Krishna K. Niyogi's research while affiliated with Howard Hughes Medical Institute and other places

Publications (273)

Article
Full-text available
Photosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme b559 iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functio...
Article
Full-text available
Regulating the central CO2-fixing enzyme Rubisco is as complex as its ancient reaction mechanism and involves interaction with a series of co-factors and auxiliary proteins that activate catalytic sites and maintain activity. A key component among the regulatory mechanisms is the binding of sugar phosphate derivatives that inhibit activity. Removal...
Article
Full-text available
Plants and algae are faced with a conundrum: harvesting sufficient light to drive their metabolic needs while dissipating light in excess to prevent photodamage, a process known as non-photochemical quenching. A slowly relaxing form of energy dissipation, termed qH, is critical for plants’ survival under abiotic stress; however, qH location in the...
Article
Crop leaves in full sunlight dissipate damaging excess absorbed light energy as heat. This protective dissipation continues after the leaf transitions to shade, reducing crop photosynthesis. A bioengineered acceleration of this adjustment increased photosynthetic efficiency and biomass in tobacco in the field. But could that also translate to incre...
Preprint
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Life on earth depends on photosynthetic primary producers that exploit sunlight to fix CO 2 into biomass. Approximately half of global primary production is associated with microalgae living in aquatic environments. Microalgae also represent a promising source of biomass to complement crop cultivation, and they could contribute to the development o...
Article
Full-text available
Photosynthetic organisms use sunlight as the primary energy source to fix CO2 . However, in nature, light energy is highly variable, reaching levels of saturation for periods ranging from milliseconds to hours. In the green microalga Chlamydomonas reinhardtii, safe dissipation of excess light energy by non-photochemical quenching (NPQ) is mediated...
Article
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p>We explore the photoprotection dynamics of Nannochloropsis oceanica using time-correlated single photon counting under regular and irregular actinic light sequences. The varying light sequences mimic natural conditions, allowing us to probe the real-time response of non-photochemical quenching (NPQ) pathways. Durations of fluctuating light exposu...
Article
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Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represen...
Preprint
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The assembly of photosystem II (PSII) requires the participation of assembly proteins that facilitate the step-wise association of its protein and pigment components into a functional complex capable of oxidizing water and reducing plastoquinone. We previously identified one such factor, the membrane-bound rubredoxin RBD1, but its precise role rema...
Article
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As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogrammin...
Preprint
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Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a drought-tolerant cereal capable of producing high yields under water scarcity conditions. Functional stay-green sorghum genotypes can maintain green leaf area and efficient grain filling in terminal post-flowerin...
Preprint
Full-text available
Photosynthetic organisms use sunlight as the primary energy source to fix CO 2 . However, in the environment, light energy fluctuates rapidly and often exceeds saturating levels for periods ranging from seconds to hours, which can lead to detrimental effects for cells. Safe dissipation of excess light energy occurs primarily by non-photochemical qu...
Preprint
Full-text available
Rice production is of paramount importance for global nutrition and potential yields will be detrimentally affected by climate change. Rice stomatal developmental genetics were explored as a mechanism to improve water use efficiency while maintaining yield under climate stress. Gene-editing of STOMAGEN and its paralog, EPFL10, using CRISPR/Cas9 in...
Article
Full-text available
When grown under cool temperature, winter annuals upregulate photosynthetic capacity as well as freezing tolerance. Here, the role of three cold-induced C-repeat-Binding Factor (CBF1–3) transcription factors in photosynthetic upregulation and freezing tolerance was examined in two Arabidopsis thaliana ecotypes originating from Italy (IT) or Sweden...
Preprint
Full-text available
As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g. phytochromes) and subsequent transduction into long-term transcriptional reprogramming...
Preprint
Full-text available
When grown under cool temperature, winter annuals upregulate photosynthetic capacity as well as freezing tolerance. Here, the role of three cold-induced C-repeat-Binding Factor (CBF1–3) transcription factors in photosynthetic upregulation and freezing tolerance was examined in two Arabidopsis thaliana ecotypes originating from Italy (IT) or Sweden...
Article
Full-text available
C4 plants frequently experience high light and high temperature conditions in the field, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridi...
Article
Full-text available
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previous...
Article
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One-sentence summary: Advances in proteomic and transcriptomic studies have made Chlamydomonas a powerful research model in redox and reactive oxygen species regulation with unique and overlapping mechanisms with plants.
