1
|
Nanes Sarfati D, Xue Y, Song ES, Byrne A, Le D, Darmanis S, Quake SR, Burlacot A, Sikes J, Wang B. Coordinated wound responses in a regenerative animal-algal holobiont. Nat Commun 2024; 15:4032. [PMID: 38740753 DOI: 10.1038/s41467-024-48366-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Animal regeneration involves coordinated responses across cell types throughout the animal body. In endosymbiotic animals, whether and how symbionts react to host injury and how cellular responses are integrated across species remain unexplored. Here, we study the acoel Convolutriloba longifissura, which hosts symbiotic Tetraselmis sp. green algae and can regenerate entire bodies from tissue fragments. We show that animal injury causes a decline in the photosynthetic efficiency of the symbiotic algae, alongside two distinct, sequential waves of transcriptional responses in acoel and algal cells. The initial algal response is characterized by the upregulation of a cohort of photosynthesis-related genes, though photosynthesis is not necessary for regeneration. A conserved animal transcription factor, runt, is induced after injury and required for acoel regeneration. Knockdown of Cl-runt dampens transcriptional responses in both species and further reduces algal photosynthetic efficiency post-injury. Our results suggest that the holobiont functions as an integrated unit of biological organization by coordinating molecular networks across species through the runt-dependent animal regeneration program.
Collapse
Affiliation(s)
| | - Yuan Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Eun Sun Song
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Daniel Le
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Adrien Burlacot
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - James Sikes
- Department of Biology, University of San Francisco, San Francisco, CA, USA.
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
2
|
Findinier J, Joubert LM, Schmid MF, Malkovskiy A, Chiu W, Burlacot A, Grossman AR. Dramatic Changes in Mitochondrial Subcellular Location and Morphology Accompany Activation of the CO 2 Concentrating Mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586705. [PMID: 38585955 PMCID: PMC10996633 DOI: 10.1101/2024.03.25.586705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Dynamic changes in intracellular ultrastructure can be critical for the ability of organisms to acclimate to environmental conditions. Microalgae, which are responsible for ~50% of global photosynthesis, compartmentalize their Rubisco into a specialized structure known as the pyrenoid when the cells experience limiting CO2 conditions; this compartmentalization appears to be a component of the CO2 Concentrating Mechanism (CCM), which facilitates photosynthetic CO2 fixation as environmental levels of inorganic carbon (Ci) decline. Changes in the spatial distribution of mitochondria in green algae have also been observed under CO2 limiting conditions, although a role for this reorganization in CCM function remains unclear. We used the green microalgae Chlamydomonas reinhardtii to monitor changes in the position and ultrastructure of mitochondrial membranes as cells transition between high CO2 (HC) and Low/Very Low CO2 (LC/VLC). Upon transferring cells to VLC, the mitochondria move from a central to a peripheral location, become wedged between the plasma membrane and chloroplast envelope, and mitochondrial membranes orient in parallel tubular arrays that extend from the cell's apex to its base. We show that these ultrastructural changes require protein and RNA synthesis, occur within 90 min of shifting cells to VLC conditions, correlate with CCM induction and are regulated by the CCM master regulator CIA5. The apico-basal orientation of the mitochondrial membrane, but not the movement of the mitochondrion to the cell periphery, is dependent on microtubules and the MIRO1 protein, which is involved in membrane-microtubule interactions. Furthermore, blocking mitochondrial electron transport in VLC acclimated cells reduces the cell's affinity for inorganic carbon. Overall, our results suggest that CIA5-dependent mitochondrial repositioning/reorientation functions in integrating cellular architecture and energetics with CCM activities and invite further exploration of how intracellular architecture can impact fitness under dynamic environmental conditions.
Collapse
Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Sciences & Engineering, Stanford, CA 94305, USA
| | - Lydia-Marie Joubert
- SLAC National Accelerator Laboratory, Division of CryoEM and Bioimaging, Menlo Park, CA 94025, USA
| | - Michael F. Schmid
- SLAC National Accelerator Laboratory, Division of CryoEM and Bioimaging, Menlo Park, CA 94025, USA
| | - Andrey Malkovskiy
- The Carnegie Institution for Science, Biosphere Sciences & Engineering, Stanford, CA 94305, USA
| | - Wah Chiu
- SLAC National Accelerator Laboratory, Division of CryoEM and Bioimaging, Menlo Park, CA 94025, USA
- Stanford University, Department of Bioengineering, Stanford, CA 94305, USA
| | - Adrien Burlacot
- The Carnegie Institution for Science, Biosphere Sciences & Engineering, Stanford, CA 94305, USA
- Stanford University, Biology Department, Stanford, CA 94305, USA
| | - Arthur R. Grossman
- The Carnegie Institution for Science, Biosphere Sciences & Engineering, Stanford, CA 94305, USA
- Stanford University, Biology Department, Stanford, CA 94305, USA
| |
Collapse
|
3
|
Atkinson N, Stringer R, Mitchell SR, Seung D, McCormick AJ. SAGA1 and SAGA2 promote starch formation around proto-pyrenoids in Arabidopsis chloroplasts. Proc Natl Acad Sci U S A 2024; 121:e2311013121. [PMID: 38241434 PMCID: PMC10823261 DOI: 10.1073/pnas.2311013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The pyrenoid is a chloroplastic microcompartment in which most algae and some terrestrial plants condense the primary carboxylase, Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) as part of a CO2-concentrating mechanism that improves the efficiency of CO2 capture. Engineering a pyrenoid-based CO2-concentrating mechanism (pCCM) into C3 crop plants is a promising strategy to enhance yield capacities and resilience to the changing climate. Many pyrenoids are characterized by a sheath of starch plates that is proposed to act as a barrier to limit CO2 diffusion. Recently, we have reconstituted a phase-separated "proto-pyrenoid" Rubisco matrix in the model C3 plant Arabidopsis thaliana using proteins from the alga with the most well-studied pyrenoid, Chlamydomonas reinhardtii [N. Atkinson, Y. Mao, K. X. Chan, A. J. McCormick, Nat. Commun. 11, 6303 (2020)]. Here, we describe the impact of introducing the Chlamydomonas proteins StArch Granules Abnormal 1 (SAGA1) and SAGA2, which are associated with the regulation of pyrenoid starch biogenesis and morphology. We show that SAGA1 localizes to the proto-pyrenoid in engineered Arabidopsis plants, which results in the formation of atypical spherical starch granules enclosed within the proto-pyrenoid condensate and adjacent plate-like granules that partially cover the condensate, but without modifying the total amount of chloroplastic starch accrued. Additional expression of SAGA2 further increases the proportion of starch synthesized as adjacent plate-like granules that fully encircle the proto-pyrenoid. Our findings pave the way to assembling a diffusion barrier as part of a functional pCCM in vascular plants, while also advancing our understanding of the roles of SAGA1 and SAGA2 in starch sheath formation and broadening the avenues for engineering starch morphology.
Collapse
Affiliation(s)
- Nicky Atkinson
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
- Centre of Engineering Biology, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
| | - Rhea Stringer
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, NorwichNR4 7UH, United Kingdom
| | - Stephen R. Mitchell
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
| | - David Seung
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, NorwichNR4 7UH, United Kingdom
| | - Alistair J. McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
- Centre of Engineering Biology, University of Edinburgh, EdinburghEH9 3BF, United Kingdom
| |
Collapse
|
4
|
Liu D, Wei L. Epigenetic Regulation in Response to CO 2 Fluctuation in Marine Microalga Nannochloropsis oceanica. MICROBIAL ECOLOGY 2023; 87:4. [PMID: 38015286 DOI: 10.1007/s00248-023-02322-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/22/2023] [Indexed: 11/29/2023]
Abstract
Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.
Collapse
Affiliation(s)
- Danmei Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Li Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
- Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Haikou, 571129, China.
- International Science and Technology Cooperation Laboratory for Marine Microalgae Ecological Carbon Sinks, Hainan Normal University, Haikou, 571158, China.
| |
Collapse
|
5
|
He S, Crans VL, Jonikas MC. The pyrenoid: the eukaryotic CO2-concentrating organelle. THE PLANT CELL 2023; 35:3236-3259. [PMID: 37279536 PMCID: PMC10473226 DOI: 10.1093/plcell/koad157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]
Abstract
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
Collapse
Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| | - Victoria L Crans
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| |
Collapse
|
6
|
Lau CS, Dowle A, Thomas GH, Girr P, Mackinder LCM. A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii. THE PLANT CELL 2023; 35:3260-3279. [PMID: 37195994 PMCID: PMC10473203 DOI: 10.1093/plcell/koad131] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 05/19/2023]
Abstract
Phase separation underpins many biologically important cellular events such as RNA metabolism, signaling, and CO2 fixation. However, determining the composition of a phase-separated organelle is often challenging due to its sensitivity to environmental conditions, which limits the application of traditional proteomic techniques like organellar purification or affinity purification mass spectrometry to understand their composition. In Chlamydomonas reinhardtii, Rubisco is condensed into a crucial phase-separated organelle called the pyrenoid that improves photosynthetic performance by supplying Rubisco with elevated concentrations of CO2. Here, we developed a TurboID-based proximity labeling technique in which proximal proteins in Chlamydomonas chloroplasts are labeled by biotin radicals generated from the TurboID-tagged protein. By fusing 2 core pyrenoid components with the TurboID tag, we generated a high-confidence pyrenoid proxiome that contains most known pyrenoid proteins, in addition to new pyrenoid candidates. Fluorescence protein tagging of 7 previously uncharacterized TurboID-identified proteins showed that 6 localized to a range of subpyrenoid regions. The resulting proxiome also suggests new secondary functions for the pyrenoid in RNA-associated processes and redox-sensitive iron-sulfur cluster metabolism. This developed pipeline can be used to investigate a broad range of biological processes in Chlamydomonas, especially at a temporally resolved suborganellar resolution.
