdom
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Dhruv Patel-Tupper
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Paolo Pesaresi
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Christine Raines
- University of Essex, School of Life Sciences, Colchester, Essex CO4 3SQ, United Kingdom
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, University Street 1, Düsseldorf, 40225, Germany
| | - Xin-Guang Zhu
- Key Laboratory of Carbon Capture, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| |
Collapse
|
2
|
Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE. A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 2024; 15:3167. [PMID: 38609367 PMCID: PMC11014987 DOI: 10.1038/s41467-024-47486-z] [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: 05/02/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
Collapse
Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Macon Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masakazu Iwai
- 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
| | - Krishna K Niyogi
- 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
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hubertus van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
3
|
Espinoza-Corral R, Iwai M, Zavřel T, Lechno-Yossef S, Sutter M, Červený J, Niyogi KK, Kerfeld CA. Phycobilisome protein ApcG interacts with PSII and regulates energy transfer in Synechocystis. Plant Physiol 2024; 194:1383-1396. [PMID: 37972281 PMCID: PMC10904348 DOI: 10.1093/plphys/kiad615] [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: 07/12/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Photosynthetic organisms harvest light using pigment-protein complexes. In cyanobacteria, these are water-soluble antennae known as phycobilisomes (PBSs). The light absorbed by PBS is transferred to the photosystems in the thylakoid membrane to drive photosynthesis. The energy transfer between these complexes implies that protein-protein interactions allow the association of PBS with the photosystems. However, the specific proteins involved in the interaction of PBS with the photosystems are not fully characterized. Here, we show in Synechocystis sp. PCC 6803 that the recently discovered PBS linker protein ApcG (sll1873) interacts specifically with PSII through its N-terminal region. Growth of cyanobacteria is impaired in apcG deletion strains under light-limiting conditions. Furthermore, complementation of these strains using a phospho-mimicking version of ApcG causes reduced growth under normal growth conditions. Interestingly, the interaction of ApcG with PSII is affected when a phospho-mimicking version of ApcG is used, targeting the positively charged residues interacting with the thylakoid membrane, suggesting a regulatory role mediated by phosphorylation of ApcG. Low-temperature fluorescence measurements showed decreased PSI fluorescence in apcG deletion and complementation strains. The PSI fluorescence was the lowest in the phospho-mimicking complementation strain, while the pull-down experiment showed no interaction of ApcG with PSI under any tested condition. Our results highlight the importance of ApcG for selectively directing energy harvested by the PBS and imply that the phosphorylation status of ApcG plays a role in regulating energy transfer from PSII to PSI.
Collapse
Affiliation(s)
- Roberto Espinoza-Corral
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Drásov 470, CZ-66424 Drásov, Czech Republic
| | - Sigal Lechno-Yossef
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Červený
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Drásov 470, CZ-66424 Drásov, Czech Republic
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
4
|
Iwai M, Patel-Tupper D, Niyogi KK. Structural Diversity in Eukaryotic Photosynthetic Light Harvesting. Annu Rev Plant Biol 2024; 75. [PMID: 38360524 DOI: 10.1146/annurev-arplant-070623-015519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Photosynthesis has been using energy from sunlight to assimilate atmospheric CO2 for at least 3.5 billion years. Through evolution and natural selection, photosynthetic organisms have flourished in almost all aquatic and terrestrial environments. This is partly due to the diversity of light-harvesting complex (LHC) proteins, which facilitate photosystem assembly, efficient excitation energy transfer, and photoprotection. Structural advances have provided Ångström-level structures of many of these proteins and have expanded our understanding of the pigments, lipids, and residues that drive LHC function. In this review, we compare and contrast recently observed cryo-electron microscopy structures across photosynthetic eukaryotes to identify structural motifs that underlie various light-harvesting strategies. We discuss subtle monomer changes that result in macroscale reorganization of LHC oligomers. Additionally, we find recurring patterns across diverse LHCs that may serve as evolutionary stepping stones for functional diversification. Advancing our understanding of LHC protein-environment interactions will improve our capacity to engineer more productive crops. Expected final online publication date for the Annual Review of Plant Biology, Volume 75 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Dhruv Patel-Tupper
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California, USA
| |
Collapse
|
5
|
Broderson M, Niyogi KK, Iwai M. Macroscale structural changes of thylakoid architecture during high light acclimation in Chlamydomonas reinhardtii. Photosynth Res 2024:10.1007/s11120-023-01067-1. [PMID: 38180578 DOI: 10.1007/s11120-023-01067-1] [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] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024]
Abstract
Photoprotection mechanisms are ubiquitous among photosynthetic organisms. The photoprotection capacity of the green alga Chlamydomonas reinhardtii is correlated with protein levels of stress-related light-harvesting complex (LHCSR) proteins, which are strongly induced by high light (HL). However, the dynamic response of overall thylakoid structure during acclimation to growth in HL has not been fully understood. Here, we combined live-cell super-resolution microscopy and analytical membrane subfractionation to investigate macroscale structural changes of thylakoid membranes during HL acclimation in Chlamydomonas. Subdiffraction-resolution live-cell imaging revealed that the overall thylakoid structures became thinned and shrunken during HL acclimation. The stromal space around the pyrenoid also became enlarged. Analytical density-dependent membrane fractionation indicated that the structural changes were partly a consequence of membrane unstacking. The analysis of both an LHCSR loss-of-function mutant, npq4 lhcsr1, and a regulatory mutant that over-expresses LHCSR, spa1-1, showed that structural changes occurred independently of LHCSR protein levels, demonstrating that LHCSR was neither necessary nor sufficient to induce the thylakoid structural changes associated with HL acclimation. In contrast, stt7-9, a mutant lacking a kinase of major light-harvesting antenna proteins, had a slower thylakoid structural response to HL relative to all other lines tested but still showed membrane unstacking. These results indicate that neither LHCSR- nor antenna-phosphorylation-dependent HL acclimation are required for the observed macroscale structural changes of thylakoid membranes in HL conditions.
Collapse
Affiliation(s)
- Mimi Broderson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
6
|
Baker CR, Cocuron JC, Alonso AP, Niyogi KK. Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light. New Phytol 2023; 240:2335-2352. [PMID: 37849025 DOI: 10.1111/nph.19324] [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] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Induction of high photosynthetic capacity is a key acclimation response to high light (HL) for many herbaceous dicot plants; however, the signaling pathways that control this response remain largely unknown. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions. Plants were grown for 5 wk in a low light (LL) regime, and time-resolved photosynthetic physiological, metabolomic, and transcriptomic responses were measured during subsequent exposure to HL. The induction of high nitrogen (N) assimilation rates early in the HL shift was strongly predictive of the induction of photosynthetic capacity later in the HL shift. Accelerated N assimilation rates depended on the mobilization of existing organic acid (OA) reserves and increased de novo OA synthesis during the induction of high photosynthetic capacity. Enhanced sucrose biosynthesis capacity increased in tandem with the induction of high photosynthetic capacity, and increased starch biosynthetic capacity was balanced by increased starch catabolism. This systems analysis supports a model in which the efficient induction of N assimilation early in the HL shift begins the cascade of events necessary for the induction of high photosynthetic capacity acclimation in HL.
Collapse
Affiliation(s)
- Christopher R Baker
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
| | | | - Ana Paula Alonso
- BioAnalytical Facility, University of North Texas, Denton, TX, 76201, USA
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76201, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| |
Collapse
|
7
|
Baker CR, Patel‐Tupper D, Cole BJ, Ching LG, Dautermann O, Kelikian AC, Allison C, Pedraza J, Sievert J, Bilbao A, Lee J, Kim Y, Kyle JE, Bloodsworth KJ, Paurus V, Hixson KK, Hutmacher R, Dahlberg J, Lemaux PG, Niyogi KK. Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum. Plant Direct 2023; 7:e545. [PMID: 37965197 PMCID: PMC10641490 DOI: 10.1002/pld3.545] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023]
Abstract
Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a relatively drought-tolerant cereal. Functional stay-green sorghum genotypes can maintain green leaf area and efficient grain filling during terminal post-flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought-tolerant genotypes, BTx642 and RTx430, were grown in replicated control and terminal post-flowering drought field plots in California's Central Valley. Photosynthetic, photoprotective, and water dynamics traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during control and drought conditions. Physiological and metabolomic data were then compared to longitudinal RNA sequencing data collected from these two genotypes. The unique metabolic and transcriptomic response to post-flowering drought in sorghum supports a role for the metabolite galactinol in controlling photosynthetic activity through regulating stomatal closure in post-flowering drought. Additionally, in the functional stay-green genotype BTx642, photoprotective responses were specifically induced in post-flowering drought, supporting a role for photoprotection in the molecular response associated with the functional stay-green trait. From these insights, new pathways are identified that can be targeted to maximize yields under growth conditions with limited water.
Collapse
Affiliation(s)
- Christopher R. Baker
- Howard Hughes Medical Institute, Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Dhruv Patel‐Tupper
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Benjamin J. Cole
- DOE‐Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Lindsey G. Ching
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Oliver Dautermann
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Armen C. Kelikian
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Cayci Allison
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Julie Pedraza
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Julie Sievert
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Aivett Bilbao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Joon‐Yong Lee
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Young‐Mo Kim
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Jennifer E. Kyle
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Kent J. Bloodsworth
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Vanessa Paurus
- Biological Sciences Division, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Robert Hutmacher
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Jeffery Dahlberg
- UC‐ANR Kearney Agricultural Research and Extension (KARE) CenterParlierCaliforniaUSA
| | - Peggy G. Lemaux
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Krishna K. Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| |
Collapse
|
8
|
Short A, Fay TP, Crisanto T, Mangal R, Niyogi KK, Limmer DT, Fleming GR. Kinetics of the xanthophyll cycle and its role in photoprotective memory and response. Nat Commun 2023; 14:6621. [PMID: 37857617 PMCID: PMC10587229 DOI: 10.1038/s41467-023-42281-8] [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: 06/09/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023] Open
Abstract
Efficiently balancing photochemistry and photoprotection is crucial for survival and productivity of photosynthetic organisms in the rapidly fluctuating light levels found in natural environments. The ability to respond quickly to sudden changes in light level is clearly advantageous. In the alga Nannochloropsis oceanica we observed an ability to respond rapidly to sudden increases in light level which occur soon after a previous high-light exposure. This ability implies a kind of memory. In this work, we explore the xanthophyll cycle in N. oceanica as a short-term photoprotective memory system. By combining snapshot fluorescence lifetime measurements with a biochemistry-based quantitative model, we show that short-term memory arises from the xanthophyll cycle. In addition, the model enables us to characterize the relative quenching abilities of the three xanthophyll cycle components. Given the ubiquity of the xanthophyll cycle in photosynthetic organisms the model described here will be of utility in improving our understanding of vascular plant and algal photoprotection with important implications for crop productivity.