Article
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The responses of plants to their environment are often dependent on the spatiotemporal dynamics of transcriptional regulation. While live-imaging tools have been used extensively to quantitatively capture rapid transcriptional dynamics in living animal cells, the lack of implementation of these technologies in plants has limited concomitant quantit...
Preprint
Full-text available
Excess light can induce photodamage to the photosynthetic machinery, therefore plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). Different NPQ components have been identified and classified based on their relaxation kinetics and molecular players. The NPQ component qE is induced and relaxed rapidly (seconds t...
Preprint
Full-text available
Photoprotection mechanisms are ubiquitous among photosynthetic organisms. The photoprotection capacity of the green alga Chlamydomonas reinhardtii is correlated with protein levels of stress-related light-harvesting complex (LHCSR) proteins, which are strongly induced by high light (HL). However, the dynamic response of overall thylakoid structure...
Preprint
Full-text available
C4 plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the...
Preprint
Full-text available
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previous...
Article
Plants in dryland ecosystems experience extreme daily and seasonal fluctuations in light, temperature, and water availability. We used an in-situ field experiment to uncover the effects of natural and reduced levels of UV on maximum PSII quantum efficiency (Fv/Fm), relative abundance of photosynthetic pigments and antioxidants, and the transcriptom...
Article
Full-text available
Significance Historically, it has been understood that for gene expression in eukaryotes, each messenger RNA encodes a single protein. With the recent development of technologies to sequence full-length transcripts en masse, we have discovered hundreds of examples in two species of green algae where two, three, or more proteins are translated from...
Article
Full-text available
Diverse algae of the red lineage possess chlorophyll a -binding proteins termed LHCR, comprising the PSI light-harvesting system, which represent an ancient antenna form that evolved in red algae and was acquired through secondary endosymbiosis. However, the function and regulation of LHCR complexes remain obscure. Here we describe isolation of a N...
Preprint
Full-text available
The induction of high photosynthetic capacity (i.e., the CO2- and light-saturated maximum photosynthetic rate) in HL is a shared response among many herbaceous dicot plants. The increase in photosynthetic capacity following a shift to growth in high light (HL) was measured across a large panel of Arabidopsis thaliana ecotypes revealing substantial...
Preprint
Photosynthetic organisms are essential for human life, yet most of their genes remain functionally uncharacterized. Single-celled photosynthetic model systems have the potential to accelerate our ability to connect genes to functions. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phe...
Article
Full-text available
The importance of green light for driving natural photosynthesis has long been underappreciated, however, under the presence of strong illumination, green light actually drives photosynthesis more efficiently than red light. This green light is absorbed by mixed vibronic Qy-Qx states, arising from chlorophyll (Chl)-Chl interactions, although almost...
Article
Protection of photosystem II against damage from excess light by nonphotochemical quenching (NPQ) includes responses on a wide range of timescales. The onset of the various phases of NPQ overlap in time making it difficult to discern if they influence each other or involve different photophysical mechanisms. To unravel the complex relationship of t...
Preprint
Full-text available
Understanding photosynthetic light harvesting requires knowledge of the molecular mechanisms that dissipate excess energy in thylakoids. However, it remains unclear how the physical environment of light-harvesting complex II (LHCII) influences the process of chlorophyll de-excitation. Here, we demonstrate that protein-protein interactions between L...
Preprint
Full-text available
The responses of plants to their environment often hinge on the spatiotemporal dynamics of transcriptional regulation. While live-imaging tools have been used extensively to quantitatively capture rapid transcriptional dynamics in living animal cells, lack of implementation of these technologies in plants has limited concomitant quantitative studie...
Preprint
Full-text available
The importance of green light for driving natural photosynthesis has long been underappreciated, however, under the presence of strong illumination, green light actually drives photosynthesis more efficiently than red light. This green light is absorbed by mixed vibronic Q y -Q x states, arising from chlorophyll (Chl)-Chl interactions, although alm...
Article
Full-text available
Significance Carotenoids are essential molecules in oxygenic photoautotrophs, and they fulfill essential requirements for human and animal nutrition. How carotenoid accumulation is regulated in the chloroplast, a cyanobacterium-derived organelle, remains poorly understood, despite significant advancements in identifying enzymes of the carotenoid bi...
