Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth

A Flashforward Look into Solutions for Fruit and Vegetable Production

One of the most important challenges facing current and future generations is how climate change and continuous population growth adversely affect food security. To address this, the food system needs a complete transformation where more is produced in non-optimal and space-limited areas while reducing negative environmental impacts. Fruits and vegetables, essential for human health, are high-value-added crops, which are grown in both greenhouses and open field environments. Here, we review potential practices to reduce the impact of climate variation and ecosystem damages on fruit and vegetable crop yield, as well as highlight current bottlenecks for indoor and outdoor agrosystems. To obtain sustainability, high-tech greenhouses are increasingly important and biotechnological means are becoming instrumental in designing the crops of tomorrow. We discuss key traits that need to be studied to improve agrosystem sustainability and fruit yield.

Contributions of species shade tolerance and individual light environment to photosynthetic induction in tropical tree seedlings

It has long been debated whether tree leaves from shady environments exhibit higher photosynthetic induction efficiency (IE) than those from sunny environments and how the shade tolerance of tree species and the light environment of leaves contribute to the dynamics of photosynthesis. To address these questions, we investigated leaf photosynthetic responses to simulated changes of light intensity in seedlings of six tree species with differential shade tolerance. The seedlings were growing under different light environments in a lowland tropical forest. We proposed an index of relative shade tolerance (RST) to assess species-specific capacity to tolerate shade, and we quantified the light environment of individual leaves by the index of daily light integral (DLI), the averaged daily total light intensity. We obtained the following results. Photosynthetic IE, which is the ratio of the achieved carbon gain to the expected carbon gain, was significantly higher for species with a higher RST than for that with a lower RST. The impacts of light environment on the IE of individual leaves within the same species varied largely among different species. In the three species with relatively low RST, the IE of individual leaves decreased at higher DLIs when DLI < 10 mol m-2 d-1. Seedlings with high initial stomatal conductance before induction (gs50) possessed a higher IE than those with low gs50 from the same species. A trade-off existed between IE and steady-state photosynthetic rates. These results suggest a complex interaction between the shade tolerance of species and the light environments of individual leaves for photosynthetic induction and provide new insights into the adaptation strategy for understory seedlings under sunfleck environments.

Tools for studying the cytoskeleton during plant cell division

The plant cytoskeleton regulates fundamental biological processes, including cell division. How to experimentally perturb the cytoskeleton is a key question if one wants to understand the role of both actin filaments (AFs) and microtubules (MTs) in a given biological process. While a myriad of mutants are available, knock-out in cytoskeleton regulators, when nonlethal, often produce little or no phenotypic perturbation because such regulators are often part of a large family, leading to functional redundancy. In this review, alternative techniques to modify the plant cytoskeleton during plant cell division are outlined. The different pharmacological and genetic approaches already developed in cell culture, transient assays, or in whole organisms are presented. Perspectives on the use of optogenetics to perturb the plant cytoskeleton are also discussed.

Quantitative System Modeling Bridges the Gap between Macro- and Microscopic Stomatal Model

An understanding of stomatal function is vital for the carbon and water cycle in nature. In the past decades, various stomatal models with different functions have been established to investigate and predict stomatal behavior and its association with plants' responses to the changing climate, but with limited biological information provided. On the other hand, many stomatal models at the molecular level focus on simulating and predicting molecular practices and ignore the dynamic quantitative information. As a result, stomatal models are often divided between the microscopic and macroscopic scales. Quantitative systems analysis offers an effective in silico approach to explore the link between microscopic gene function and macroscopic physiological traits. As a first step, a systems model, OnGuard, is developed for the investigation of guard cell ion homeostasis and its relevance to the dynamic stomatal movements. The system model has already yielded a series of important predictions to guide molecular physiological studies in stomata. It also exhibits great potential in breeding practice, which represents a key step toward "Breeding by design" of improving plant carbon-water use efficiency. Here, the development of stomatal models is reviewed, and the future perspectives on stomatal modeling for agricultural and ecological applications are discussed.