Collapse
Affiliation(s)
- Audrey Short
- Graduate Group in Biophysics, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy Nanoscience Institute, Berkeley, CA, 94720, USA
| | - Thomas P Fay
- Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Thien Crisanto
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Ratul Mangal
- Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - David T Limmer
- Kavli Energy Nanoscience Institute, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA
- Chemical Science Division Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Material Science Division Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Graham R Fleming
- Graduate Group in Biophysics, University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Kavli Energy Nanoscience Institute, Berkeley, CA, 94720, USA.
- Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.
| |
Collapse
|
9
|
Teh JT, Leitz V, Holzer VJC, Neusius D, Marino G, Meitzel T, García-Cerdán JG, Dent RM, Niyogi KK, Geigenberger P, Nickelsen J. NTRC regulates CP12 to activate Calvin-Benson cycle during cold acclimation. Proc Natl Acad Sci U S A 2023; 120:e2306338120. [PMID: 37549282 PMCID: PMC10433458 DOI: 10.1073/pnas.2306338120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 08/09/2023] Open
Abstract
NADPH-dependent thioredoxin reductase C (NTRC) is a chloroplast redox regulator in algae and plants. Here, we used site-specific mutation analyses of the thioredoxin domain active site of NTRC in the green alga Chlamydomonas reinhardtii to show that NTRC mediates cold tolerance in a redox-dependent manner. By means of coimmunoprecipitation and mass spectrometry, a redox- and cold-dependent binding of the Calvin-Benson Cycle Protein 12 (CP12) to NTRC was identified. NTRC was subsequently demonstrated to directly reduce CP12 of C. reinhardtii as well as that of the vascular plant Arabidopsis thaliana in vitro. As a scaffold protein, CP12 joins the Calvin-Benson cycle enzymes phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to form an autoinhibitory supracomplex. Using size-exclusion chromatography, NTRC from both organisms was shown to control the integrity of this complex in vitro and thereby PRK and GAPDH activities in the cold. Thus, NTRC apparently reduces CP12, hence triggering the dissociation of the PRK/CP12/GAPDH complex in the cold. Like the ntrc::aphVIII mutant, CRISPR-based cp12::emx1 mutants also exhibited a redox-dependent cold phenotype. In addition, CP12 deletion resulted in robust decreases in both PRK and GAPDH protein levels implying a protein protection effect of CP12. Both CP12 functions are critical for preparing a repertoire of enzymes for rapid activation in response to environmental changes. This provides a crucial mechanism for cold acclimation.
Collapse
Affiliation(s)
- Jing Tsong Teh
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Verena Leitz
- Department of Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Victoria J. C. Holzer
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Daniel Neusius
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Giada Marino
- Department of Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Tobias Meitzel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben06466, Germany
| | - José G. García-Cerdán
- HHMI, University of California, Berkeley, CA94720-3102
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
| | - Rachel M. Dent
- HHMI, University of California, Berkeley, CA94720-3102
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
| | - Krishna K. Niyogi
- HHMI, University of California, Berkeley, CA94720-3102
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Peter Geigenberger
- Department of Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Jörg Nickelsen
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| |
Collapse
|
10
|
Perin G, Bellan A, Michelberger T, Lyska D, Wakao S, Niyogi KK, Morosinotto T. Modulation of xanthophyll cycle impacts biomass productivity in the marine microalga Nannochloropsis. Proc Natl Acad Sci U S A 2023; 120:e2214119120. [PMID: 37307488 DOI: 10.1073/pnas.2214119120] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/15/2023] [Indexed: 06/14/2023] Open
Abstract
Life on earth depends on photosynthetic primary producers that exploit sunlight to fix CO2 into biomass. Approximately half of global primary production is associated with microalgae living in aquatic environments. Microalgae also represent a promising source of biomass to complement crop cultivation, and they could contribute to the development of a more sustainable bioeconomy. Photosynthetic organisms evolved multiple mechanisms involved in the regulation of photosynthesis to respond to highly variable environmental conditions. While essential to avoid photodamage, regulation of photosynthesis results in dissipation of absorbed light energy, generating a complex trade-off between protection from stress and light-use efficiency. This work investigates the impact of the xanthophyll cycle, the light-induced reversible conversion of violaxanthin into zeaxanthin, on the protection from excess light and on biomass productivity in the marine microalgae of the genus Nannochloropsis. Zeaxanthin is shown to have an essential role in protection from excess light, contributing to the induction of nonphotochemical quenching and scavenging of reactive oxygen species. On the contrary, the overexpression of zeaxanthin epoxidase enables a faster reconversion of zeaxanthin to violaxanthin that is shown to be advantageous for biomass productivity in dense cultures in photobioreactors. These results demonstrate that zeaxanthin accumulation is critical to respond to strong illumination, but it may lead to unnecessary energy losses in light-limiting conditions and accelerating its reconversion to violaxanthin provides an advantage for biomass productivity in microalgae.
Collapse
Affiliation(s)
- Giorgio Perin
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Tim Michelberger
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Dagmar Lyska
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Setsuko Wakao
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- HHMI, University of California, Berkeley, CA 94720-3102
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | | |
Collapse
|
11
|
Karavolias NG, Patel-Tupper D, Seong K, Tjahjadi M, Gueorguieva GA, Tanaka J, Gallegos Cruz A, Lieberman S, Litvak L, Dahlbeck D, Cho MJ, Niyogi KK, Staskawicz BJ. Paralog editing tunes rice stomatal density to maintain photosynthesis and improve drought tolerance. Plant Physiol 2023; 192:1168-1182. [PMID: 36960567 PMCID: PMC10231365 DOI: 10.1093/plphys/kiad183] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 06/01/2023]
Abstract
Rice (Oryza sativa) is of paramount importance for global nutrition, supplying at least 20% of global calories. However, water scarcity and increased drought severity are anticipated to reduce rice yields globally. We explored stomatal developmental genetics as a mechanism for improving drought resilience in rice while maintaining yield under climate stress. CRISPR/Cas9-mediated knockouts of the positive regulator of stomatal development STOMAGEN and its paralog EPIDERMAL PATTERNING FACTOR-LIKE10 (EPFL10) yielded lines with ∼25% and 80% of wild-type stomatal density, respectively. epfl10 lines with moderate reductions in stomatal density were able to conserve water to similar extents as stomagen lines but did not suffer from the concomitant reductions in stomatal conductance, carbon assimilation, or thermoregulation observed in stomagen knockouts. Moderate reductions in stomatal density achieved by editing EPFL10 present a climate-adaptive approach for safeguarding yield in rice. Editing the paralog of STOMAGEN in other species may provide a means for tuning stomatal density in agriculturally important crops beyond rice.
Collapse
Affiliation(s)
- Nicholas G Karavolias
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Dhruv Patel-Tupper
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kyungyong Seong
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
| | | | - Gloria-Alexandra Gueorguieva
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Jaclyn Tanaka
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | | | | | | | - Douglas Dahlbeck
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Krishna K Niyogi
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brian J Staskawicz
- Plant and Microbial Biology Department, UC Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| |
Collapse
|
12
|
De Souza AP, Burgess SJ, Doran L, Manukyan L, Hansen J, Maryn N, Leonelli L, Niyogi KK, Stephen SP. Response to Comments on "Soybean photosynthesis and crop yield is improved by accelerating recovery from photoprotection". Science 2023; 379:eadf2189. [PMID: 36821655 DOI: 10.1126/science.adf2189] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
We recently demonstrated that accelerating the relaxation of nonphotochemical quenching leads to higher soybean photosynthetic efficiency and yield. In response, Sinclair et al. assert that improved photosynthesis cannot improve crop yields and that there is only one valid experimental design for proving a genetic improvement in yield. We explain here why neither assertion is valid.
Collapse
Affiliation(s)
- Amanda P De Souza
- Departments of Plant Biology and of Crop Sciences, Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steven J Burgess
- Departments of Plant Biology and of Crop Sciences, Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lynn Doran
- Departments of Plant Biology and of Crop Sciences, Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lusya Manukyan
- Departments of Plant Biology and of Crop Sciences, Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jeffrey Hansen
- Departments of Plant Biology and of Crop Sciences, Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nina Maryn
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Lauribel Leonelli
- Departments of Plant Biology and of Crop Sciences, Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, 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
| | - Stephen P Stephen
- Departments of Plant Biology and of Crop Sciences, Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| |
Collapse
|
13
|
Calderon RH, de Vitry C, Wollman FA, Niyogi KK. Rubredoxin 1 promotes the proper folding of D1 and is not required for heme b 559 assembly in Chlamydomonas photosystem II. J Biol Chem 2023; 299:102968. [PMID: 36736898 PMCID: PMC9986647 DOI: 10.1016/j.jbc.2023.102968] [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: 10/24/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Photosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme b559 iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome b559, using the RBD1-lacking 2pac mutant from Chlamydomonas reinhardtii, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant 2pac ftsh1-1, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the 2pac ftsh1-1 background and found that α and β cytochrome b559 subunits are still present and coordinate heme b559 as in the WT. Interestingly, immunoblot analysis of dark- and low light-grown 2pac ftsh1-1 showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme b559 assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly via delivery or reduction of the nonheme iron during PSII assembly.