Article
Full-text available
Significance The light reactions of photosynthesis in algae and plants occur in thylakoid membranes within the chloroplast. Previous studies have implicated membrane contact sites, vesicle trafficking, and lipid-binding proteins in the formation of thylakoids at the chloroplast inner envelope, but the molecular basis of thylakoid biogenesis and mai...
Article
Full-text available
Since the discovery of quantum beats in the two-dimensional electronic spectra of photosynthetic pigment-protein complexes over a decade ago, the origin and mechanistic function of these beats in photosynthetic light-harvesting has been extensively debated. The current consensus is that these long-lived oscillatory features likely result from elect...
Article
Full-text available
Fucoxanthin and its derivatives are the main light-harvesting pigments in the photosynthetic apparatus of many chromalveolate algae and represent the most abundant carotenoids in the world’s oceans, thus being major facilitators of marine primary production. A central step in fucoxanthin biosynthesis that has been elusive so far is the conversion o...
Article
Full-text available
Thylakoid membranes in chloroplasts contain photosynthetic protein complexes that convert light energy into chemical energy. Photosynthetic protein complexes are considered to undergo structural reorganization to maintain the efficiency of photochemical reactions. A detailed description of the mobility of photosynthetic complexes in real-time is ne...
Article
Full-text available
Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid...
Conference Paper
This work reinvestigates the subpicosecond energy transfer (ET) dynamics of light-harvesting complex II with two-dimensional electronic-vibrational spectroscopy (2DEV). With the help of a straightforward theoretical model, emphasis is also more generally placed on the manifestation of ET in 2DEV.
Article
Full-text available
Drought is the most important environmental stress limiting crop yields. The C4 cereal sorghum [ Sorghum bicolor (L.) Moench] is a critical food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing preflowering and postflowering drought stress on 2 genotypes of sorghum across a...
Article
Full-text available
Global primary production is driven largely by oxygenic photosynthesis, with algae as major contributors. The green alga Chromochloris zofingiensis reversibly switches off photosynthesis in the presence of glucose in the light and augments production of biofuel precursors (triacylglycerols) and the high-value antioxidant astaxanthin. Here we used f...
Article
Full-text available
Photosynthetic organisms use nonphotochemical quenching (NPQ) mechanisms to dissipate excess absorbed light energy and protect themselves from photooxidation. In the model green alga Chlamy-domonas reinhardtii, the capacity for rapidly reversible NPQ (qE) is induced by high light, blue light, and UV light via increased expression of LHCSR and PSBS...
Article
Full-text available
Significance Photosystem II (PSII) catalyzes the light-driven oxidation of water in photosynthesis, supplying energy and oxygen to many life-forms on earth. During PSII assembly and repair, PSII intermediate complexes are prone to photooxidative damage, requiring mechanisms to minimize this damage. Here, we report the functional characterization of...
Article
Light and nutrients are critical regulators of photosynthesis and metabolism in plants and algae. Many algae have the metabolic flexibility to grow photoautotrophically, heterotrophically, or mixotrophically. Here, we describe reversible glucose-dependent repression/activation of oxygenic photosynthesis in the unicellular green alga Chromochloris z...
Article
Significance Manipulating the nonphotochemical quenching (NPQ) capabilities of photosynthetic organisms is known to result in increased crop productivity. However, optimization of yields also requires a detailed molecular understanding of the mechanism of NPQ in vivo with specific attention to the roles of the carotenoid zeaxanthin and various ∆pH-...
Article
Full-text available
The photosynthesis machinery in chloroplast thylakoid membranes is comprised of multiple protein complexes and supercomplexes1,2. Here, we show a novel supramolecular organization of photosystem I (PSI) in the moss Physcomitrella patens by single-particle cryo-electron microscopy. The moss-specific light-harvesting complex (LHC) protein Lhcb9 is in...
Preprint
Full-text available
Thylakoid membranes in chloroplasts contain photosynthetic protein complexes that convert light energy into chemical energy. Photosynthetic protein complexes are considered to undergo structural reorganization to maintain the efficiency of photochemical reactions. A detailed description of the mobility of photosynthetic complexes in real-time is ne...
Article
Nonphotochemical quenching (NPQ) provides an essential photoprotection in plants, assuring safe dissipation of excess energy as heat under high light. Although excitation energy transfer (EET) between chlorophyll (Chl) and carotenoid (Car) molecules plays an important role in NPQ, detailed information on the EET quenching mechanism under in vivo co...