Collapse
Affiliation(s)
- Chun Sing Lau
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Adam Dowle
- Department of Biology, University of York, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Luke C M Mackinder
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
7
|
Findinier J, Grossman AR. Chlamydomonas: Fast tracking from genomics. JOURNAL OF PHYCOLOGY 2023; 59:644-652. [PMID: 37417760 DOI: 10.1111/jpy.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
Collapse
Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| | - Arthur R Grossman
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| |
Collapse
|
8
|
Burlacot A, Peltier G. Energy crosstalk between photosynthesis and the algal CO 2-concentrating mechanisms. TRENDS IN PLANT SCIENCE 2023; 28:795-807. [PMID: 37087359 DOI: 10.1016/j.tplants.2023.03.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/03/2023]
Abstract
Microalgal photosynthesis is responsible for nearly half of the CO2 annually captured by Earth's ecosystems. In aquatic environments where the CO2 availability is low, the CO2-fixing efficiency of microalgae greatly relies on mechanisms - called CO2-concentrating mechanisms (CCMs) - for concentrating CO2 at the catalytic site of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). While the transport of inorganic carbon (Ci) across membrane bilayers against a concentration gradient consumes part of the chemical energy generated by photosynthesis, the bioenergetics and cellular mechanisms involved are only beginning to be elucidated. Here, we review the current knowledge relating to the energy requirement of CCMs in the light of recent advances in photosynthesis regulatory mechanisms and the spatial organization of CCM components.
Collapse
Affiliation(s)
- Adrien Burlacot
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Gilles Peltier
- Aix-Marseille Université, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France.
| |
Collapse
|
9
|
Arend M, Yuan Y, Ruiz-Sola MÁ, Omranian N, Nikoloski Z, Petroutsos D. Widening the landscape of transcriptional regulation of green algal photoprotection. Nat Commun 2023; 14:2687. [PMID: 37164999 PMCID: PMC10172295 DOI: 10.1038/s41467-023-38183-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/17/2023] [Indexed: 05/12/2023] Open
Abstract
Availability of light and CO2, substrates of microalgae photosynthesis, is frequently far from optimal. Microalgae activate photoprotection under strong light, to prevent oxidative damage, and the CO2 Concentrating Mechanism (CCM) under low CO2, to raise intracellular CO2 levels. The two processes are interconnected; yet, the underlying transcriptional regulators remain largely unknown. Employing a large transcriptomic data compendium of Chlamydomonas reinhardtii's responses to different light and carbon supply, we reconstruct a consensus genome-scale gene regulatory network from complementary inference approaches and use it to elucidate transcriptional regulators of photoprotection. We show that the CCM regulator LCR1 also controls photoprotection, and that QER7, a Squamosa Binding Protein, suppresses photoprotection- and CCM-gene expression under the control of the blue light photoreceptor Phototropin. By demonstrating the existence of regulatory hubs that channel light- and CO2-mediated signals into a common response, our study provides an accessible resource to dissect gene expression regulation in this microalga.
Collapse
Affiliation(s)
- Marius Arend
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Yizhong Yuan
- University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - M Águila Ruiz-Sola
- University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, 41092, Sevilla, Spain
| | - Nooshin Omranian
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
- Systems Biology and Mathematical Modeling Group, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
- Bioinformatics and Mathematical Modeling Department, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Dimitris Petroutsos
- University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France.
| |
Collapse
|
10
|
Shimamura D, Yamano T, Niikawa Y, Hu D, Fukuzawa H. A pyrenoid-localized protein SAGA1 is necessary for Ca 2+-binding protein CAS-dependent expression of nuclear genes encoding inorganic carbon transporters in Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 2023; 156:181-192. [PMID: 36656499 DOI: 10.1007/s11120-022-00996-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/14/2022] [Indexed: 05/03/2023]
Abstract
Microalgae induce a CO2-concentrating mechanism (CCM) to maintain photosynthetic affinity for dissolved inorganic carbon (Ci) under CO2-limiting conditions. In the model alga Chlamydomonas reinhardtii, the pyrenoid-localized Ca2+-binding protein CAS is required to express genes encoding the Ci-transporters, high-light activated 3 (HLA3), and low-CO2-inducible protein A (LCIA). To identify new factors related to the regulation or components of the CCM, we isolated CO2-requiring mutants KO-60 and KO-62. These mutants had insertions of a hygromycin-resistant cartridge in the StArch Granules Abnormal 1 (SAGA1) gene, which is necessary to maintain the number of pyrenoids and the structure of pyrenoid tubules in the chloroplast. In both KO-60 and the previously identified saga1 mutant, expression levels of 532 genes were significantly reduced. Among them, 10 CAS-dependent genes, including HLA3 and LCIA, were not expressed in the saga1 mutants. While CAS was expressed normally at the protein levels, the localization of CAS was dispersed through the chloroplast rather than in the pyrenoid, even under CO2-limiting conditions. These results suggest that SAGA1 is necessary not only for maintenance of the pyrenoid structure but also for regulation of the nuclear genes encoding Ci-transporters through CAS-dependent retrograde signaling under CO2-limiting stress.
Collapse
Affiliation(s)
- Daisuke Shimamura
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan.
| | - Yuki Niikawa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Donghui Hu
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan.
| |
Collapse
|
11
|
Águila Ruiz-Sola M, Flori S, Yuan Y, Villain G, Sanz-Luque E, Redekop P, Tokutsu R, Küken A, Tsichla A, Kepesidis G, Allorent G, Arend M, Iacono F, Finazzi G, Hippler M, Nikoloski Z, Minagawa J, Grossman AR, Petroutsos D. Light-independent regulation of algal photoprotection by CO 2 availability. Nat Commun 2023; 14:1977. [PMID: 37031262 PMCID: PMC10082802 DOI: 10.1038/s41467-023-37800-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.
Collapse
Affiliation(s)
- M Águila Ruiz-Sola
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, Sevilla, Spain
| | - Serena Flori
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Yizhong Yuan
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Gaelle Villain
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Emanuel Sanz-Luque
- The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
- University of Cordoba, Department of Biochemistry and Molecular Biology, Cordoba, Spain
| | - Petra Redekop
- The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | - Ryutaro Tokutsu
- Division of Environmental photobiology, National Institute for Basic Biology (NIBB), Nishigonaka 38, Myodaiji, Okazaki, 444-8585, Japan
| | - Anika Küken
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Angeliki Tsichla
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Georgios Kepesidis
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Guillaume Allorent
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Marius Arend
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Fabrizio Iacono
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000, Grenoble, France
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms Universität, 48143, Münster, Germany
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Jun Minagawa
- Division of Environmental photobiology, National Institute for Basic Biology (NIBB), Nishigonaka 38, Myodaiji, Okazaki, 444-8585, Japan
| | - Arthur R Grossman
- The Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, USA
| | | |
Collapse
|
12
|
Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
Collapse
|
13
|
Förster B, Rourke LM, Weerasooriya HN, Pabuayon ICM, Rolland V, Au EK, Bala S, Bajsa-Hirschel J, Kaines S, Kasili R, LaPlace L, Machingura MC, Massey B, Rosati VC, Stuart-Williams H, Badger MR, Price GD, Moroney JV. The Chlamydomonas reinhardtii chloroplast envelope protein LCIA transports bicarbonate in planta. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad116. [PMID: 36987927 DOI: 10.1093/jxb/erad116] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 06/19/2023]
Abstract
LCIA is a chloroplast envelope protein associated with the CO2 concentrating mechanism of the green alga Chlamydomonas reinhardtii. LCIA is postulated to be a HCO3- channel, but previous studies were unable to show that LCIA was actively transporting bicarbonate in planta. Therefore, LCIA activity was investigated more directly in two heterologous systems: an E. coli mutant (DCAKO) lacking both native carbonic anhydrases and an Arabidopsis mutant (βca5) missing the plastid carbonic anhydrase βCA5. Both DCAKO and βca5 cannot grow in ambient CO2 conditions, as they lack carbonic anhydrase-catalyzed production of the necessary HCO3- concentration for lipid and nucleic acid biosynthesis. Expression of LCIA restored growth in both systems in ambient CO2 conditions, which strongly suggests that LCIA is facilitating HCO3- uptake in each system. To our knowledge, this is the first direct evidence that LCIA moves HCO3- across membranes in bacteria and plants. Furthermore, the βca5 plant bioassay used in this study is the first system for testing HCO3- transport activity in planta, an experimental breakthrough that will be valuable for future studies aimed at improving the photosynthetic efficiency of crop plants using components from algal CO2 concentrating mechanisms.