Collapse
Affiliation(s)
- Robert H Calderon
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA; Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden.
| | - Catherine de Vitry
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
| | - Francis-André Wollman
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA
| |
Collapse
|
14
|
Orr DJ, Robijns AKJ, Baker CR, Niyogi KK, Carmo-Silva E. Dynamics of Rubisco regulation by sugar phosphate derivatives and their phosphatases. J Exp Bot 2023; 74:581-590. [PMID: 36173669 PMCID: PMC9833046 DOI: 10.1093/jxb/erac386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 06/07/2022] [Accepted: 09/28/2022] [Indexed: 05/31/2023]
Abstract
Regulating the central CO2-fixing enzyme Rubisco is as complex as its ancient reaction mechanism and involves interaction with a series of cofactors and auxiliary proteins that activate catalytic sites and maintain activity. A key component among the regulatory mechanisms is the binding of sugar phosphate derivatives that inhibit activity. Removal of inhibitors via the action of Rubisco activase is required to restore catalytic competency. In addition, specific phosphatases dephosphorylate newly released inhibitors, rendering them incapable of binding to Rubisco catalytic sites. The best studied inhibitor is 2-carboxy-d-arabinitol 1-phosphate (CA1P), a naturally occurring nocturnal inhibitor that accumulates in most species during darkness and low light, progressively binding to Rubisco. As light increases, Rubisco activase removes CA1P from Rubisco, and the specific phosphatase CA1Pase dephosphorylates CA1P to CA, which cannot bind Rubisco. Misfire products of Rubisco's complex reaction chemistry can also act as inhibitors. One example is xylulose-1,5-bisphosphate (XuBP), which is dephosphorylated by XuBPase. Here we revisit key findings related to sugar phosphate derivatives and their specific phosphatases, highlighting outstanding questions and how further consideration of these inhibitors and their role is important for better understanding the regulation of carbon assimilation.
Collapse
Affiliation(s)
| | - Alice K J Robijns
- Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Christopher R Baker
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, 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
| | | |
Collapse
|
15
|
Bru P, Steen CJ, Park S, Amstutz CL, Sylak-Glassman EJ, Lam L, Fekete A, Mueller MJ, Longoni F, Fleming GR, Niyogi KK, Malnoë A. The major trimeric antenna complexes serve as a site for qH-energy dissipation in plants. J Biol Chem 2022; 298:102519. [PMID: 36152752 PMCID: PMC9615032 DOI: 10.1016/j.jbc.2022.102519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/26/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/28/2022] Open
Abstract
Plants and algae are faced with a conundrum: harvesting sufficient light to drive their metabolic needs while dissipating light in excess to prevent photodamage, a process known as nonphotochemical quenching. A slowly relaxing form of energy dissipation, termed qH, is critical for plants’ survival under abiotic stress; however, qH location in the photosynthetic membrane is unresolved. Here, we tested whether we could isolate subcomplexes from plants in which qH was induced that would remain in an energy-dissipative state. Interestingly, we found that chlorophyll (Chl) fluorescence lifetimes were decreased by qH in isolated major trimeric antenna complexes, indicating that they serve as a site for qH-energy dissipation and providing a natively quenched complex with physiological relevance to natural conditions. Next, we monitored the changes in thylakoid pigment, protein, and lipid contents of antenna with active or inactive qH but did not detect any evident differences. Finally, we investigated whether specific subunits of the major antenna complexes were required for qH but found that qH was insensitive to trimer composition. Because we previously observed that qH can occur in the absence of specific xanthophylls, and no evident changes in pigments, proteins, or lipids were detected, we tentatively propose that the energy-dissipative state reported here may stem from Chl–Chl excitonic interaction.
Collapse
Affiliation(s)
- Pierrick Bru
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Collin J Steen
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division (formerly Physical Biosciences Division), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Kavli Energy Nanoscience Institute, Berkeley, CA 94720, USA
| | - Soomin Park
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division (formerly Physical Biosciences Division), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Kavli Energy Nanoscience Institute, Berkeley, CA 94720, USA; School of Energy, Materials and Chemical Engineering, Korea University of Technology and Education, Cheonan, Chungnam 31253, Republic of Korea
| | - Cynthia L Amstutz
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Emily J Sylak-Glassman
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division (formerly Physical Biosciences Division), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lam Lam
- Molecular Biophysics and Integrated Bioimaging Division (formerly Physical Biosciences Division), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Kavli Energy Nanoscience Institute, Berkeley, CA 94720, USA; Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
| | - Agnes Fekete
- Julius-von-Sachs-Institute, Biocenter, Pharmaceutical Biology, University of Wuerzburg, D-97082 Wuerzburg, Germany
| | - Martin J Mueller
- Julius-von-Sachs-Institute, Biocenter, Pharmaceutical Biology, University of Wuerzburg, D-97082 Wuerzburg, Germany
| | - Fiamma Longoni
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division (formerly Physical Biosciences Division), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Kavli Energy Nanoscience Institute, Berkeley, CA 94720, USA; Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division (formerly Physical Biosciences Division), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Alizée Malnoë
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden.
| |
Collapse
|
16
|
De Souza AP, Burgess SJ, Doran L, Hansen J, Manukyan L, Maryn N, Gotarkar D, Leonelli L, Niyogi KK, Long SP. Soybean photosynthesis and crop yield are improved by accelerating recovery from photoprotection. Science 2022; 377:851-854. [PMID: 35981033 DOI: 10.1126/science.adc9831] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Crop leaves in full sunlight dissipate damaging excess absorbed light energy as heat. This protective dissipation continues after the leaf transitions to shade, reducing crop photosynthesis. A bioengineered acceleration of this adjustment increased photosynthetic efficiency and biomass in tobacco in the field. But could that also translate to increased yield in a food crop? Here we bioengineered the same change into soybean. In replicated field trials, photosynthetic efficiency in fluctuating light was higher and seed yield in five independent transformation events increased by up to 33%. Despite increased seed quantity, seed protein and oil content were unaltered. This validates increasing photosynthetic efficiency as a much needed strategy toward sustainably increasing crop yield in support of future global food security.
Collapse
Affiliation(s)
- Amanda P De Souza
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steven J Burgess
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Plant Biology, Morrill Hall, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lynn Doran
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jeffrey Hansen
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lusya Manukyan
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nina Maryn
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Dhananjay Gotarkar
- Department of Plant Biology, Morrill Hall, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lauriebeth Leonelli
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, 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
| | - Stephen P Long
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Lancaster Environment Centre, Lancaster University, Lancaster, UK
| |
Collapse
|
17
|
Steen CJ, Burlacot A, Short AH, Niyogi KK, Fleming GR. Interplay between LHCSR proteins and state transitions governs the NPQ response in Chlamydomonas during light fluctuations. Plant Cell Environ 2022; 45:2428-2445. [PMID: 35678230 PMCID: PMC9540987 DOI: 10.1111/pce.14372] [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: 04/01/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 05/19/2023]
Abstract
Photosynthetic organisms use sunlight as the primary energy source to fix CO2 . However, in nature, light energy is highly variable, reaching levels of saturation for periods ranging from milliseconds to hours. In the green microalga Chlamydomonas reinhardtii, safe dissipation of excess light energy by nonphotochemical quenching (NPQ) is mediated by light-harvesting complex stress-related (LHCSR) proteins and redistribution of light-harvesting antennae between the photosystems (state transition). Although each component underlying NPQ has been documented, their relative contributions to NPQ under fluctuating light conditions remain unknown. Here, by monitoring NPQ in intact cells throughout high light/dark cycles of various illumination periods, we find that the dynamics of NPQ depend on the timescales of light fluctuations. We show that LHCSRs play a major role during the light phases of light fluctuations and describe their role in growth under rapid light fluctuations. We further reveal an activation of NPQ during the dark phases of all high light/dark cycles and show that this phenomenon arises from state transition. Finally, we show that LHCSRs and state transition synergistically cooperate to enable NPQ response during light fluctuations. These results highlight the dynamic functioning of photoprotection under light fluctuations and open a new way to systematically characterize the photosynthetic response to an ever-changing light environment.
Collapse
Affiliation(s)
- Collin J. Steen
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Kavli Energy Nanoscience InstituteBerkeleyCaliforniaUSA
| | - Adrien Burlacot
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
| | - Audrey H. Short
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Kavli Energy Nanoscience InstituteBerkeleyCaliforniaUSA
- Graduate Group in BiophysicsUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Krishna K. Niyogi
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Graham R. Fleming
- Department of ChemistryUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Kavli Energy Nanoscience InstituteBerkeleyCaliforniaUSA
- Graduate Group in BiophysicsUniversity of CaliforniaBerkeleyCaliforniaUSA
| |
Collapse
|
18
|
Short AH, Fay TP, Crisanto T, Hall J, Steen CJ, Niyogi KK, Limmer DT, Fleming GR. Xanthophyll-cycle based model of the rapid photoprotection of Nannochloropsis in response to regular and irregular light/dark sequences. J Chem Phys 2022; 156:205102. [DOI: 10.1063/5.0089335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract <p>We explore the photoprotection dynamics of Nannochloropsis oceanica using time-correlated single photon counting under regular and irregular actinic light sequences. The varying light sequences mimic natural conditions, allowing us to probe the real-time response of non-photochemical quenching (NPQ) pathways. Durations of fluctuating light exposure during a fixed total experimental time and prior light exposure of the algae are both found to have a profound effect on NPQ. These observations are rationalized with a quantitative model based on the xanthophyll cycle and the protonation of LHCX1. The model is able to accurately describe the dynamics of non-photochemical quenching across a variety of light sequences. The combined model and observations suggest that the accumulation of a quenching complex, likely zeaxanthin bound to a protonated LHCX1, is responsible for the gradual rise in NPQ. Additionally, the model makes specific predictions for the light sequence dependence of xanthophyll concentrations that are in reasonable agreement with independent chromatography measurements taken during a specific light/dark sequence.