Article
The chloroplast is the chlorophyll‐containing organelle that produces energy through photosynthesis. Within the chloroplast is an intricate network of thylakoid membranes containing photosynthetic membrane proteins that mediate electron transport and generate chemical energy. Historically, electron microscopy has been a powerful tool to visualize t...
Article
The GreenCut encompasses a suite of nucleus‐encoded proteins with orthologs among green lineage organisms (plants, green algae), but that are absent or poorly conserved in non‐photosynthetic/heterotrophic organisms. In Chlamydomonas reinhardtii, CPLD49 (Conserved in Plant Lineage and Diatoms49) is an uncharacterized GreenCut protein that is critica...
Article
Full-text available
Insufficient water availability for crop production is a mounting barrier to achieving the 70% increase in food production that will be needed by 2050. One solution is to develop crops that require less water per unit mass of production. Water vapor transpires from leaves through stomata, which also facilitate the influx of CO2during photosynthetic...
Article
Full-text available
Light utilization is finely tuned in photosynthetic organisms to prevent cellular damage. The dissipation of excess absorbed light energy, a process termed NPQ, plays an important role in photoprotection. Little is known about the sustained or slowly reversible form(s) of NPQ and whether they are photoprotective, in part due to the lack of mutants....
Article
Non-photochemical quenching mechanisms regulate light harvesting in oxygenic photosynthesis. Measurement techniques for non-photochemical quenching have typically focused on downstream effects of quenching, such as measuring reduced chlorophyll fluorescence. Here, to directly measure a species involved in quenching, we report snapshot transient abs...
Article
Significance Optimizing the balance between light harvesting and photoprotection holds great promise for improving photosynthetic efficiency and ultimately crop yields. The switch between these two states is regulated by xanthophyll cycling, which occurs in response to changing light conditions. Two xanthophyll cycles have been described in vascula...
Article
Significance The balance between light harvesting and photoprotection is a critical component of photosynthetic efficiency and must be maintained in fluctuating light conditions. Two xanthophylls play key roles in the vascular plant response to changes in light intensity: zeaxanthin and lutein. Chlorophyll fluorescence decay studies of Arabidopsis...
Data
Gene annotation. (A) Annotation Edit Distance (AED) distribution of gene models in the first annotation set after eliminating entries with AED = 1. (B). AED distribution of gene models in the second annotation after eliminating entries with AED = 1. (C) Proportion of gene models with protein domain hits in different heterokonts (abbreviated as indi...
Article
Significance The growing human population generates increasing demand for food and energy. Microalgae are a promising source of sustainable bioproducts whose production may not exacerbate worsening environmental problems. The green alga Chromochloris zofingiensis has potential as a biofuel feedstock and source of high-value nutraceutical molecules,...
Article
Full-text available
Main conclusion: Evidence shows that decreasing the light-harvesting antenna size of the photosystems in tobacco helps to increase the photosynthetic productivity and plant canopy biomass accumulation under high-density cultivation conditions. Decreasing, or truncating, the chlorophyll antenna size of the photosystems can theoretically improve pho...
Article
Full-text available
Significance Algae account for a large proportion of global primary productivity, and the carbon that they fix supports many ecosystems and associated services used by humans. Green algae overcome various physical limitations on the rate of CO 2 supply for photosynthesis by the action of carbon-concentrating mechanisms (CCM) that deliver CO 2 to th...
Article
Oxygenic photoautotrophs require mechanisms for rapidly matching the level of chlorophyll excited states from light harvesting with the rate of electron transport from water to carbon dioxide. These photoprotective reactions prevent formation of reactive excited states and photoinhibition. The fastest response to excess illumination is the so-calle...
Article
Full-text available
Significance Life on earth largely depends on the capture of light energy by plants through photosynthesis. Light is essential, but excess light is dangerous. Energy dissipation as heat is a major mechanism induced to protect the photosynthetic machinery. We report that UV-B perception by a specific photoreceptor in the nucleocytosolic compartment...
Article
Full-text available
Faster light adaptation improves productivity Crop plants protect themselves from excess sunlight by dissipating some light energy as heat, readjusting their systems when shadier conditions prevail. But the photosynthetic systems do not adapt to fluctuating light conditions as rapidly as a cloud passes overhead, resulting in suboptimal photosynthet...