Collapse
Affiliation(s)
- Britta Förster
- The Australian National University, Canberra, ACT 2600, Australia
| | - Loraine M Rourke
- The Australian National University, Canberra, ACT 2600, Australia
| | - Hiruni N Weerasooriya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Isaiah C M Pabuayon
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Vivien Rolland
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Eng Kee Au
- The Australian National University, Canberra, ACT 2600, Australia
| | - Soumi Bala
- The Australian National University, Canberra, ACT 2600, Australia
| | - Joanna Bajsa-Hirschel
- Natural Products Utilization Research Unit, United States Department of Agriculture, University, MS 38677, USA
| | - Sarah Kaines
- The Australian National University, Canberra, ACT 2600, Australia
| | - Remmy Kasili
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Lillian LaPlace
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Baxter Massey
- The Australian National University, Canberra, ACT 2600, Australia
| | - Viviana C Rosati
- Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | | | - Murray R Badger
- The Australian National University, Canberra, ACT 2600, Australia
| | - G Dean Price
- The Australian National University, Canberra, ACT 2600, Australia
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
14
|
Wang L, Tonsager AJ, Zheng W, Wang Y, Stessman D, Fang W, Stenback KE, Campbell A, Tanvir R, Zhang J, Cothron S, Wan D, Meng Y, Spalding MH, Nikolau BJ, Li L. Single-cell genetic models to evaluate orphan gene function: The case of QQS regulating carbon and nitrogen allocation. FRONTIERS IN PLANT SCIENCE 2023; 14:1126139. [PMID: 37051080 PMCID: PMC10084940 DOI: 10.3389/fpls.2023.1126139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
We demonstrate two synthetic single-cell systems that can be used to better understand how the acquisition of an orphan gene can affect complex phenotypes. The Arabidopsis orphan gene, Qua-Quine Starch (QQS) has been identified as a regulator of carbon (C) and nitrogen (N) partitioning across multiple plant species. QQS modulates this important biotechnological trait by replacing NF-YB (Nuclear Factor Y, subunit B) in its interaction with NF-YC. In this study, we expand on these prior findings by developing Chlamydomonas reinhardtii and Saccharomyces cerevisiae strains, to refactor the functional interactions between QQS and NF-Y subunits to affect modulations in C and N allocation. Expression of QQS in C. reinhardtii modulates C (i.e., starch) and N (i.e., protein) allocation by affecting interactions between NF-YC and NF-YB subunits. Studies in S. cerevisiae revealed similar functional interactions between QQS and the NF-YC homolog (HAP5), modulating C (i.e., glycogen) and N (i.e., protein) allocation. However, in S. cerevisiae both the NF-YA (HAP2) and NF-YB (HAP3) homologs appear to have redundant functions to enable QQS and HAP5 to affect C and N allocation. The genetically tractable systems that developed herein exhibit the plasticity to modulate highly complex phenotypes.
Collapse
Affiliation(s)
- Lei Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Andrew J. Tonsager
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Wenguang Zheng
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Yingjun Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Dan Stessman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Wei Fang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Kenna E. Stenback
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Alexis Campbell
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Rezwan Tanvir
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Jinjiang Zhang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
- Mississippi School for Mathematics and Science, Columbus, MS, United States
| | - Samuel Cothron
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Dongli Wan
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yan Meng
- Department of Agriculture, Alcorn State University, Lorman, MS, United States
| | - Martin H. Spalding
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| |
Collapse
|
15
|
Yamada R, Yokota M, Matsumoto T, Hankamer B, Ogino H. Promoting cell growth and characterizing partial symbiotic relationships in the co-cultivation of green alga Chlamydomonas reinhardtii and Escherichia coli. Biotechnol J 2023; 18:e2200099. [PMID: 36479591 DOI: 10.1002/biot.202200099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND By co-culturing selected microalgae and heterotrophic microorganisms, the growth rate of microalgae can be improved even under atmospheric conditions with a low CO2 concentration. However, the detailed mechanism of improvement of proliferative capacity by co-culture has not been elucidated. In this study, we investigated changes in the proliferative capacity of the green alga Chlamydomonas reinhardtii by co-culturing with Escherichia coli. MAIN METHODS AND MAJOR RESULTS In the co-culture, the number of C. reinhardtii cells reached 2.22 × 1010 cell/L on day 14 of culture. This was about 1.9 times the number of cells (1.16 × 1010 cell/L) on day 14 compared to C. reinhardtii cells in monoculture. The starch content per cell in the co-culture of C. reinhardtii and E. coli on the 14th day (2.09 × 10-11 g/cell) was 1.3 times higher than that in the C. reinhardtii monoculture (1.59 × 10-11 g/cell), and the starch content per culture medium improved 2.5 times with co-cultivation. By analyzing the gene transcription profiles and key media components, we clarified that E. coli produced CO2 from the organic carbon in the medium and the organic carbon produced by photosynthesis of C. reinhardtii, and this CO2 likely enhanced the growth of C. reinhardtii. CONCLUSIONS Consequently, E. coli plays a key role in promoting the growth of C. reinhardtii as well as the accumulation of starch which is a valuable intermediate for the production of a range of useful chemicals from CO2 .
Collapse
Affiliation(s)
- Ryosuke Yamada
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Moe Yokota
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
| |
Collapse
|
16
|
Mao Y, Catherall E, Díaz-Ramos A, Greiff GRL, Azinas S, Gunn L, McCormick AJ. The small subunit of Rubisco and its potential as an engineering target. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:543-561. [PMID: 35849331 PMCID: PMC9833052 DOI: 10.1093/jxb/erac309] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 05/06/2023]
Abstract
Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.
Collapse
Affiliation(s)
| | | | - Aranzazú Díaz-Ramos
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, King’s Buildings, University of Edinburgh, Edingburgh EH9 3BF, UK
| | - George R L Greiff
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Stavros Azinas
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
| | - Laura Gunn
- Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | |
Collapse
|
17
|
Adler L, Díaz-Ramos A, Mao Y, Pukacz KR, Fei C, McCormick AJ. New horizons for building pyrenoid-based CO2-concentrating mechanisms in plants to improve yields. PLANT PHYSIOLOGY 2022; 190:1609-1627. [PMID: 35961043 PMCID: PMC9614477 DOI: 10.1093/plphys/kiac373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 05/06/2023]
Abstract
Many photosynthetic species have evolved CO2-concentrating mechanisms (CCMs) to improve the efficiency of CO2 assimilation by Rubisco and reduce the negative impacts of photorespiration. However, the majority of plants (i.e. C3 plants) lack an active CCM. Thus, engineering a functional heterologous CCM into important C3 crops, such as rice (Oryza sativa) and wheat (Triticum aestivum), has become a key strategic ambition to enhance yield potential. Here, we review recent advances in our understanding of the pyrenoid-based CCM in the model green alga Chlamydomonas reinhardtii and engineering progress in C3 plants. We also discuss recent modeling work that has provided insights into the potential advantages of Rubisco condensation within the pyrenoid and the energetic costs of the Chlamydomonas CCM, which, together, will help to better guide future engineering approaches. Key findings include the potential benefits of Rubisco condensation for carboxylation efficiency and the need for a diffusional barrier around the pyrenoid matrix. We discuss a minimal set of components for the CCM to function and that active bicarbonate import into the chloroplast stroma may not be necessary for a functional pyrenoid-based CCM in planta. Thus, the roadmap for building a pyrenoid-based CCM into plant chloroplasts to enhance the efficiency of photosynthesis now appears clearer with new challenges and opportunities.
Collapse
Affiliation(s)
| | | | - Yuwei Mao
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krzysztof Robin Pukacz
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | | |
Collapse
|
18
|
Koletti A, Dervisi I, Kalloniati C, Zografaki ME, Rennenberg H, Roussis A, Flemetakis E. Selenium-binding Protein 1 (SBD1): A stress response regulator in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2022; 189:2368-2381. [PMID: 35579367 PMCID: PMC9342975 DOI: 10.1093/plphys/kiac230] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/04/2022] [Indexed: 05/20/2023]
Abstract
Selenium-binding proteins (SBPs) represent a ubiquitous protein family implicated in various environmental stress responses, although the exact molecular and physiological role of the SBP family remains elusive. In this work, we report the identification and characterization of CrSBD1, an SBP homolog from the model microalgae Chlamydomonas reinhardtii. Growth analysis of the C. reinhardtii sbd1 mutant strain revealed that the absence of a functional CrSBD1 resulted in increased growth under mild oxidative stress conditions, although cell viability rapidly declined at higher hydrogen peroxide (H2O2) concentrations. Furthermore, a combined global transcriptomic and metabolomic analysis indicated that the sbd1 mutant exhibited a dramatic quenching of the molecular and biochemical responses upon H2O2-induced oxidative stress when compared to the wild-type. Our results indicate that CrSBD1 represents a cell regulator, which is involved in the modulation of C. reinhardtii early responses to oxidative stress. We assert that CrSBD1 acts as a member of an extensive and conserved protein-protein interaction network including Fructose-bisphosphate aldolase 3, Cysteine endopeptidase 2, and Glutaredoxin 6 proteins, as indicated by yeast two-hybrid assays.
Collapse
Affiliation(s)
- Aikaterini Koletti
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Irene Dervisi
- Department of Botany, Faculty of Biology, National & Kapodistrian University of Athens, Athens 15784, Greece
| | - Chrysanthi Kalloniati
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Maria-Eleftheria Zografaki
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Chongqing 400715, China
| | | | | |
Collapse
|
19
|
Rai AK, DiMario RJ, Kasili RW, Groszmann M, Cousins AB, Donze D, Moroney JV. A Rapid Method for Detecting Normal or Modified Plant and Algal Carbonic Anhydrase Activity Using Saccharomyces cerevisiae. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11141882. [PMID: 35890517 PMCID: PMC9320139 DOI: 10.3390/plants11141882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 05/19/2023]
Abstract
In recent years, researchers have attempted to improve photosynthesis by introducing components from cyanobacterial and algal CO2-concentrating mechanisms (CCMs) into terrestrial C3 plants. For these attempts to succeed, we need to understand the CCM components in more detail, especially carbonic anhydrase (CA) and bicarbonate (HCO3−) transporters. Heterologous complementation systems capable of detecting carbonic anhydrase activity (i.e., catalysis of the pH-dependent interconversion between CO2 and HCO3−) or active HCO3− transport can be of great value in the process of introducing CCM components into terrestrial C3 plants. In this study, we generated a Saccharomyces cerevisiae CA knock-out (ΔNCE103 or ΔCA) that has a high-CO2-dependent phenotype (5% (v/v) CO2 in air). CAs produce HCO3− for anaplerotic pathways in S. cerevisiae; therefore, the unavailability of HCO3− for neutral lipid biosynthesis is a limitation for the growth of ΔCA in ambient levels of CO2 (0.04% (v/v) CO2 in air). ΔCA can be complemented for growth at ambient levels of CO2 by expressing a CA from human red blood cells. ΔCA was also successfully complemented for growth at ambient levels of CO2 through the expression of CAs from Chlamydomonas reinhardtii and Arabidopsis thaliana. The ΔCA strain is also useful for investigating the activity of modified CAs, allowing for quick screening of modified CAs before putting them into the plants. CA activity in the complemented ΔCA strains can be probed using the Wilbur−Anderson assay and by isotope exchange membrane-inlet mass spectrometry (MIMS). Other potential uses for this new ΔCA-based screening system are also discussed.