Collapse
Affiliation(s)
- Audrey H Short
- University of California Berkeley, United States of America
| | - Thomas Patrick Fay
- Department of Chemistry, University of California Berkeley Department of Chemistry, United States of America
| | - Thien Crisanto
- University of California Berkeley, United States of America
| | - Johanna Hall
- Georgia Institute of Technology, United States of America
| | - Collin J Steen
- Chemistry, University of California Berkeley, United States of America
| | | | - David T Limmer
- Chemistry, University of California Berkeley Department of Chemistry, United States of America
| | - Graham R. Fleming
- Department of Chemistry, University of California Berkeley College of Chemistry, United States of America
| |
Collapse
|
19
|
Baker CR, Stewart JJ, Amstutz CL, Ching LG, Johnson JD, Niyogi KK, Adams WW, Demmig‐Adams B. Genotype-dependent contribution of CBF transcription factors to long-term acclimation to high light and cool temperature. Plant Cell Environ 2022; 45:392-411. [PMID: 34799867 PMCID: PMC9299779 DOI: 10.1111/pce.14231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
When grown under cool temperature, winter annuals upregulate photosynthetic capacity as well as freezing tolerance. Here, the role of three cold-induced C-repeat-binding factor (CBF1-3) transcription factors in photosynthetic upregulation and freezing tolerance was examined in two Arabidopsis thaliana ecotypes originating from Italy (IT) or Sweden (SW), and their corresponding CBF1-3-deficient mutant lines it:cbf123 and sw:cbf123. Photosynthetic, morphological and freezing-tolerance phenotypes, as well as gene expression profiles, were characterized in plants grown from the seedling stage under different combinations of light level and temperature. Under high light and cool (HLC) growth temperature, a greater role of CBF1-3 in IT versus SW was evident from both phenotypic and transcriptomic data, especially with respect to photosynthetic upregulation and freezing tolerance of whole plants. Overall, features of SW were consistent with a different approach to HLC acclimation than seen in IT, and an ability of SW to reach the new homeostasis through the involvement of transcriptional controls other than CBF1-3. These results provide tools and direction for further mechanistic analysis of the transcriptional control of approaches to cold acclimation suitable for either persistence through brief cold spells or for maximisation of productivity in environments with continuous low temperatures.
Collapse
Affiliation(s)
- Christopher R. Baker
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jared J. Stewart
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Cynthia L. Amstutz
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Lindsey G. Ching
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jeffrey D. Johnson
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - William W. Adams
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Barbara Demmig‐Adams
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| |
Collapse
|
20
|
González-Grandío E, Álamos S, Zhang Y, Dalton-Roesler J, Niyogi KK, García HG, Quail PH. Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light. Front Plant Sci 2022; 13:803441. [PMID: 35251080 PMCID: PMC8891703 DOI: 10.3389/fpls.2022.803441] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/27/2022] [Indexed: 05/11/2023]
Abstract
As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.
Collapse
Affiliation(s)
- Eduardo González-Grandío
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
- *Correspondence: Eduardo González-Grandío,
| | - Simón Álamos
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States
| | - Yu Zhang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Jutta Dalton-Roesler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Hernán G. García
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Physics, University of California, Berkeley, Berkeley, CA, United States
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, United States
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, United States
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
- Peter H. Quail,
| |
Collapse
|
21
|
Wakao S, Niyogi KK. Chlamydomonas as a model for reactive oxygen species signaling and thiol redox regulation in the green lineage. Plant Physiol 2021; 187:687-698. [PMID: 35237823 PMCID: PMC8491031 DOI: 10.1093/plphys/kiab355] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/13/2021] [Indexed: 05/15/2023]
Abstract
One-sentence summary: Advances in proteomic and transcriptomic studies have made Chlamydomonas a powerful research model in redox and reactive oxygen species regulation with unique and overlapping mechanisms with plants.
Collapse
Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Author for communication: Senior author
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| |
Collapse
|
22
|
Anderson CM, Mattoon EM, Zhang N, Becker E, McHargue W, Yang J, Patel D, Dautermann O, McAdam SAM, Tarin T, Pathak S, Avenson TJ, Berry J, Braud M, Niyogi KK, Wilson M, Nusinow DA, Vargas R, Czymmek KJ, Eveland AL, Zhang R. High light and temperature reduce photosynthetic efficiency through different mechanisms in the C 4 model Setaria viridis. Commun Biol 2021; 4:1092. [PMID: 34531541 PMCID: PMC8446033 DOI: 10.1038/s42003-021-02576-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/03/2021] [Indexed: 11/09/2022] Open
Abstract
C4 plants frequently experience high light and high temperature conditions in the field, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour high light or high temperature treatment at photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in high light or high temperature treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to high light and high temperature. We provide a systematic analysis of high light and high temperature responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.
Collapse
Affiliation(s)
| | - Erin M Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO, USA.,Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO, USA
| | - Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Eric Becker
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Jiani Yang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Dhruv Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Oliver Dautermann
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Scott A M McAdam
- Purdue Center for Plant Biology, Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Tonantzin Tarin
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sunita Pathak
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Tom J Avenson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Jeffrey Berry
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Maxwell Braud
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Howard Hughes Medical Institute, Berkeley, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Rodrigo Vargas
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
| |
Collapse
|
23
|
Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK. Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009725. [PMID: 34492001 PMCID: PMC8448359 DOI: 10.1371/journal.pgen.1009725] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 03/02/2021] [Revised: 09/17/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
Collapse
Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Katharine Guan
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Wendy Schackwitz
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joshua Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Dhruv Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Robert M. Shih
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rachel M. Dent
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Mansi Chovatia
- Joint Genome Institute, Berkeley, California, United States of America
| | - Aditi Sharma
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joel Martin
- Joint Genome Institute, Berkeley, California, United States of America
| | - Chia-Lin Wei
- Joint Genome Institute, Berkeley, California, United States of America
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| |
Collapse
|
24
|
Alamos S, Reimer A, Niyogi KK, Garcia HG. Quantitative imaging of RNA polymerase II activity in plants reveals the single-cell basis of tissue-wide transcriptional dynamics. Nat Plants 2021; 7:1037-1049. [PMID: 34373604 PMCID: PMC8616715 DOI: 10.1038/s41477-021-00976-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/22/2021] [Indexed: 05/18/2023]
Abstract
The responses of plants to their environment are often dependent on the spatiotemporal dynamics of transcriptional regulation. While live-imaging tools have been used extensively to quantitatively capture rapid transcriptional dynamics in living animal cells, the lack of implementation of these technologies in plants has limited concomitant quantitative studies in this kingdom. Here, we applied the PP7 and MS2 RNA-labelling technologies for the quantitative imaging of RNA polymerase II activity dynamics in single cells of living plants as they respond to experimental treatments. Using this technology, we counted nascent RNA transcripts in real time in Nicotiana benthamiana (tobacco) and Arabidopsis thaliana. Examination of heat shock reporters revealed that plant tissues respond to external signals by modulating the proportion of cells that switch from an undetectable basal state to a high-transcription state, instead of modulating the rate of transcription across all cells in a graded fashion. This switch-like behaviour, combined with cell-to-cell variability in transcription rate, results in mRNA production variability spanning three orders of magnitude. We determined that cellular heterogeneity stems mainly from stochasticity intrinsic to individual alleles instead of variability in cellular composition. Together, our results demonstrate that it is now possible to quantitatively study the dynamics of transcriptional programs in single cells of living plants.
Collapse
Affiliation(s)
- Simon Alamos
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Physics, University of California Berkeley, Berkeley, CA, USA.
- Institute for Quantitative Biosciences-QB3, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
25
|
Ekwealor JTB, Clark TA, Dautermann O, Russell A, Ebrahimi S, Stark LR, Niyogi KK, Mishler BD. Natural ultraviolet radiation exposure alters photosynthetic biology and improves recovery from desiccation in a desert moss. J Exp Bot 2021; 72:4161-4179. [PMID: 33595636 DOI: 10.1093/jxb/erab051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/01/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Plants in dryland ecosystems experience extreme daily and seasonal fluctuations in light, temperature, and water availability. We used an in situ field experiment to uncover the effects of natural and reduced levels of ultraviolet radiation (UV) on maximum PSII quantum efficiency (Fv/Fm), relative abundance of photosynthetic pigments and antioxidants, and the transcriptome in the desiccation-tolerant desert moss Syntrichia caninervis. We tested the hypotheses that: (i) S. caninervis plants undergo sustained thermal quenching of light [non-photochemical quenching (NPQ)] while desiccated and after rehydration; (ii) a reduction of UV will result in improved recovery of Fv/Fm; but (iii) 1 year of UV removal will de-harden plants and increase vulnerability to UV damage, indicated by a reduction in Fv/Fm. All field-collected plants had extremely low Fv/Fm after initial rehydration but recovered over 8 d in lab-simulated winter conditions. UV-filtered plants had lower Fv/Fm during recovery, higher concentrations of photoprotective pigments and antioxidants such as zeaxanthin and tocopherols, and lower concentrations of neoxanthin and Chl b than plants exposed to near natural UV levels. Field-grown S. caninervis underwent sustained NPQ that took days to relax and for efficient photosynthesis to resume. Reduction of solar UV radiation adversely affected recovery of Fv/Fm following rehydration.
Collapse
Affiliation(s)
- Jenna T B Ekwealor
- Department of Integrative Biology, and University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Theresa A Clark
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Oliver Dautermann
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Sotodeh Ebrahimi
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Lloyd R Stark
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brent D Mishler
- Department of Integrative Biology, and University and Jepson Herbaria, University of California, Berkeley, CA, USA
| |
Collapse
|
26
|
Lu Y, Gan Q, Iwai M, Alboresi A, Burlacot A, Dautermann O, Takahashi H, Crisanto T, Peltier G, Morosinotto T, Melis A, Niyogi KK. Role of an ancient light-harvesting protein of PSI in light absorption and photoprotection. Nat Commun 2021; 12:679. [PMID: 33514722 PMCID: PMC7846763 DOI: 10.1038/s41467-021-20967-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/05/2021] [Indexed: 12/18/2022] Open
Abstract
Diverse algae of the red lineage possess chlorophyll a-binding proteins termed LHCR, comprising the PSI light-harvesting system, which represent an ancient antenna form that evolved in red algae and was acquired through secondary endosymbiosis. However, the function and regulation of LHCR complexes remain obscure. Here we describe isolation of a Nannochloropsis oceanica LHCR mutant, named hlr1, which exhibits a greater tolerance to high-light (HL) stress compared to the wild type. We show that increased tolerance to HL of the mutant can be attributed to alterations in PSI, making it less prone to ROS production, thereby limiting oxidative damage and favoring growth in HL. HLR1 deficiency attenuates PSI light-harvesting capacity and growth of the mutant under light-limiting conditions. We conclude that HLR1, a member of a conserved and broadly distributed clade of LHCR proteins, plays a pivotal role in a dynamic balancing act between photoprotection and efficient light harvesting for photosynthesis. LHCR proteins are ancient chlorophyll a-binding antennas that evolved in diverse algae of the red lineage. Here Lu et al. characterize a red lineage LHCR mutant and show reduced oxidative damage in high light but attenuated growth under low light, thus demonstrating how LHCR proteins impact the balance between photoprotection and light harvesting.
Collapse
Affiliation(s)
- Yandu Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, Hainan, China. .,Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
| | - Qinhua Gan
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, Hainan, China
| | - Masakazu Iwai
- Howard Hughes Medical Institute, 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
| | | | - Adrien Burlacot
- CEA, CNRS, Aix-Marseille Université, Institut de Biosciences et Biotechnologies Aix-Marseille, UMR 7265, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, CEA Cadarache, Saint-Paul-lezDurance, France
| | - Oliver Dautermann
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Hiroko Takahashi
- Department of Biochemistry and Molecular Biology, Graduate school of Science and Engineering, Saitama University, Saitama, Japan
| | - Thien Crisanto
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Gilles Peltier
- CEA, CNRS, Aix-Marseille Université, Institut de Biosciences et Biotechnologies Aix-Marseille, UMR 7265, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, CEA Cadarache, Saint-Paul-lezDurance, France
| | | | - Anastasios Melis
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, 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.
| |
Collapse
|
27
|
Steen CJ, Morris JM, Short AH, Niyogi KK, Fleming GR. Complex Roles of PsbS and Xanthophylls in the Regulation of Nonphotochemical Quenching in Arabidopsis thaliana under Fluctuating Light. J Phys Chem B 2020; 124:10311-10325. [PMID: 33166148 DOI: 10.1021/acs.jpcb.0c06265] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protection of photosystem II against damage from excess light by nonphotochemical quenching (NPQ) includes responses on a wide range of timescales. The onset of the various phases of NPQ overlap in time making it difficult to discern if they influence each other or involve different photophysical mechanisms. To unravel the complex relationship of the known actors in NPQ, we perform fluorescence lifetime snapshot measurements throughout multiple cycles of alternating 2 min periods of high light and darkness. By comparing the data with an empirically based mathematical model that describes both fast and slow quenching responses, we suggest that the rapidly reversible quenching response depends on the state of the slower response. By studying a series of Arabidopsis thaliana mutants, we find that removing zeaxanthin (Zea) or enhancing PsbS concentration, for example, influences the amplitudes of the slow quenching induction and recovery, but not the timescales. The plants' immediate response to high light appears independent of the illumination history, while PsbS and Zea have distinct roles in both quenching and recovery. We further identify two parameters in our model that predominately influence the recovery amplitude and propose that our approach may prove useful for screening new mutants or overexpressors with enhanced biomass yields under field conditions.
Collapse
Affiliation(s)
- Collin J Steen
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States
| | - Jonathan M Morris
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States.,Graduate Group in Applied Science & Technology, University of California, Berkeley, California 94720, United States
| | - Audrey H Short
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States.,Graduate Group in Biophysics, University of California, Berkeley, California 94720, United States
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Howard Hughes Medical Institute and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States.,Graduate Group in Applied Science & Technology, University of California, Berkeley, California 94720, United States.,Graduate Group in Biophysics, University of California, Berkeley, California 94720, United States
| |
Collapse
|
28
|
Hertle AP, García-Cerdán JG, Armbruster U, Shih R, Lee JJ, Wong W, Niyogi KK. A Sec14 domain protein is required for photoautotrophic growth and chloroplast vesicle formation in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2020; 117:9101-9111. [PMID: 32245810 PMCID: PMC7183190 DOI: 10.1073/pnas.1916946117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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] [Indexed: 01/29/2023] Open
Abstract
In eukaryotic photosynthetic organisms, the conversion of solar into chemical energy occurs in thylakoid membranes in the chloroplast. How thylakoid membranes are formed and maintained is poorly understood. However, previous observations of vesicles adjacent to the stromal side of the inner envelope membrane of the chloroplast suggest a possible role of membrane transport via vesicle trafficking from the inner envelope to the thylakoids. Here we show that the model plant Arabidopsis thaliana has a chloroplast-localized Sec14-like protein (CPSFL1) that is necessary for photoautotrophic growth and vesicle formation at the inner envelope membrane of the chloroplast. The cpsfl1 mutants are seedling lethal, show a defect in thylakoid structure, and lack chloroplast vesicles. Sec14 domain proteins are found only in eukaryotes and have been well characterized in yeast, where they regulate vesicle budding at the trans-Golgi network. Like the yeast Sec14p, CPSFL1 binds phosphatidylinositol phosphates (PIPs) and phosphatidic acid (PA) and acts as a phosphatidylinositol transfer protein in vitro, and expression of Arabidopsis CPSFL1 can complement the yeast sec14 mutation. CPSFL1 can transfer PIP into PA-rich membrane bilayers in vitro, suggesting that CPSFL1 potentially facilitates vesicle formation by trafficking PA and/or PIP, known regulators of membrane trafficking between organellar subcompartments. These results underscore the role of vesicles in thylakoid biogenesis and/or maintenance. CPSFL1 appears to be an example of a eukaryotic cytosolic protein that has been coopted for a function in the chloroplast, an organelle derived from endosymbiosis of a cyanobacterium.
Collapse
Affiliation(s)
- Alexander P Hertle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
| | - José G García-Cerdán
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Ute Armbruster
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Robert Shih
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jimmy J Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Winnie Wong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| |
Collapse
|
29
|
Onoa B, Fukuda S, Iwai M, Bustamante C, Niyogi KK. Atomic Force Microscopy Visualizes Mobility of Photosynthetic Proteins in Grana Thylakoid Membranes. Biophys J 2020; 118:1876-1886. [PMID: 32224302 PMCID: PMC7175462 DOI: 10.1016/j.bpj.2020.02.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/10/2020] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Thylakoid membranes in chloroplasts contain photosynthetic protein complexes that convert light energy into chemical energy. Photosynthetic protein complexes are considered to undergo structural reorganization to maintain the efficiency of photochemical reactions. A detailed description of the mobility of photosynthetic complexes in real time is necessary to understand how macromolecular organization of the membrane is altered by environmental fluctuations. Here, we used high-speed atomic force microscopy to visualize and characterize the in situ mobility of individual protein complexes in grana thylakoid membranes isolated from Spinacia oleracea. Our observations reveal that these membranes can harbor complexes with at least two distinctive classes of mobility. A large fraction of grana membranes contained proteins with quasistatic mobility exhibiting molecular displacements smaller than 10 nm2. In the remaining fraction, the protein mobility is variable with molecular displacements of up to 100 nm2. This visualization at high spatiotemporal resolution enabled us to estimate an average diffusion coefficient of ∼1 nm2 s-1. Interestingly, both confined and Brownian diffusion models could describe the protein mobility of the second group of membranes. We also provide the first direct evidence, to our knowledge, of rotational diffusion of photosynthetic complexes. The rotational diffusion of photosynthetic complexes could be an adaptive response to the high protein density in the membrane to guarantee the efficiency of electron transfer reactions. This characterization of the mobility of individual photosynthetic complexes in grana membranes establishes a foundation that could be adapted to study the dynamics of the complexes inside intact and photosynthetically functional thylakoid membranes to be able to understand its structural responses to diverse environmental fluctuations.
Collapse
Affiliation(s)
- Bibiana Onoa
- Howard Hughes Medical Institute, University of California, Berkeley, California.
| | - Shingo Fukuda
- Howard Hughes Medical Institute, University of California, Berkeley, California
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California; Department of Plant and Microbial Biology, University of California, Berkeley, California
| | - Carlos Bustamante
- Howard Hughes Medical Institute, University of California, Berkeley, California; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California; Jason L. Choy Laboratory of Single Molecule Biophysics, University of California, Berkeley, California; Department of Molecular and Cell Biology, University of California, Berkeley, California; Department of Physics, University of California, Berkeley, California; Kavli Energy NanoScience Institute, Lawrence Berkeley National Laboratory, University of California, Berkeley, California
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, University of California, Berkeley, California; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California; Department of Plant and Microbial Biology, University of California, Berkeley, California.
| |
Collapse
|
30
|
Arsenault EA, Yoneda Y, Iwai M, Niyogi KK, Fleming GR. Vibronic mixing enables ultrafast energy flow in light-harvesting complex II. Nat Commun 2020; 11:1460. [PMID: 32193383 PMCID: PMC7081214 DOI: 10.1038/s41467-020-14970-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [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: 09/12/2019] [Accepted: 02/12/2020] [Indexed: 11/09/2022] Open
Abstract
Since the discovery of quantum beats in the two-dimensional electronic spectra of photosynthetic pigment-protein complexes over a decade ago, the origin and mechanistic function of these beats in photosynthetic light-harvesting has been extensively debated. The current consensus is that these long-lived oscillatory features likely result from electronic-vibrational mixing, however, it remains uncertain if such mixing significantly influences energy transport. Here, we examine the interplay between the electronic and nuclear degrees of freedom (DoF) during the excitation energy transfer (EET) dynamics of light-harvesting complex II (LHCII) with two-dimensional electronic-vibrational spectroscopy. Particularly, we show the involvement of the nuclear DoF during EET through the participation of higher-lying vibronic chlorophyll states and assign observed oscillatory features to specific EET pathways, demonstrating a significant step in mapping evolution from energy to physical space. These frequencies correspond to known vibrational modes of chlorophyll, suggesting that electronic-vibrational mixing facilitates rapid EET over moderately size energy gaps.
Collapse
Affiliation(s)
- Eric A Arsenault
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Yoneda
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Kavli Energy Nanoscience Institute at Berkeley, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Roth MS, Westcott DJ, Iwai M, Niyogi KK. Hexokinase is necessary for glucose-mediated photosynthesis repression and lipid accumulation in a green alga. Commun Biol 2019; 2:347. [PMID: 31552300 PMCID: PMC6753101 DOI: 10.1038/s42003-019-0577-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 05/15/2019] [Accepted: 08/14/2019] [Indexed: 12/24/2022] Open
Abstract
Global primary production is driven largely by oxygenic photosynthesis, with algae as major contributors. The green alga Chromochloris zofingiensis reversibly switches off photosynthesis in the presence of glucose in the light and augments production of biofuel precursors (triacylglycerols) and the high-value antioxidant astaxanthin. Here we used forward genetics to reveal that this photosynthetic and metabolic switch is mediated by the glycolytic enzyme hexokinase (CzHXK1). In contrast to wild-type, glucose-treated hxk1 mutants do not shut off photosynthesis or accumulate astaxanthin, triacylglycerols, or cytoplasmic lipid droplets. We show that CzHXK1 is critical for the regulation of genes related to photosynthesis, ketocarotenoid synthesis and fatty acid biosynthesis. Sugars play fundamental regulatory roles in gene expression, physiology, metabolism, and growth in plants and animals, and we introduce a relatively simple, emerging model system to investigate conserved eukaryotic sugar sensing and signaling at the base of the green lineage.