Collapse
Affiliation(s)
- Ashwani K. Rai
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (A.K.R.); (R.W.K.); (D.D.)
| | - Robert J. DiMario
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA; (R.J.D.); (A.B.C.)
| | - Remmy W. Kasili
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (A.K.R.); (R.W.K.); (D.D.)
| | - Michael Groszmann
- ARC Centre of Excellence in Translational Photosynthesis, Research School of Biology, Australian National University, Linnaeus Building, 134 Linnaeus Way, Canberra, ACT 2601, Australia;
| | - Asaph B. Cousins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA; (R.J.D.); (A.B.C.)
| | - David Donze
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (A.K.R.); (R.W.K.); (D.D.)
| | - James V. Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; (A.K.R.); (R.W.K.); (D.D.)
- Correspondence:
| |
Collapse
|
20
|
Redekop P, Sanz-Luque E, Yuan Y, Villain G, Petroutsos D, Grossman AR. Transcriptional regulation of photoprotection in dark-to-light transition-More than just a matter of excess light energy. SCIENCE ADVANCES 2022; 8:eabn1832. [PMID: 35658034 PMCID: PMC9166400 DOI: 10.1126/sciadv.abn1832] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/18/2022] [Indexed: 05/22/2023]
Abstract
In nature, photosynthetic organisms are exposed to different light spectra and intensities depending on the time of day and atmospheric and environmental conditions. When photosynthetic cells absorb excess light, they induce nonphotochemical quenching to avoid photodamage and trigger expression of "photoprotective" genes. In this work, we used the green alga Chlamydomonas reinhardtii to assess the impact of light intensity, light quality, photosynthetic electron transport, and carbon dioxide on induction of the photoprotective genes (LHCSR1, LHCSR3, and PSBS) during dark-to-light transitions. Induction (mRNA accumulation) occurred at very low light intensity and was independently modulated by blue and ultraviolet B radiation through specific photoreceptors; only LHCSR3 was strongly controlled by carbon dioxide levels through a putative enhancer function of CIA5, a transcription factor that controls genes of the carbon concentrating mechanism. We propose a model that integrates inputs of independent signaling pathways and how they may help the cells anticipate diel conditions and survive in a dynamic light environment.
Collapse
Affiliation(s)
- Petra Redekop
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama St, Stanford, CA 94305, USA
- Corresponding author. (E.S.-L.); (P.R.)
| | - Emanuel Sanz-Luque
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama St, Stanford, CA 94305, USA
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain
- Corresponding author. (E.S.-L.); (P.R.)
| | - Yizhong Yuan
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38000 Grenoble, France
| | - Gaelle Villain
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38000 Grenoble, France
| | - Dimitris Petroutsos
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38000 Grenoble, France
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, 260 Panama St, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
21
|
Li B, Hou L, Song C, Wang Z, Xue Q, Li Y, Qin J, Cao N, Jia C, Zhang Y, Shi W. Biological function of calcium-sensing receptor (CAS) and its coupling calcium signaling in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 180:74-80. [PMID: 35398653 DOI: 10.1016/j.plaphy.2022.03.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/09/2022] [Accepted: 03/26/2022] [Indexed: 05/23/2023]
Abstract
The calcium-sensing receptor (CAS), as a chloroplast thylakoid membrane protein, is involved in the process of external Ca2+-induced cytosolic Ca2+ increase in plants. However, the underlying mechanism regulating this process is lacking. Furthermore, recent evidence suggests that CAS may perform additional roles in plants. Here, we provided an update covering the multiple roles of CAS in stomatal movement regulation and Ca2+ signaling in plants. We also analyzed the possible phosphorylation mechanism of CAS by light and discuss the role of CAS in abiotic stress (drought, salt stress) and biotic stresses (plant immune signaling). Finally, we proposed a perspective for future experiments that are required to fill gaps in our understanding of the biological function of CAS in plants.
Collapse
Affiliation(s)
- Bin Li
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Liyuan Hou
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Chenggang Song
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Zhengbiao Wang
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Qiyang Xue
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Yuanyang Li
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Jianchun Qin
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Ning Cao
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Chengguo Jia
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China
| | - Yubin Zhang
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China.
| | - Wuliang Shi
- Center for Emerging Agricultural Education & Advanced Interdisciplinary Science, College of Plant Science, Jilin University, Changchun, 130062, PR China.
| |
Collapse
|
22
|
Schad A, Rössler S, Nagel R, Wagner H, Wilhelm C. Crossing and selection of Chlamydomonas reinhardtii strains for biotechnological glycolate production. Appl Microbiol Biotechnol 2022; 106:3539-3554. [PMID: 35511277 PMCID: PMC9151519 DOI: 10.1007/s00253-022-11933-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 11/27/2022]
Abstract
Abstract As an alternative to chemical building blocks derived from algal biomass, the excretion of glycolate has been proposed. This process has been observed in green algae such as Chlamydomonas reinhardtii as a product of the photorespiratory pathway. Photorespiration generally occurs at low CO2 and high O2 concentrations, through the key enzyme RubisCO initiating the pathway via oxygenation of 1.5-ribulose-bisphosphate. In wild-type strains, photorespiration is usually suppressed in favour of carboxylation due to the cellular carbon concentrating mechanisms (CCMs) controlling the internal CO2 concentration. Additionally, newly produced glycolate is directly metabolized in the C2 cycle. Therefore, both the CCMs and the C2 cycle are the key elements which limit the glycolate production in wild-type cells. Using conventional crossing techniques, we have developed Chlamydomonas reinhardtii double mutants deficient in these two key pathways to direct carbon flux to glycolate excretion. Under aeration with ambient air, the double mutant D6 showed a significant and stable glycolate production when compared to the non-producing wild type. Interestingly, this mutant can act as a carbon sink by fixing atmospheric CO2 into glycolate without requiring any additional CO2 supply. Thus, the double-mutant strain D6 can be used as a photocatalyst to produce chemical building blocks and as a future platform for algal-based biotechnology. Key Points • Chlamydomonas reinhardtii cia5 gyd double mutants were developed by sexual crossing • The double mutation eliminates the need for an inhibitor in glycolate production • The strain D6 produces significant amounts of glycolate with ambient air only Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11933-y.
Collapse
Affiliation(s)
- Antonia Schad
- Department of Algal Biotechnology, Faculty of Life Science, University of Leipzig, Permoserstraße 15, D-04318, Leipzig, Germany
| | - Sonja Rössler
- Department of Algal Biotechnology, Faculty of Life Science, University of Leipzig, Permoserstraße 15, D-04318, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Faculty of Life Science, University of Leipzig, Johannisallee 21-23, D-04103, Leipzig, Germany
| | - Heiko Wagner
- Department of Algal Biotechnology, Faculty of Life Science, University of Leipzig, Permoserstraße 15, D-04318, Leipzig, Germany
| | - Christian Wilhelm
- Department of Algal Biotechnology, Faculty of Life Science, University of Leipzig, Permoserstraße 15, D-04318, Leipzig, Germany.
| |
Collapse
|
23
|
Wei L, Liu B, Liu D, Xu Z, Wang R, Zhang W. Identification and expression analysis of genome-wide long noncoding RNA responsive CO 2 fluctuated environment in marine microalga Nannochloropsis oceanica. MARINE POLLUTION BULLETIN 2022; 176:113419. [PMID: 35152114 DOI: 10.1016/j.marpolbul.2022.113419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to participate in plant growth and development as well as response to different biotic and abiotic stresses. However, the knowledge of lncRNA was limited in microalgae. In this study, by RNA deep sequencing, 134 lncRNAs were identified in marine Nannochloropsis oceanica in response to carbon dioxide fluctuation. Among them, there were 51 lncRNAs displayed differentially expressed between low and high CO2 treatments, including 33 upregulation and 18 downregulation lncRNAs. Cellulose metabolic process, glucan metabolic process, polysaccharide metabolic process, and transmembrane transporter activity were functionally enriched. Multiple potential target genes of lncRNA and lncRNA-mRNA co-located gene network were analyzed. Subsequent analysis had demonstrated that lncRNAs would participate in many biological molecular processes, including gene expression, transcriptional regulation, protein expression and epigenetic regulation. In addition, alternative splicing events were firstly analyzed in response to CO2 fluctuation. There were 2051 alternative splicing (AS events) identified, which might be associated with lncRNA. These observations will provide a novel insight into lncRNA function in Nannochloropsis and provide a series of targets for lncRNA-based gene editing in future.