Collapse
Affiliation(s)
- Melissa S. Roth
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Daniel J. Westcott
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Masakazu Iwai
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Krishna K. Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102 USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| |
Collapse
|
33
|
Gabilly ST, Baker CR, Wakao S, Crisanto T, Guan K, Bi K, Guiet E, Guadagno CR, Niyogi KK. Regulation of photoprotection gene expression in Chlamydomonas by a putative E3 ubiquitin ligase complex and a homolog of CONSTANS. Proc Natl Acad Sci U S A 2019; 116:17556-17562. [PMID: 31405963 PMCID: PMC6717296 DOI: 10.1073/pnas.1821689116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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] [Indexed: 12/22/2022] Open
Abstract
Photosynthetic organisms use nonphotochemical quenching (NPQ) mechanisms to dissipate excess absorbed light energy and protect themselves from photooxidation. In the model green alga Chlamydomonas reinhardtii, the capacity for rapidly reversible NPQ (qE) is induced by high light, blue light, and UV light via increased expression of LHCSR and PSBS genes that are necessary for qE. Here, we used a forward genetics approach to identify SPA1 and CUL4, components of a putative green algal E3 ubiquitin ligase complex, as critical factors in a signaling pathway that controls light-regulated expression of the LHCSR and PSBS genes in C. reinhardtii The spa1 and cul4 mutants accumulate increased levels of LHCSR1 and PSBS proteins in high light, and unlike the wild type, they express LHCSR1 and exhibit qE capacity even when grown in low light. The spa1-1 mutation resulted in constitutively high expression of LHCSR and PSBS RNAs in both low light and high light. The qE and gene expression phenotypes of spa1-1 are blocked by mutation of CrCO, a B-box Zn-finger transcription factor that is a homolog of CONSTANS, which controls flowering time in plants. CONSTANS-like cis-regulatory sequences were identified proximal to the qE genes, consistent with CrCO acting as a direct activator of qE gene expression. We conclude that SPA1 and CUL4 are components of a conserved E3 ubiquitin ligase that acts upstream of CrCO, whose regulatory function is wired differently in C. reinhardtii to control qE capacity via cis-regulatory CrCO-binding sites at key photoprotection genes.
Collapse
Affiliation(s)
- Stéphane T Gabilly
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Christopher R Baker
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Setsuko Wakao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Thien Crisanto
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Katharine Guan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Ke Bi
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Elodie Guiet
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Carmela R Guadagno
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Iwai M, Grob P, Iavarone AT, Nogales E, Niyogi KK. A unique supramolecular organization of photosystem I in the moss Physcomitrella patens. Nat Plants 2018; 4:904-909. [PMID: 30374090 PMCID: PMC7806276 DOI: 10.1038/s41477-018-0271-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/05/2018] [Indexed: 05/03/2023]
Abstract
The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes1,2. Here, we show a novel supramolecular organization of photosystem I (PSI) in the moss Physcomitrella patens by single-particle cryo-electron microscopy. The moss-specific light-harvesting complex (LHC) protein Lhcb9 is involved in this PSI supercomplex, which has been shown to have a molecular density similar to that of the green alga Chlamydomonas reinhardtii3. Our results show that the structural organization is unexpectedly different-two rows of the LHCI belt exist as in C. reinhardtii4, but the outer one is shifted toward the PsaK side. Furthermore, one trimeric LHC protein and one monomeric LHC protein position alongside PsaL/K, filling the gap between these subunits and the outer LHCI belt. We provide evidence showing that Lhcb9 is a key factor, acting as a linkage between the PSI core and the outer LHCI belt to form the unique supramolecular organization of the PSI supercomplex in P. patens.
Collapse
Affiliation(s)
- Masakazu Iwai
- 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.
| | - Patricia Grob
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, CA, USA
| | - Eva Nogales
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Krishna K Niyogi
- 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.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
| |
Collapse
|
36
|
Iwai M, Roth MS, Niyogi KK. Subdiffraction-resolution live-cell imaging for visualizing thylakoid membranes. Plant J 2018; 96:233-243. [PMID: 29982996 PMCID: PMC6150804 DOI: 10.1111/tpj.14021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 06/01/2018] [Revised: 06/18/2018] [Accepted: 06/25/2018] [Indexed: 05/19/2023]
Abstract
The chloroplast is the chlorophyll-containing organelle that produces energy through photosynthesis. Within the chloroplast is an intricate network of thylakoid membranes containing photosynthetic membrane proteins that mediate electron transport and generate chemical energy. Historically, electron microscopy (EM) has been a powerful tool for visualizing the macromolecular structure and organization of thylakoid membranes. However, an understanding of thylakoid membrane dynamics remains elusive because EM requires fixation and sectioning. To improve our knowledge of thylakoid membrane dynamics we need to consider at least two issues: (i) the live-cell imaging conditions needed to visualize active processes in vivo; and (ii) the spatial resolution required to differentiate the characteristics of thylakoid membranes. Here, we utilize three-dimensional structured illumination microscopy (3D-SIM) to explore the optimal imaging conditions for investigating the dynamics of thylakoid membranes in living plant and algal cells. We show that 3D-SIM is capable of examining broad characteristics of thylakoid structures in chloroplasts of the vascular plant Arabidopsis thaliana and distinguishing the structural differences between wild-type and mutant strains. Using 3D-SIM, we also visualize thylakoid organization in whole cells of the green alga Chlamydomonas reinhardtii. These data reveal that high light intensity changes thylakoid membrane structure in C. reinhardtii. Moreover, we observed the green alga Chromochloris zofingiensis and the moss Physcomitrella patens to show the applicability of 3D-SIM. This study demonstrates that 3D-SIM is a promising approach for studying the dynamics of thylakoid membranes in photoautotrophic organisms during photoacclimation processes.
Collapse
Affiliation(s)
- Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720-3102, USA
- Contact Author: Masakazu Iwai
| | - Melissa S. Roth
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720-3102, USA
| | - Krishna K. Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720-3102, USA
- For correspondence ( or )
| |
Collapse
|
37
|
Park S, Fischer AL, Steen CJ, Iwai M, Morris JM, Walla PJ, Niyogi KK, Fleming GR. Chlorophyll-Carotenoid Excitation Energy Transfer in High-Light-Exposed Thylakoid Membranes Investigated by Snapshot Transient Absorption Spectroscopy. J Am Chem Soc 2018; 140:11965-11973. [DOI: 10.1021/jacs.8b04844] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Soomin Park
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States
| | - Alexandra L. Fischer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States
| | - Collin J. Steen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Jonathan M. Morris
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States
| | - Peter Jomo Walla
- Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States
- Department for Biophysical Chemistry, Technische Universität Braunschweig, Institute for Physical and Theoretical Chemistry, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany
- Department of Neurobiology, Research Group Biomolecular Spectroscopy and Single Molecule Detection, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Krishna K. Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, United States
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute, Berkeley, California 94720, United States
| |
Collapse
|
38
|
Wittkopp TM, Saroussi S, Yang W, Johnson X, Kim RG, Heinnickel ML, Russell JJ, Phuthong W, Dent RM, Broeckling CD, Peers G, Lohr M, Wollman FA, Niyogi KK, Grossman AR. GreenCut protein CPLD49 of Chlamydomonas reinhardtii associates with thylakoid membranes and is required for cytochrome b 6 f complex accumulation. Plant J 2018; 94:1023-1037. [PMID: 29602195 DOI: 10.1111/tpj.13915] [Citation(s) in RCA: 3] [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: 10/27/2017] [Revised: 02/23/2018] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
The GreenCut encompasses a suite of nucleus-encoded proteins with orthologs among green lineage organisms (plants, green algae), but that are absent or poorly conserved in non-photosynthetic/heterotrophic organisms. In Chlamydomonas reinhardtii, CPLD49 (Conserved in Plant Lineage and Diatoms49) is an uncharacterized GreenCut protein that is critical for maintaining normal photosynthetic function. We demonstrate that a cpld49 mutant has impaired photoautotrophic growth under high-light conditions. The mutant exhibits a nearly 90% reduction in the level of the cytochrome b6 f complex (Cytb6 f), which impacts linear and cyclic electron transport, but does not compromise the ability of the strain to perform state transitions. Furthermore, CPLD49 strongly associates with thylakoid membranes where it may be part of a membrane protein complex with another GreenCut protein, CPLD38; a mutant null for CPLD38 also impacts Cytb6 f complex accumulation. We investigated several potential functions of CPLD49, with some suggested by protein homology. Our findings are congruent with the hypothesis that CPLD38 and CPLD49 are part of a novel thylakoid membrane complex that primarily modulates accumulation, but also impacts the activity of the Cytb6 f complex. Based on motifs of CPLD49 and the activities of other CPLD49-like proteins, we suggest a role for this putative dehydrogenase in the synthesis of a lipophilic thylakoid membrane molecule or cofactor that influences the assembly and activity of Cytb6 f.
Collapse
Affiliation(s)
- Tyler M Wittkopp
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Wenqiang Yang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Xenie Johnson
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, CEA Cadarache, Saint Paul lez Durance, France
| | - Rick G Kim
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Mark L Heinnickel
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - James J Russell
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Witchukorn Phuthong
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Rachel M Dent
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Martin Lohr
- Institut für Molekulare Physiologie - Pflanzenbiochemie, Johannes Gutenberg-Universität, 55099, Mainz, Germany
| | | | - Krishna K Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| |
Collapse
|
39
|
Głowacka K, Kromdijk J, Kucera K, Xie J, Cavanagh AP, Leonelli L, Leakey ADB, Ort DR, Niyogi KK, Long SP. Photosystem II Subunit S overexpression increases the efficiency of water use in a field-grown crop. Nat Commun 2018; 9:868. [PMID: 29511193 PMCID: PMC5840416 DOI: 10.1038/s41467-018-03231-x] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/26/2018] [Indexed: 12/29/2022] Open
Abstract
Insufficient water availability for crop production is a mounting barrier to achieving the 70% increase in food production that will be needed by 2050. One solution is to develop crops that require less water per unit mass of production. Water vapor transpires from leaves through stomata, which also facilitate the influx of CO2 during photosynthetic assimilation. Here, we hypothesize that Photosystem II Subunit S (PsbS) expression affects a chloroplast-derived signal for stomatal opening in response to light, which can be used to improve water-use efficiency. Transgenic tobacco plants with a range of PsbS expression, from undetectable to 3.7 times wild-type are generated. Plants with increased PsbS expression show less stomatal opening in response to light, resulting in a 25% reduction in water loss per CO2 assimilated under field conditions. Since the role of PsbS is universal across higher plants, this manipulation should be effective across all crops.
Collapse
Affiliation(s)
- Katarzyna Głowacka
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
| | - Johannes Kromdijk
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Katherine Kucera
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Jiayang Xie
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Amanda P Cavanagh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Lauriebeth Leonelli
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Andrew D B Leakey
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
- Photosynthesis Research Unit, US Department of Agriculture-Agricultural Research Service, University of Illinois, Urbana, IL, 61801, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Stephen P Long
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
- Lancaster Environment Centre, University of Lancaster, Lancaster, LA1 1YX, UK.
| |
Collapse
|
40
|
Onoa B, Fukuda S, Iwai M, Niyogi KK, Bustamante C. Dynamic Characterization of Photosynthetic Proteins on Thylakoid Membranes by High-Speed AFM. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
41
|
Malnoë A, Schultink A, Shahrasbi S, Rumeau D, Havaux M, Niyogi KK. The Plastid Lipocalin LCNP Is Required for Sustained Photoprotective Energy Dissipation in Arabidopsis. Plant Cell 2018; 30:196-208. [PMID: 29233855 PMCID: PMC5810567 DOI: 10.1105/tpc.17.00536] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 11/01/2017] [Accepted: 12/08/2017] [Indexed: 05/18/2023]
Abstract
Light utilization is finely tuned in photosynthetic organisms to prevent cellular damage. The dissipation of excess absorbed light energy, a process termed nonphotochemical quenching (NPQ), plays an important role in photoprotection. Little is known about the sustained or slowly reversible form(s) of NPQ and whether they are photoprotective, in part due to the lack of mutants. The Arabidopsis thaliana suppressor of quenching1 (soq1) mutant exhibits enhanced sustained NPQ, which we term qH. To identify molecular players involved in qH, we screened for suppressors of soq1 and isolated mutants affecting either chlorophyllide a oxygenase or the chloroplastic lipocalin, now renamed plastid lipocalin (LCNP). Analysis of the mutants confirmed that qH is localized to the peripheral antenna (LHCII) of photosystem II and demonstrated that LCNP is required for qH, either directly (by forming NPQ sites) or indirectly (by modifying the LHCII membrane environment). qH operates under stress conditions such as cold and high light and is photoprotective, as it reduces lipid peroxidation levels. We propose that, under stress conditions, LCNP protects the thylakoid membrane by enabling sustained NPQ in LHCII, thereby preventing singlet oxygen stress.
Collapse
Affiliation(s)
- Alizée Malnoë
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Alex Schultink
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Sanya Shahrasbi
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Dominique Rumeau
- CEA, CNRS UMR 7265, Biologie Végétale et Microbiologie Environnementales, Aix-Marseille Université, Laboratoire d'Ecophysiologie Moléculaire des Plantes, Saint-Paul-lez-Durance 13108, France
| | - Michel Havaux
- CEA, CNRS UMR 7265, Biologie Végétale et Microbiologie Environnementales, Aix-Marseille Université, Laboratoire d'Ecophysiologie Moléculaire des Plantes, Saint-Paul-lez-Durance 13108, France
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| |
Collapse
|
42
|
Park S, Fischer AL, Li Z, Bassi R, Niyogi KK, Fleming GR. Snapshot Transient Absorption Spectroscopy of Carotenoid Radical Cations in High-Light-Acclimating Thylakoid Membranes. J Phys Chem Lett 2017; 8:5548-5554. [PMID: 29083901 DOI: 10.1021/acs.jpclett.7b02486] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nonphotochemical quenching mechanisms regulate light harvesting in oxygenic photosynthesis. Measurement techniques for nonphotochemical quenching have typically focused on downstream effects of quenching, such as measuring reduced chlorophyll fluorescence. Here, to directly measure a species involved in quenching, we report snapshot transient absorption (TA) spectroscopy, which rapidly tracks carotenoid radical cation signals as samples acclimate to excess light. The formation of zeaxanthin radical cations, which is possible evidence of zeaxanthin-chlorophyll charge-transfer (CT) quenching, was investigated in spinach thylakoids. Together with fluorescence lifetime snapshot data and time-resolved high-performance liquid chromatography (HPLC) measurements, snapshot TA reveals that Zea•+ formation is closely related to energy-dependent quenching (qE) in nonphotochemical quenching. Quantitative and dynamic information on CT quenching discussed in this work give insight into the design principles of photoprotection in natural photosynthesis.
Collapse
Affiliation(s)
- Soomin Park
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute , Berkeley, California 94720, United States
| | - Alexandra L Fischer
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute , Berkeley, California 94720, United States
| | - Zhirong Li
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Universitá di Verona , Strada Le Grazie, I-37134 Verona, Italia
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California , Berkeley, California 94720, United States
| | - Graham R Fleming
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy Nanoscience Institute , Berkeley, California 94720, United States
| |
Collapse
|
43
|
Abstract
Although sunlight provides the energy necessary for plants to survive and grow, light can also damage reaction centers of photosystem II (PSII) and reduce photochemical efficiency. To prevent damage, plants possess photoprotective mechanisms that dissipate excess excitation. A subset of these mechanisms is collectively referred to as NPQ, or nonphotochemical quenching of chlorophyll a fluorescence. The regulation of NPQ is intrinsically linked to the cycling of xanthophylls that affects the kinetics and extent of the photoprotective response. The violaxanthin cycle (VAZ cycle) and the lutein epoxide cycle (LxL cycle) are two xanthophyll cycles found in vascular plants. The VAZ cycle has been studied extensively, owing in large part to its presence in model plant species where mutants are available to aid in its characterization. In contrast, the LxL cycle is not found in model plants, and its role in photosynthetic processes has been more difficult to define. To address this challenge, we introduced the LxL cycle into Arabidopsis thaliana and functionally isolated it from the VAZ cycle. Using these plant lines, we showed an increase in dark-acclimated PSII efficiency associated with Lx accumulation and demonstrated that violaxanthin deepoxidase is responsible for the light-driven deepoxidation of Lx. Conversion of Lx to L was reversible during periods of low light and occurred considerably faster than rates previously described in nonmodel species. Finally, we present clear evidence of the LxL cycle's role in modulating a rapid component of NPQ that is necessary to prevent photoinhibition in excess light.
Collapse
Affiliation(s)
- Lauriebeth Leonelli
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Matthew D Brooks
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720;
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| |
Collapse
|
44
|
Leuenberger M, Morris JM, Chan AM, Leonelli L, Niyogi KK, Fleming GR. Dissecting and modeling zeaxanthin- and lutein-dependent nonphotochemical quenching in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2017; 114:E7009-E7017. [PMID: 28652334 PMCID: PMC5565437 DOI: 10.1073/pnas.1704502114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 11/18/2022] Open
Abstract
Photosynthetic organisms use various photoprotective mechanisms to dissipate excess photoexcitation as heat in a process called nonphotochemical quenching (NPQ). Regulation of NPQ allows for a rapid response to changes in light intensity and in vascular plants, is primarily triggered by a pH gradient across the thylakoid membrane (∆pH). The response is mediated by the PsbS protein and various xanthophylls. Time-correlated single-photon counting (TCSPC) measurements were performed on Arabidopsis thaliana to quantify the dependence of the response of NPQ to changes in light intensity on the presence and accumulation of zeaxanthin and lutein. Measurements were performed on WT and mutant plants deficient in one or both of the xanthophylls as well as a transgenic line that accumulates lutein via an engineered lutein epoxide cycle. Changes in the response of NPQ to light acclimation in WT and mutant plants were observed between two successive light acclimation cycles, suggesting that the character of the rapid and reversible response of NPQ in fully dark-acclimated plants is substantially different from in conditions plants are likely to experience caused by changes in light intensity during daylight. Mathematical models of the response of zeaxanthin- and lutein-dependent reversible NPQ were constructed that accurately describe the observed differences between the light acclimation periods. Finally, the WT response of NPQ was reconstructed from isolated components present in mutant plants with a single common scaling factor, which enabled deconvolution of the relative contributions of zeaxanthin- and lutein-dependent NPQ.
Collapse
Affiliation(s)
- Michelle Leuenberger
- Department of Chemistry, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Kavli Energy Nanoscience Institute, Berkeley, CA 94720
| | - Jonathan M Morris
- Department of Chemistry, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Kavli Energy Nanoscience Institute, Berkeley, CA 94720
- Graduate Group in Applied Science & Technology, University of California, Berkeley, CA 94720
| | - Arnold M Chan
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Lauriebeth Leonelli
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, CA 94720;
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Kavli Energy Nanoscience Institute, Berkeley, CA 94720
- Graduate Group in Applied Science & Technology, University of California, Berkeley, CA 94720
| |
Collapse
|
45
|
Niyogi KK. Editorial overview: Physiology and metabolism: Light responses from photoreceptors to photosynthesis and photoprotection. Curr Opin Plant Biol 2017; 37:iv-vi. [PMID: 28606394 DOI: 10.1016/j.pbi.2017.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720-3102, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
46
|
Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Simpson JP, TerBush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C. Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. PLoS Genet 2017; 13:e1006802. [PMID: 28542203 PMCID: PMC5441573 DOI: 10.1371/journal.pgen.1006802] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1003064.].