Collapse
Affiliation(s)
- Li Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Bingqing Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Danmei Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Zhengru Xu
- College of Foreign Language, Hainan Normal University, Haikou 571157, China
| | - Ruiping Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Wenfei Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| |
Collapse
|
24
|
Choi BY, Kim H, Shim D, Jang S, Yamaoka Y, Shin S, Yamano T, Kajikawa M, Jin E, Fukuzawa H, Lee Y. The Chlamydomonas bZIP transcription factor BLZ8 confers oxidative stress tolerance by inducing the carbon-concentrating mechanism. THE PLANT CELL 2022; 34:910-926. [PMID: 34893905 PMCID: PMC8824676 DOI: 10.1093/plcell/koab293] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/28/2021] [Indexed: 05/19/2023]
Abstract
Photosynthetic organisms are exposed to various environmental sources of oxidative stress. Land plants have diverse mechanisms to withstand oxidative stress, but how microalgae do so remains unclear. Here, we characterized the Chlamydomonas reinhardtii basic leucine zipper (bZIP) transcription factor BLZ8, which is highly induced by oxidative stress. Oxidative stress tolerance increased with increasing BLZ8 expression levels. BLZ8 regulated the expression of genes likely involved in the carbon-concentrating mechanism (CCM): HIGH-LIGHT ACTIVATED 3 (HLA3), CARBONIC ANHYDRASE 7 (CAH7), and CARBONIC ANHYDRASE 8 (CAH8). BLZ8 expression increased the photosynthetic affinity for inorganic carbon under alkaline stress conditions, suggesting that BLZ8 induces the CCM. BLZ8 expression also increased the photosynthetic linear electron transfer rate, reducing the excitation pressure of the photosynthetic electron transport chain and in turn suppressing reactive oxygen species (ROS) production under oxidative stress conditions. A carbonic anhydrase inhibitor, ethoxzolamide, abolished the enhanced tolerance to alkaline stress conferred by BLZ8 overexpression. BLZ8 directly regulated the expression of the three target genes and required bZIP2 as a dimerization partner in activating CAH8 and HLA3. Our results suggest that a CCM-mediated increase in the CO2 supply for photosynthesis is critical to minimize oxidative damage in microalgae, since slow gas diffusion in aqueous environments limits CO2 availability for photosynthesis, which can trigger ROS formation.
Collapse
Affiliation(s)
| | | | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134 Korea
| | - Sunghoon Jang
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | | | - Seungjun Shin
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | | | - EonSeon Jin
- Department of Life Science, Hanyang University, Seoul 133-791, South Korea
| | | | | |
Collapse
|
25
|
Knockout of Cia5 gene using CRISPR/Cas9 technique in Chlamydomonas reinhardtii and evaluating CO2 sequestration in control and mutant isolates. J Genet 2022. [DOI: 10.1007/s12041-021-01350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
26
|
Shimakawa G, Shoguchi E, Burlacot A, Ifuku K, Che Y, Kumazawa M, Tanaka K, Nakanishi S. Coral symbionts evolved a functional polycistronic flavodiiron gene. PHOTOSYNTHESIS RESEARCH 2022; 151:113-124. [PMID: 34309771 DOI: 10.1007/s11120-021-00867-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/17/2021] [Indexed: 05/26/2023]
Abstract
Photosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O2. In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O2 photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are the only algae to harbor FLV in photosynthetic red plastid lineage, only one gene is found in transcriptomes and its role and activity remain unknown. Here, we characterized the FLV genes in Symbiodiniaceae and found that its coding region is composed of tandemly repeated FLV sequences. By measuring the O2-dependent electron flow and P700 oxidation, we suggest that this atypical FLV is active in vivo. Based on the amino-acid sequence alignment and the phylogenetic analysis, we conclude that in coral symbionts, the gene pair for FLVA and FLVB have been fused to construct one coding region for a hybrid enzyme, which presumably occurred when or after both genes were inherited from basal green algae to the dinoflagellate. Immunodetection suggested the FLV polypeptide to be cleaved by a post-translational mechanism, adding it to the rare cases of polycistronic genes in eukaryotes. Our results demonstrate that FLV are active in coral symbionts with genomic arrangement that is unique to these species. The implication of these unique features on their symbiotic living environment is discussed.
Collapse
Affiliation(s)
- Ginga Shimakawa
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Adrien Burlacot
- Aix Marseille University, CEA, CNRS, Institut de Biosciences Et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, 111 Koshland Hall, Berkeley, CA, 94720-3102, USA
| | - Kentaro Ifuku
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Yufen Che
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Minoru Kumazawa
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Kenya Tanaka
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
| |
Collapse
|
27
|
Neofotis P, Temple J, Tessmer OL, Bibik J, Norris N, Pollner E, Lucker B, Weraduwage SM, Withrow A, Sears B, Mogos G, Frame M, Hall D, Weissman J, Kramer DM. The induction of pyrenoid synthesis by hyperoxia and its implications for the natural diversity of photosynthetic responses in Chlamydomonas. eLife 2021; 10:67565. [PMID: 34936552 PMCID: PMC8694700 DOI: 10.7554/elife.67565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/13/2021] [Indexed: 12/31/2022] Open
Abstract
In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO2. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO2 or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO2 or hyperoxia. Consistent with this view, the photorespiratory by-product, H2O2, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H2O2 signaling, and pyrenoid morphologies.
Collapse
Affiliation(s)
- Peter Neofotis
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Joshua Temple
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| | - Oliver L Tessmer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Jacob Bibik
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Nicole Norris
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Eric Pollner
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Ben Lucker
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Sarathi M Weraduwage
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States.,Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, United States
| | - Alecia Withrow
- Center for Advanced Microscopy, Michigan State University, East Lansing, United States
| | - Barbara Sears
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Greg Mogos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Melinda Frame
- Center for Advanced Microscopy, Michigan State University, East Lansing, United States
| | - David Hall
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Joseph Weissman
- Corporate Strategic Research, ExxonMobil, Annandale, United States
| | - David M Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| |
Collapse
|
28
|
Wu S, Gu W, Jia S, Wang L, Wang L, Liu X, Zhou L, Huang A, Wang G. Proteomic and biochemical responses to different concentrations of CO 2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:235. [PMID: 34906223 PMCID: PMC8670125 DOI: 10.1186/s13068-021-02088-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Diatoms are well known for high photosynthetic efficiency and rapid growth rate, which are not only important oceanic primary producer, but also ideal feedstock for microalgae industrialization. Their high success is mainly due to the rapid response of photosynthesis to inorganic carbon fluctuations. Thus, an in-depth understanding of the photosynthetic carbon fixation mechanism of diatoms will be of great help to microalgae-based applications. This work directed toward the analysis of whether C4 photosynthetic pathway functions in the model marine diatom Phaeodactylum tricornutum, which possesses biophysical CO2-concentrating mechanism (CCM) as well as metabolic enzymes potentially involved in C4 photosynthetic pathway. RESULTS For P. tricornutum, differential proteome, enzyme activities and transcript abundance of carbon metabolism-related genes especially biophysical and biochemical CCM-related genes in response to different concentrations of CO2 were tracked in this study. The upregulated protein abundance of a carbonic anhydrases and a bicarbonate transporter suggested biophysical CCM activated under low CO2 (LC). The upregulation of a number of key C4-related enzymes in enzymatic activity, transcript and protein abundance under LC indicated the induction of a mitochondria-mediated CCM in P. tricornutum. Moreover, protein abundance of a number of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine-urea cycle related proteins upregulated under LC, while numbers of proteins involved in the Calvin cycle and pentose phosphate pathway were downregulated. Under high CO2 (HC), protein abundance of most central carbon metabolism and photosynthesis-related proteins were upregulated. CONCLUSIONS The proteomic and biochemical responses to different concentrations of CO2 suggested multiple carbon metabolism strategies exist in P. tricornutum. Namely, LC might induce a mitochondrial-mediated C4-like CCM and the improvement of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine-urea cycle activity contribute to the energy supply and carbon and nitrogen recapture in P. tricornutum to cope with the CO2 limitation, while P. tricornutum responds to the HC environment by improving photosynthesis and central carbon metabolism activity. These findings can not only provide evidences for revealing the global picture of biophysical and biochemical CCM in P. tricornutum, but also provide target genes for further microalgal strain modification to improve carbon fixation and biomass yield in algal-based industry.
Collapse
Affiliation(s)
- Songcui Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Wenhui Gu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Shuao Jia
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lepu Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijun Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xuehua Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Zhou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aiyou Huang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- College of Marine Sciences, Hainan University, Haikou, 570228, China.
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| |
Collapse
|
29
|
Kselíková V, Singh A, Bialevich V, Čížková M, Bišová K. Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet. Biotechnol Adv 2021; 58:107885. [PMID: 34906670 DOI: 10.1016/j.biotechadv.2021.107885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.
Collapse
Affiliation(s)
- Veronika Kselíková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anjali Singh
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Vitali Bialevich
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Mária Čížková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic.
| |
Collapse
|
30
|
Examining the impact of carbon dioxide levels and modulation of resulting hydrogen peroxide in Chlorella vulgaris. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
31
|
Rai AK, Chen T, Moroney JV. Mitochondrial carbonic anhydrases are needed for optimal photosynthesis at low CO2 levels in Chlamydomonas. PLANT PHYSIOLOGY 2021; 187:1387-1398. [PMID: 34618049 PMCID: PMC8566214 DOI: 10.1093/plphys/kiab351] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/05/2021] [Indexed: 05/19/2023]
Abstract
Chlamydomonas reinhardtii can grow photosynthetically using CO2 or in the dark using acetate as the carbon source. In the light in air, the CO2 concentrating mechanism (CCM) of C. reinhardtii accumulates CO2, enhancing photosynthesis. A combination of carbonic anhydrases (CAs) and bicarbonate transporters in the CCM of C. reinhardtii increases the CO2 concentration at Ribulose 1,5-bisphosphate carboxylase oxygenase (Rubisco) in the chloroplast pyrenoid. Previously, CAs important to the CCM have been found in the periplasmic space, surrounding the pyrenoid and inside the thylakoid lumen. Two almost identical mitochondrial CAs, CAH4 and CAH5, are also highly expressed when the CCM is made, but their role in the CCM is not understood. Here, we adopted an RNAi approach to reduce the expression of CAH4 and CAH5 to study their possible physiological functions. RNAi mutants with low expression of CAH4 and CAH5 had impaired rates of photosynthesis under ambient levels of CO2 (0.04% CO2 [v/v] in air). These strains were not able to grow at very low CO2 (<0.02% CO2 [v/v] in air), and their ability to accumulate inorganic carbon (Ci = CO2 + HCO3-) was reduced. At low CO2 concentrations, the CCM is needed to both deliver Ci to Rubisco and to minimize the leak of CO2 generated by respiration and photorespiration. We hypothesize that CAH4 and CAH5 in the mitochondria convert the CO2 released from respiration and photorespiration as well as the CO2 leaked from the chloroplast to HCO3- thus "recapturing" this potentially lost CO2.
Collapse
Affiliation(s)
- Ashwani K Rai
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Timothy Chen
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
- Author for communication:
| |
Collapse
|
32
|
Rottet S, Förster B, Hee WY, Rourke LM, Price GD, Long BM. Engineered Accumulation of Bicarbonate in Plant Chloroplasts: Known Knowns and Known Unknowns. FRONTIERS IN PLANT SCIENCE 2021; 12:727118. [PMID: 34531888 PMCID: PMC8438413 DOI: 10.3389/fpls.2021.727118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/06/2021] [Indexed: 05/10/2023]
Abstract
Heterologous synthesis of a biophysical CO2-concentrating mechanism (CCM) in plant chloroplasts offers significant potential to improve the photosynthetic efficiency of C3 plants and could translate into substantial increases in crop yield. In organisms utilizing a biophysical CCM, this mechanism efficiently surrounds a high turnover rate Rubisco with elevated CO2 concentrations to maximize carboxylation rates. A critical feature of both native biophysical CCMs and one engineered into a C3 plant chloroplast is functional bicarbonate (HCO3 -) transporters and vectorial CO2-to-HCO3 - converters. Engineering strategies aim to locate these transporters and conversion systems to the C3 chloroplast, enabling elevation of HCO3 - concentrations within the chloroplast stroma. Several CCM components have been identified in proteobacteria, cyanobacteria, and microalgae as likely candidates for this approach, yet their successful functional expression in C3 plant chloroplasts remains elusive. Here, we discuss the challenges in expressing and regulating functional HCO3 - transporter, and CO2-to-HCO3 - converter candidates in chloroplast membranes as an essential step in engineering a biophysical CCM within plant chloroplasts. We highlight the broad technical and physiological concerns which must be considered in proposed engineering strategies, and present our current status of both knowledge and knowledge-gaps which will affect successful engineering outcomes.
Collapse
Affiliation(s)
- Sarah Rottet
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
| | - Britta Förster
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Wei Yih Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
| | - Loraine M. Rourke
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
| | - G. Dean Price
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Benedict M. Long
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
33
|
The impact of photorespiration on plant primary metabolism through metabolic and redox regulation. Biochem Soc Trans 2021; 48:2495-2504. [PMID: 33300978 DOI: 10.1042/bst20200055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
Photorespiration is an inevitable trait of all oxygenic phototrophs, being the only known metabolic route that converts the inhibitory side-product of Rubisco's oxygenase activity 2-phosphoglycolate (2PG) back into the Calvin-Benson (CB) cycle's intermediate 3-phosphoglycerate (3PGA). Through this function of metabolite repair, photorespiration is able to protect photosynthetic carbon assimilation from the metabolite intoxication that would occur in the present-day oxygen-rich atmosphere. In recent years, much plant research has provided compelling evidence that photorespiration safeguards photosynthesis and engages in cross-talk with a number of subcellular processes. Moreover, the potential of manipulating photorespiration to increase the photosynthetic yield potential has been demonstrated in several plant species. Considering this multifaceted role, it is tempting to presume photorespiration itself is subject to a suite of regulation mechanisms to eventually exert a regulatory impact on other processes, and vice versa. The identification of potential pathway interactions and underlying regulatory aspects has been facilitated via analysis of the photorespiratory mutant phenotype, accompanied by the emergence of advanced omics' techniques and biochemical approaches. In this mini-review, I focus on the identification of enzymatic steps which control the photorespiratory flux, as well as levels of transcriptional, posttranslational, and metabolic regulation. Most importantly, glycine decarboxylase (GDC) and 2PG are identified as being key photorespiratory determinants capable of controlling photorespiratory flux and communicating with other branches of plant primary metabolism.
Collapse
|
34
|
Shukshina AK, Terentyev VV. Involvement of Carbonic Anhydrase CAH3 in the Structural and Functional Stabilization of the Water-Oxidizing Complex of Photosystem II from Chlamydomonas reinhardtii. BIOCHEMISTRY (MOSCOW) 2021; 86:867-877. [PMID: 34284710 DOI: 10.1134/s0006297921070075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The involvement of carbonic anhydrases (CA) and CA activity in the functioning of photosystem II (PSII) has been studied for a long time and has been shown in many works. However, so far only for CAH3 from Chlamydomonas reinhardtii there is evidence for its association with the donor side of PSII, where the CA activity of CAH3 can influence the functioning of the water-oxidizing complex (WOC). Our results suggest that CAH3 is also involved in the organization of the native structure of WOC independently of its CA activity. It was shown that in PSII preparations from wild type (WT) the high O2-evolving activity of WOC was observed up to 100 mM NaCl in the medium and practically did not decrease with increasing incubation time with NaCl. At the same time, the WOC function in PSII preparations from CAH3-deficient mutant cia3 is significantly inhibited already at NaCl concentrations above 35 mM, reaching 50% at 100 mM NaCl and increased incubation time. It is suggested that the absence of CAH3 in PSII from cia3 causes disruption of the native structure of WOC, allowing more pronounced conformational changes of its proteins and, consequently, suppression of the WOC active center function, when the ionic strength of the medium is increased. The results of Western blot analysis indicate a more difficult removal of PsbP protein from PSII of cia3 at higher NaCl concentrations, apparently due to the changes in the intermolecular interactions between proteins of WOC in the absence of CAH3. At the same time, the values of the maximum quantum yield of PSII did not practically differ between preparations from WT and cia3, indicating no effect of CAH3 on the photoinduced electron transfer in the reaction center of PSII. The obtained results indicate the involvement of the CAH3 protein in the native organization of the WOC and, as a consequence, in the stabilization of its functional state in PSII from C. reinhardtii.
Collapse
Affiliation(s)
- Anna K Shukshina
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Vasily V Terentyev
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| |
Collapse
|
35
|
Spät P, Barske T, Maček B, Hagemann M. Alterations in the CO 2 availability induce alterations in the phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2021; 231:1123-1137. [PMID: 34058021 DOI: 10.1111/nph.17423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Cyanobacteria are the only prokaryotes that perform plant-like oxygenic photosynthesis. They evolved an inorganic carbon-concentrating mechanism to adapt to low CO2 conditions. Quantitative phosphoproteomics was applied to analyze regulatory features during the acclimation to low CO2 conditions in the model cyanobacterium Synechocystis sp. PCC 6803. Overall, more than 2500 proteins were quantified, equivalent to c. 70% of the Synechocystis theoretical proteome. Proteins with changing abundances correlated largely with mRNA expression levels. Functional annotation of the noncorrelating proteins revealed an enrichment of key metabolic processes fundamental for maintaining cellular homeostasis. Furthermore, 105 phosphoproteins harboring over 200 site-specific phosphorylation events were identified. Subunits of the bicarbonate transporter BCT1 and the redox switch protein CP12 were among phosphoproteins with reduced phosphorylation levels at lower CO2 , whereas the serine/threonine protein kinase SpkC revealed increased phosphorylation levels. The corresponding ΔspkC mutant was characterized and showed decreased ability to acclimate to low CO2 conditions. Possible phosphorylation targets of SpkC including a BCT1 subunit were identified by phosphoproteomics. Collectively, our study highlights the importance of posttranscriptional regulation of protein abundances as well as posttranslational regulation by protein phosphorylation for the successful acclimation towards low CO2 conditions in Synechocystis and possibly among cyanobacteria.
Collapse
Affiliation(s)
- Philipp Spät
- Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, D-72076, Germany
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Thomas Barske
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
- Department Life, Light and Matter, Interdisciplinary Faculty, University of Rostock, Rostock, D-18059, Germany
| |
Collapse
|
36
|
Santhanagopalan I, Wong R, Mathur T, Griffiths H. Orchestral manoeuvres in the light: crosstalk needed for regulation of the Chlamydomonas carbon concentration mechanism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4604-4624. [PMID: 33893473 PMCID: PMC8320531 DOI: 10.1093/jxb/erab169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 05/19/2023]
Abstract
The inducible carbon concentration mechanism (CCM) in Chlamydomonas reinhardtii has been well defined from a molecular and ultrastructural perspective. Inorganic carbon transport proteins, and strategically located carbonic anhydrases deliver CO2 within the chloroplast pyrenoid matrix where Rubisco is packaged. However, there is little understanding of the fundamental signalling and sensing processes leading to CCM induction. While external CO2 limitation has been believed to be the primary cue, the coupling between energetic supply and inorganic carbon demand through regulatory feedback from light harvesting and photorespiration signals could provide the original CCM trigger. Key questions regarding the integration of these processes are addressed in this review. We consider how the chloroplast functions as a crucible for photosynthesis, importing and integrating nuclear-encoded components from the cytoplasm, and sending retrograde signals to the nucleus to regulate CCM induction. We hypothesize that induction of the CCM is associated with retrograde signals associated with photorespiration and/or light stress. We have also examined the significance of common evolutionary pressures for origins of two co-regulated processes, namely the CCM and photorespiration, in addition to identifying genes of interest involved in transcription, protein folding, and regulatory processes which are needed to fully understand the processes leading to CCM induction.