Collapse
|
47
|
Xu CS, Hayworth KJ, Lu Z, Grob P, Hassan AM, García-Cerdán JG, Niyogi KK, Nogales E, Weinberg RJ, Hess HF. Enhanced FIB-SEM systems for large-volume 3D imaging. eLife 2017; 6. [PMID: 28500755 PMCID: PMC5476429 DOI: 10.7554/elife.25916] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 106 µm3. These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology. DOI:http://dx.doi.org/10.7554/eLife.25916.001 Precise three-dimensional imaging can help make sense of microscopic details in biology. These images are usually built up from many two-dimensional images stacked on top of each other. One approach for examining particularly fine details, such as the connections between nerve cells in the brain, is called focused ion beam scanning electron microscopy (or FIB-SEM for short). This approach works by creating an image of the surface layer of a sample, which is then stripped away using a beam of charged particles to reveal the layer beneath. The new surface can then be imaged and so on, through the whole sample. Unfortunately, FIB-SEM devices are currently slow and can only run for a short time, leading to a lack of continuity in the stack of images. FIB-SEM would allow faster, more accurate and detailed studies of connections between brain cells, and other elaborate biological systems, if the technology could be made faster and more reliable over months of continuous operation. The current technical challenge is to create a system that can, for example, successfully image and analyse all the connections between the more than 100 thousand cells that make up the brain of a fruit fly – a common model organism in neurobiology. Xu et al. aimed to create a technique to image a complete fly brain, with gaps of just 8 nanometres between each image in a stack, within a reasonable timeframe. By improving how FIB-SEM signals are detected, making use of advances in ion beam controls, and by engineering ways to recover from system malfunctions, Xu et al. developed an enhanced FIB-SEM device. To demonstrate its value, the new technology was used to create images of a third of a fruit fly’s brain, parts of a mouse’s brain, and cells of a single-celled alga called Chlamydomonas reinhardtii. The results show that large and complex samples can be successfully imaged in their entirety to adequate detail, enabling high-quality reconstruction of the connections between nerve cells. The level of detail, which can be further increased for smaller samples, offers advantages in precision and image quality over other comparable techniques. As well as helping to study the brain, this approach could also be used to examine details inside cells. Future work to advance this technology will enable larger and more complete imaging of elaborate biological structures. DOI:http://dx.doi.org/10.7554/eLife.25916.002
Collapse
Affiliation(s)
- C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Kenneth J Hayworth
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Zhiyuan Lu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Department of Psychology and Neuroscience, Dalhousie University, Halifax, Canada
| | - Patricia Grob
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, United States
| | - Ahmed M Hassan
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, United States
| | - José G García-Cerdán
- Howard Hughes Medical Institute, Plant and Microbial Biology Department, University of California, Berkeley, United States
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Plant and Microbial Biology Department, University of California, Berkeley, United States.,Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Eva Nogales
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, United States.,Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Richard J Weinberg
- Department of Cell Biology and Physiology, University of North Carolina, North Carolina, United States
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| |
Collapse
|
48
|
Kirst H, Gabilly ST, Niyogi KK, Lemaux PG, Melis A. Photosynthetic antenna engineering to improve crop yields. Planta 2017; 245:1009-1020. [PMID: 28188423 DOI: 10.1007/s00425-017-2659-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [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: 01/09/2017] [Accepted: 02/03/2017] [Indexed: 05/05/2023]
Abstract
MAIN CONCLUSION Evidence shows that decreasing the light-harvesting antenna size of the photosystems in tobacco helps to increase the photosynthetic productivity and plant canopy biomass accumulation under high-density cultivation conditions. Decreasing, or truncating, the chlorophyll antenna size of the photosystems can theoretically improve photosynthetic solar energy conversion efficiency and productivity in mass cultures of algae or plants by up to threefold. A Truncated Light-harvesting chlorophyll Antenna size (TLA), in all classes of photosynthetic organisms, would help to alleviate excess absorption of sunlight and the ensuing wasteful non-photochemical dissipation of excitation energy. Thus, solar-to-biomass energy conversion efficiency and photosynthetic productivity in high-density cultures can be increased. Applicability of the TLA concept was previously shown in green microalgae and cyanobacteria, but it has not yet been demonstrated in crop plants. In this work, the TLA concept was applied in high-density tobacco canopies. The work showed a 25% improvement in stem and leaf biomass accumulation for the TLA tobacco canopies over that measured with their wild-type counterparts grown under the same ambient conditions. Distinct canopy appearance differences are described between the TLA and wild type tobacco plants. Findings are discussed in terms of concept application to crop plants, leading to significant improvements in agronomy, agricultural productivity, and application of photosynthesis for the generation of commodity products in crop leaves.
Collapse
Affiliation(s)
- Henning Kirst
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, MC-3102, Berkeley, CA, 94720-3102, USA
| | - Stéphane T Gabilly
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, MC-3102, Berkeley, CA, 94720-3102, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, MC-3102, Berkeley, CA, 94720-3102, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peggy G Lemaux
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, MC-3102, Berkeley, CA, 94720-3102, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, MC-3102, Berkeley, CA, 94720-3102, USA.
| |
Collapse
|
49
|
Dall'Osto L, Cazzaniga S, Bressan M, Paleček D, Židek K, Niyogi KK, Fleming GR, Zigmantas D, Bassi R. Two mechanisms for dissipation of excess light in monomeric and trimeric light-harvesting complexes. Nat Plants 2017; 3:17033. [PMID: 28394312 DOI: 10.1038/nplants.2017.33] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/14/2017] [Indexed: 05/19/2023]
Abstract
Oxygenic photoautotrophs require mechanisms for rapidly matching the level of chlorophyll excited states from light harvesting with the rate of electron transport from water to carbon dioxide. These photoprotective reactions prevent formation of reactive excited states and photoinhibition. The fastest response to excess illumination is the so-called non-photochemical quenching which, in higher plants, requires the luminal pH sensor PsbS and other yet unidentified components of the photosystem II antenna. Both trimeric light-harvesting complex II (LHCII) and monomeric LHC proteins have been indicated as site(s) of the heat-dissipative reactions. Different mechanisms have been proposed: energy transfer to a lutein quencher in trimers, formation of a zeaxanthin radical cation in monomers. Here, we report on the construction of a mutant lacking all monomeric LHC proteins but retaining LHCII trimers. Its non-photochemical quenching induction rate was substantially slower with respect to the wild type. A carotenoid radical cation signal was detected in the wild type, although it was lost in the mutant. We conclude that non-photochemical quenching is catalysed by two independent mechanisms, with the fastest activated response catalysed within monomeric LHC proteins depending on both zeaxanthin and lutein and on the formation of a radical cation. Trimeric LHCII was responsible for the slowly activated quenching component whereas inclusion in supercomplexes was not required. This latter activity does not depend on lutein nor on charge transfer events, whereas zeaxanthin was essential.
Collapse
Affiliation(s)
- Luca Dall'Osto
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Stefano Cazzaniga
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Mauro Bressan
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - David Paleček
- Department of Chemical Physics, Lund University, Getingevägen 60, Lund S-22241, Sweden
| | - Karel Židek
- Department of Chemical Physics, Lund University, Getingevägen 60, Lund S-22241, Sweden
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley 94720-3102, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley 94720, California, USA
| | - Graham R Fleming
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley 94720, California, USA
- Graduate Group in Applied Science and Technology, University of California, Berkeley 94720, California, USA
- Department of Chemistry, Hildebrand B77, University of California, Berkeley 94720-1460, California, USA
| | - Donatas Zigmantas
- Department of Chemical Physics, Lund University, Getingevägen 60, Lund S-22241, Sweden
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134 Verona, Italy
- Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione delle Piante (IPP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Firenze, Italy
| |
Collapse
|
50
|
Kromdijk J, Głowacka K, Leonelli L, Gabilly ST, Iwai M, Niyogi KK, Long SP. Improving photosynthesis and crop productivity by accelerating recovery from photoprotection. Science 2016; 354:857-861. [PMID: 27856901 DOI: 10.1126/science.aai8878] [Citation(s) in RCA: 650] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 09/28/2016] [Indexed: 01/06/2023]
Abstract
Crop leaves in full sunlight dissipate damaging excess absorbed light energy as heat. When sunlit leaves are shaded by clouds or other leaves, this protective dissipation continues for many minutes and reduces photosynthesis. Calculations have shown that this could cost field crops up to 20% of their potential yield. Here, we describe the bioengineering of an accelerated response to natural shading events in Nicotiana (tobacco), resulting in increased leaf carbon dioxide uptake and plant dry matter productivity by about 15% in fluctuating light. Because the photoprotective mechanism that has been altered is common to all flowering plants and crops, the findings provide proof of concept for a route to obtaining a sustainable increase in productivity for food crops and a much-needed yield jump.
Collapse
MESH Headings
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Bioengineering
- Carbon Dioxide/metabolism
- Crops, Agricultural/genetics
- Crops, Agricultural/growth & development
- Crops, Agricultural/metabolism
- Crops, Agricultural/radiation effects
- Darkness
- Light-Harvesting Protein Complexes/genetics
- Light-Harvesting Protein Complexes/metabolism
- Magnoliopsida/genetics
- Magnoliopsida/growth & development
- Magnoliopsida/metabolism
- Magnoliopsida/radiation effects
- Oxidoreductases/genetics
- Oxidoreductases/metabolism
- Photosynthesis
- Photosystem II Protein Complex/genetics
- Photosystem II Protein Complex/metabolism
- Plant Leaves/growth & development
- Plant Leaves/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- Plants, Genetically Modified/metabolism
- Plants, Genetically Modified/radiation effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sunlight
- Nicotiana/genetics
- Nicotiana/growth & development
- Nicotiana/metabolism
- Nicotiana/radiation effects
Collapse
Affiliation(s)
- Johannes Kromdijk
- Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Katarzyna Głowacka
- Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL 61801, USA.
- Institute of Plant Genetics, Polish Academy of Sciences, Ulica Strzeszyńska 34, 60-479 Poznań, Poland
| | - Lauriebeth Leonelli
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, 111 Koshland Hall, University of California Berkeley, Berkeley, CA 94720-3102, USA
| | - Stéphane T Gabilly
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, 111 Koshland Hall, University of California Berkeley, Berkeley, CA 94720-3102, USA
| | - Masakazu Iwai
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, 111 Koshland Hall, University of California Berkeley, Berkeley, CA 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, 111 Koshland Hall, University of California Berkeley, Berkeley, CA 94720-3102, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen P Long
- Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL 61801, USA.
- Lancaster Environment Centre, University of Lancaster, Lancaster LA1 1YX, UK
| |
Collapse
|