Collapse
Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Rachel Wong
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | - Tanya Mathur
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, UK
| | | |
Collapse
|
37
|
Yun EJ, Zhang GC, Atkinson C, Lane S, Liu JJ, Ort DR, Jin YS. Glycolate production by a Chlamydomonas reinhardtii mutant lacking carbon-concentrating mechanism. J Biotechnol 2021; 335:39-46. [PMID: 34090947 DOI: 10.1016/j.jbiotec.2021.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022]
Abstract
The green alga Chlamydomonas reinhardtii serves as a model organism for plant and photosynthesis research due to many commonalities in metabolism and to the fast growth rate of C. reinhardtii which accelerates experimental turnaround time. In addition, C. reinhardtii is a focus of research efforts in metabolic engineering and synthetic biology for the potential production of biofuels and value-added chemicals. Here, we report that the C. reinhardtii cia5 mutant, which lacks a functional carbon-concentrating mechanism (CCM), can produce substantial amounts of glycolate, a high-value cosmetic ingredient, when the mutant is cultured under ambient air conditions. In order to reveal the metabolic basis of glycolate accumulation by the cia5 mutant, we investigated the metabolomes of the cia5 mutant and a wild type strain CC-125 (WT) through the global metabolic profiling of intracellular and extracellular fractions using gas chromatography and mass spectrometry. We observed the intracellular and extracellular metabolic profiles of the WT and the cia5 mutant were similar during the mixotrophic phase at 30 h. However, when the cells entered the photoautotrophic phase (i.e., 96 h and 120 h), both the intracellular and extracellular metabolic profiles of cia5 mutant differed significantly when compared to WT. In the cia5 mutant strain, a group of photorespiration pathway intermediates including glycolate, glyoxylate, glycine, and serine accumulated to significantly higher levels compared to WT. In the photorespiration pathway, glycolate is metabolized to glyoxylate and glycine leading to NH3 and CO2 generation during the mitochondrial conversion of glycine to serine. This result provides further evidence that the CIA5 mutation increased the photorespiration rate. Because the cia5 mutant lacks a CCM, and C. reinhardtii might harbor an inefficient or incomplete photorespiration pathway, glycolate may accumulate when the CCM is not functional. We envision that investigating photorespiration controls in C. reinhardtii provides tools for producers to use the cia5 mutant to produce glycolate as well as platform to engineer alternative pathways for glycolate metabolism.
Collapse
Affiliation(s)
- Eun Ju Yun
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guo-Chang Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christine Atkinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stephan Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
38
|
Salomé PA, Merchant SS. Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery. THE PLANT CELL 2021; 33:1058-1082. [PMID: 33793846 PMCID: PMC8226298 DOI: 10.1093/plcell/koab042] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/25/2021] [Indexed: 05/18/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.
Collapse
|
39
|
Blifernez-Klassen O, Berger H, Mittmann BGK, Klassen V, Schelletter L, Buchholz T, Baier T, Soleimani M, Wobbe L, Kruse O. A gene regulatory network for antenna size control in carbon dioxide-deprived Chlamydomonas reinhardtii cells. THE PLANT CELL 2021; 33:1303-1318. [PMID: 33793853 DOI: 10.1093/plcell/koab012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
In green microalgae, prolonged exposure to inorganic carbon depletion requires long-term acclimation responses, involving modulated gene expression and the adjustment of photosynthetic activity to the prevailing supply of carbon dioxide. Here, we describe a microalgal regulatory cycle that adjusts the light-harvesting capacity at photosystem II (PSII) to the prevailing supply of carbon dioxide in Chlamydomonas (Chlamydomonas reinhardtii). It engages low carbon dioxide response factor (LCRF), a member of the squamosa promoter-binding protein (SBP) family of transcription factors, and the previously characterized cytosolic translation repressor nucleic acid-binding protein 1 (NAB1). LCRF combines a DNA-binding SBP domain with a conserved domain for protein-protein interaction. LCRF transcription is rapidly induced by carbon dioxide depletion. LCRF activates NAB1 transcription by specifically binding to tetranucleotide motifs present in its promoter. Accumulation of the NAB1 protein enhances translational repression of its prime target mRNA, encoding the PSII-associated major light-harvesting protein LHCBM6. The resulting truncation of the PSII antenna size helps maintaining a low excitation during carbon dioxide limitation. Analyses of low carbon dioxide acclimation in nuclear insertion mutants devoid of a functional LCRF gene confirm the essentiality of this novel transcription factor for the regulatory circuit.
Collapse
Affiliation(s)
- Olga Blifernez-Klassen
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Hanna Berger
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Birgit Gerlinde Katharina Mittmann
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Viktor Klassen
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Louise Schelletter
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Tatjana Buchholz
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Maryna Soleimani
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Lutz Wobbe
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany
| |
Collapse
|
40
|
Emrich-Mills TZ, Yates G, Barrett J, Girr P, Grouneva I, Lau CS, Walker CE, Kwok TK, Davey JW, Johnson MP, Mackinder LCM. A recombineering pipeline to clone large and complex genes in Chlamydomonas. THE PLANT CELL 2021; 33:1161-1181. [PMID: 33723601 PMCID: PMC8633747 DOI: 10.1093/plcell/koab024] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/18/2021] [Indexed: 05/10/2023]
Abstract
The ability to clone genes has greatly advanced cell and molecular biology research, enabling researchers to generate fluorescent protein fusions for localization and confirm genetic causation by mutant complementation. Most gene cloning is polymerase chain reaction (PCR)�or DNA synthesis-dependent, which can become costly and technically challenging as genes increase in size, particularly if they contain complex regions. This has been a long-standing challenge for the Chlamydomonas reinhardtii research community, as this alga has a high percentage of genes containing complex sequence structures. Here we overcame these challenges by developing a recombineering pipeline for the rapid parallel cloning of genes from a Chlamydomonas bacterial artificial chromosome collection. To generate fluorescent protein fusions for localization, we applied the pipeline at both batch and high-throughput scales to 203 genes related to the Chlamydomonas CO2 concentrating mechanism (CCM), with an overall cloning success rate of 77%. Cloning success was independent of gene size and complexity, with cloned genes as large as 23 kb. Localization of a subset of CCM targets confirmed previous mass spectrometry data, identified new pyrenoid components, and enabled complementation of mutants. We provide vectors and detailed protocols to facilitate easy adoption of this technology, which we envision will open up new possibilities in algal and plant research.
Collapse
Affiliation(s)
- Tom Z Emrich-Mills
- Department of Biology, University of York, York YO10 5DD, UK
- Department Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Gary Yates
- Department of Biology, University of York, York YO10 5DD, UK
| | - James Barrett
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Department of Biology, University of York, York YO10 5DD, UK
| | - Irina Grouneva
- Department of Biology, University of York, York YO10 5DD, UK
| | - Chun Sing Lau
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Tsz Kam Kwok
- Department of Biology, University of York, York YO10 5DD, UK
| | - John W Davey
- Department of Biology, University of York, York YO10 5DD, UK
| | - Matthew P Johnson
- Department Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Luke C M Mackinder
- Department of Biology, University of York, York YO10 5DD, UK
- Author for correspondence: (L.C.M.M.)
| |
Collapse
|
41
|
Barrett J, Girr P, Mackinder LCM. Pyrenoids: CO 2-fixing phase separated liquid organelles. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118949. [PMID: 33421532 DOI: 10.1016/j.bbamcr.2021.118949] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023]
Abstract
Pyrenoids are non-membrane bound organelles found in chloroplasts of algae and hornwort plants that can be seen by light-microscopy. Pyrenoids are formed by liquid-liquid phase separation (LLPS) of Rubisco, the primary CO2 fixing enzyme, with an intrinsically disordered multivalent Rubisco-binding protein. Pyrenoids are the heart of algal and hornwort biophysical CO2 concentrating mechanisms, which accelerate photosynthesis and mediate about 30% of global carbon fixation. Even though LLPS may underlie the apparent convergent evolution of pyrenoids, our current molecular understanding of pyrenoid formation comes from a single example, the model alga Chlamydomonas reinhardtii. In this review, we summarise current knowledge about pyrenoid assembly, regulation and structural organization in Chlamydomonas and highlight evidence that LLPS is the general principle underlying pyrenoid formation across algal lineages and hornworts. Detailed understanding of the principles behind pyrenoid assembly, regulation and structural organization within diverse lineages will provide a fundamental understanding of this biogeochemically important organelle and help guide ongoing efforts to engineer pyrenoids into crops to increase photosynthetic performance and yields.2.
Collapse
Affiliation(s)
- James Barrett
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Department of Biology, University of York, York YO10 5DD, UK
| | | |
Collapse
|
42
|
Treves H, Siemiatkowska B, Luzarowska U, Murik O, Fernandez-Pozo N, Moraes TA, Erban A, Armbruster U, Brotman Y, Kopka J, Rensing SA, Szymanski J, Stitt M. Multi-omics reveals mechanisms of total resistance to extreme illumination of a desert alga. NATURE PLANTS 2020; 6:1031-1043. [PMID: 32719473 DOI: 10.1038/s41477-020-0729-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/24/2020] [Indexed: 05/25/2023]
Abstract
The unparalleled performance of Chlorella ohadii under irradiances of twice full sunlight underlines the gaps in our understanding of how the photosynthetic machinery operates, and what sets its upper functional limit. Rather than succumbing to photodamage under extreme irradiance, unique features of photosystem II function allow C. ohadii to maintain high rates of photosynthesis and growth, accompanied by major changes in composition and cellular structure. This remarkable resilience allowed us to investigate the systems response of photosynthesis and growth to extreme illumination in a metabolically active cell. Using redox proteomics, transcriptomics, metabolomics and lipidomics, we explored the cellular mechanisms that promote dissipation of excess redox energy, protein S-glutathionylation, inorganic carbon concentration, lipid and starch accumulation, and thylakoid stacking. C. ohadii possesses a readily available capacity to utilize a sudden excess of reducing power and carbon for growth and reserve formation, and post-translational redox regulation plays a pivotal role in this rapid response. Frequently the response in C. ohadii deviated from that of model species, reflecting its life history in desert sand crusts. Comparative global and case-specific analyses provided insights into the potential evolutionary role of effective reductant utilization in this extreme resistance of C. ohadii to extreme irradiation.
Collapse
Affiliation(s)
- Haim Treves
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany.
| | | | | | - Omer Murik
- Department of Plant & Environmental Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | | | - Alexander Erban
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Ute Armbruster
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Stefan Andreas Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Jedrzej Szymanski
- Department of Network Analysis and Modelling, IPK, Gatersleben, Germany
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| |
Collapse
|
43
|
Timm S, Hagemann M. Photorespiration-how is it regulated and how does it regulate overall plant metabolism? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3955-3965. [PMID: 32274517 DOI: 10.1093/jxb/eraa183] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/08/2020] [Indexed: 05/03/2023]
Abstract
Under the current atmospheric conditions, oxygenic photosynthesis requires photorespiration to operate. In the presence of low CO2/O2 ratios, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) performs an oxygenase side reaction, leading to the formation of high amounts of 2-phosphoglycolate during illumination. Given that 2-phosphoglycolate is a potent inhibitor of photosynthetic carbon fixation, it must be immediately removed through photorespiration. The core photorespiratory cycle is orchestrated across three interacting subcellular compartments, namely chloroplasts, peroxisomes, and mitochondria, and thus cross-talks with a multitude of other cellular processes. Over the past years, the metabolic interaction of photorespiration and photosynthetic CO2 fixation has attracted major interest because research has demonstrated the enhancement of C3 photosynthesis and growth through the genetic manipulation of photorespiration. However, to optimize future engineering approaches, it is also essential to improve our current understanding of the regulatory mechanisms of photorespiration. Here, we summarize recent progress regarding the steps that control carbon flux in photorespiration, eventually involving regulatory proteins and metabolites. In this regard, both genetic engineering and the identification of various layers of regulation point to glycine decarboxylase as the key enzyme to regulate and adjust the photorespiratory carbon flow. Potential implications of the regulation of photorespiration for acclimation to environmental changes along with open questions are also discussed.
Collapse
Affiliation(s)
- Stefan Timm
- University of Rostock, Plant Physiology Department, Rostock, Germany
| | - Martin Hagemann
- University of Rostock, Plant Physiology Department, Rostock, Germany
| |
Collapse
|
44
|
|
45
|
Metabolic, Physiological, and Transcriptomics Analysis of Batch Cultures of the Green Microalga Chlamydomonas Grown on Different Acetate Concentrations. Cells 2019; 8:cells8111367. [PMID: 31683711 PMCID: PMC6912441 DOI: 10.3390/cells8111367] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 01/13/2023] Open
Abstract
Acetate can be efficiently metabolized by the green microalga Chlamydomonas reinhardtii. The regular concentration is 17 mM, although higher concentrations are reported to increase starch and fatty acid content. To understand the responses to higher acetate concentrations, Chlamydomonas cells were cultivated in batch mode in the light at 17, 31, 44, and 57 mM acetate. Metabolic analyses show that cells grown at 57 mM acetate possess increased contents of all components analyzed (starch, chlorophylls, fatty acids, and proteins), with a three-fold increased volumetric biomass yield compared to cells cultivated at 17 mM acetate at the entry of stationary phase. Physiological analyses highlight the importance of photosynthesis for the low-acetate and exponential-phase samples. The stationary phase is reached when acetate is depleted, except for the cells grown at 57 mM acetate, which still divide until ammonium exhaustion. Surprisal analysis of the transcriptomics data supports the biological significance of our experiments. This allows the establishment of a model for acetate assimilation, its transcriptional regulation and the identification of candidates for genetic engineering of this metabolic pathway. Altogether, our analyses suggest that growing at high-acetate concentrations could increase biomass productivities in low-light and CO2-limiting air-bubbled medium for biotechnology.
Collapse
|
46
|
Mukherjee A, Lau CS, Walker CE, Rai AK, Prejean CI, Yates G, Emrich-Mills T, Lemoine SG, Vinyard DJ, Mackinder LCM, Moroney JV. Thylakoid localized bestrophin-like proteins are essential for the CO 2 concentrating mechanism of Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2019; 116:16915-16920. [PMID: 31391312 DOI: 10.1073/pnas.190970611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
The green alga Chlamydomonas reinhardtii possesses a CO2 concentrating mechanism (CCM) that helps in successful acclimation to low CO2 conditions. Current models of the CCM postulate that a series of ion transporters bring HCO3- from outside the cell to the thylakoid lumen, where the carbonic anhydrase 3 (CAH3) dehydrates accumulated HCO3- to CO2, raising the CO2 concentration for Ribulose bisphosphate carboxylase/oxygenase (Rubisco). Previously, HCO3- transporters have been identified at both the plasma membrane and the chloroplast envelope, but the transporter thought to be on the thylakoid membrane has not been identified. Three paralogous genes (BST1, BST2, and BST3) belonging to the bestrophin family have been found to be up-regulated in low CO2 conditions, and their expression is controlled by CIA5, a transcription factor that controls many CCM genes. YFP fusions demonstrate that all 3 proteins are located on the thylakoid membrane, and interactome studies indicate that they might associate with chloroplast CCM components. A single mutant defective in BST3 has near-normal growth on low CO2, indicating that the 3 bestrophin-like proteins may have redundant functions. Therefore, an RNA interference (RNAi) approach was adopted to reduce the expression of all 3 genes at once. RNAi mutants with reduced expression of BST1-3 were unable to grow at low CO2 concentrations, exhibited a reduced affinity to inorganic carbon (Ci) compared with the wild-type cells, and showed reduced Ci uptake. We propose that these bestrophin-like proteins are essential components of the CCM that deliver HCO3- accumulated in the chloroplast stroma to CAH3 inside the thylakoid lumen.
Collapse
Affiliation(s)
- Ananya Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Chun Sing Lau
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Charlotte E Walker
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Ashwani K Rai
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Camille I Prejean
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Gary Yates
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Thomas Emrich-Mills
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer G Lemoine
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - David J Vinyard
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Luke C M Mackinder
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803;
| |
Collapse
|
47
|
Thylakoid localized bestrophin-like proteins are essential for the CO 2 concentrating mechanism of Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2019; 116:16915-16920. [PMID: 31391312 PMCID: PMC6708349 DOI: 10.1073/pnas.1909706116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Models of the CO2 concentrating mechanism (CCM) of green algae and diatoms postulate that chloroplast CO2 is generated from HCO3− brought into the acidic thylakoid lumen and converted to CO2 by specific thylakoid carbonic anhydrases. However, the identity of the transporter required for thylakoid HCO3− uptake has remained elusive. In this work, 3 bestrophin-like proteins, BST1–3, located on the thylakoid membrane have been found to be essential to the CCM of Chlamydomonas. Reduction in expression of BST1–3 markedly reduced the inorganic carbon affinity of the alga. These proteins are prime candidates to be thylakoid HCO3− transporters, a critical currently missing step of the CCM required for future engineering efforts of the Chlamydomonas CCM into plants to improve photosynthesis. The green alga Chlamydomonas reinhardtii possesses a CO2 concentrating mechanism (CCM) that helps in successful acclimation to low CO2 conditions. Current models of the CCM postulate that a series of ion transporters bring HCO3− from outside the cell to the thylakoid lumen, where the carbonic anhydrase 3 (CAH3) dehydrates accumulated HCO3− to CO2, raising the CO2 concentration for Ribulose bisphosphate carboxylase/oxygenase (Rubisco). Previously, HCO3− transporters have been identified at both the plasma membrane and the chloroplast envelope, but the transporter thought to be on the thylakoid membrane has not been identified. Three paralogous genes (BST1, BST2, and BST3) belonging to the bestrophin family have been found to be up-regulated in low CO2 conditions, and their expression is controlled by CIA5, a transcription factor that controls many CCM genes. YFP fusions demonstrate that all 3 proteins are located on the thylakoid membrane, and interactome studies indicate that they might associate with chloroplast CCM components. A single mutant defective in BST3 has near-normal growth on low CO2, indicating that the 3 bestrophin-like proteins may have redundant functions. Therefore, an RNA interference (RNAi) approach was adopted to reduce the expression of all 3 genes at once. RNAi mutants with reduced expression of BST1–3 were unable to grow at low CO2 concentrations, exhibited a reduced affinity to inorganic carbon (Ci) compared with the wild-type cells, and showed reduced Ci uptake. We propose that these bestrophin-like proteins are essential components of the CCM that deliver HCO3− accumulated in the chloroplast stroma to CAH3 inside the thylakoid lumen.
Collapse
|
48
|
Salomé PA, Merchant SS. A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism. THE PLANT CELL 2019; 31:1682-1707. [PMID: 31189738 PMCID: PMC6713297 DOI: 10.1105/tpc.18.00952] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/20/2019] [Accepted: 06/08/2019] [Indexed: 05/13/2023]
Abstract
The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.
Collapse
Affiliation(s)
- Patrice A Salomé
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
| | - Sabeeha S Merchant
- University of California, Los Angeles, Department of Chemistry and Biochemistry, Los Angeles, CA 90095
- University of California, Berkeley, Departments of Plant and Microbial Biology and Molecular and Cell Biology, Berkeley, CA 94720
| |
Collapse
|
49
|
Knockdown of carbonate anhydrase elevates Nannochloropsis productivity at high CO2 level. Metab Eng 2019; 54:96-108. [DOI: 10.1016/j.ymben.2019.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 01/07/2023]
|
50
|
Terentyev VV, Shukshina AK, Shitov AV. Carbonic anhydrase CAH3 supports the activity of photosystem II under increased pH. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:582-590. [DOI: 10.1016/j.bbabio.2019.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/05/2019] [Accepted: 06/15/2019] [Indexed: 11/24/2022]
|