Strategies of tree species to adapt to drought from leaf stomatal regulation and stem embolism resistance to root properties

Considerable evidences highlight the occurrence of increasing widespread tree mortality as a result of global climate change-associated droughts. However, knowledge about the mechanisms underlying divergent strategies of various tree species to adapt to drought has remained remarkably insufficient. Leaf stomatal regulation and embolism resistance of stem xylem serves as two important strategies for tree species to prevent hydraulic failure and carbon starvation, as comprising interconnected physiological mechanisms underlying drought-induced tree mortality. Hence, the physiological and anatomical determinants of leaf stomatal regulation and stems xylem embolism resistance are evaluated and discussed. In addition, root properties related to drought tolerance are also reviewed. Species with greater investment in leaves and stems tend to maintain stomatal opening and resist stem embolism under drought conditions. The coordination between stomatal regulation and stem embolism resistance are summarized and discussed. Previous studies showed that hydraulic safety margin (HSM, the difference between minimum water potential and that causing xylem dysfunction) is a significant predictor of tree species mortality under drought conditions. Compared with HSM, stomatal safety margin (the difference between water potential at stomatal closure and that causing xylem dysfunction) more directly merge stomatal regulation strategies with xylem hydraulic strategies, illustrating a comprehensive framework to characterize plant response to drought. A combination of plant traits reflecting species' response and adaptation to drought should be established in the future, and we propose four specific urgent issues as future research priorities.

Plant optogenetics: Applications and perspectives

To understand cell biological processes, like signalling pathways, protein movements, or metabolic processes, precise tools for manipulation are desired. Optogenetics allows to control cellular processes by light and can be applied at a high temporal and spatial resolution. In the last three decades, various optogenetic applications have been developed for animal, fungal, and prokaryotic cells. However, using optogenetics in plants has been difficult due to biological and technical issues, like missing cofactors, the presence of endogenous photoreceptors, or the necessity of light for photosynthesis, which potentially activates optogenetic tools constitutively. Recently developed tools overcome these limitations, making the application of optogenetics feasible also in plants. Here, we highlight the most useful recent applications in plants and give a perspective for future optogenetic approaches in plants science.

An extremely low stomatal density mutant overcomes cooling limitations at supra-optimal temperature by adjusting stomatal size and leaf thickness

The impact of global warming on transpiration and photosynthesis would compromise plant fitness, impacting on crop yields and ecosystem functioning. In this frame, we explored the performance of a set of Arabidopsis mutants carrying partial or total loss-of-function alleles of stomatal development genes and displaying distinct stomatal abundances. Using microscopy and non-invasive imaging techniques on this genotype collection, we examined anatomical leaf and stomatal traits, plant growth and development, and physiological performance at optimal (22°C) and supra-optimal (30°C) temperatures. All genotypes showed thermomorphogenetic responses but no signs of heat stress. Data analysis singled out an extremely low stomatal abundance mutant, spch-5. At 22°C, spch-5 had lower transpiration and warmer leaves than the wild type. However, at 30°C, this mutant developed larger stomata and thinner leaves, paralleled by a notable cooling capacity, similar to that of the wild type. Despite their low stomatal density (SD), spch-5 plants grown at 30°C showed no photosynthesis or growth penalties. The behavior of spch-5 at supra-optimal temperature exemplifies how the effect of very low stomatal numbers can be counteracted by a combination of larger stomata and thinner leaves. Furthermore, it provides a novel strategy for coping with high growth temperatures.

Optogenetics for light control of biological systems

Optogenetic techniques have been developed to allow control over the activity of selected cells within a highly heterogeneous tissue, using a combination of genetic engineering and light. Optogenetics employs natural and engineered photoreceptors, mostly of microbial origin, to be genetically introduced into the cells of interest. As a result, cells that are naturally light-insensitive can be made photosensitive and addressable by illumination and precisely controllable in time and space. The selectivity of expression and subcellular targeting in the host is enabled by applying control elements such as promoters, enhancers and specific targeting sequences to the employed photoreceptor-encoding DNA. This powerful approach allows precise characterization and manipulation of cellular functions and has motivated the development of advanced optical methods for patterned photostimulation. Optogenetics has revolutionized neuroscience during the past 15 years and is primed to have a similar impact in other fields, including cardiology, cell biology and plant sciences. In this Primer, we describe the principles of optogenetics, review the most commonly used optogenetic tools, illumination approaches and scientific applications and discuss the possibilities and limitations associated with optogenetic manipulations across a wide variety of optical techniques, cells, circuits and organisms.

Electrifying rhythms in plant cells

Physiological oscillations (or rhythms) pervade all spatiotemporal scales of biological organization, either because they perform critical functions or simply because they can arise spontaneously and may be difficult to prevent. Regardless of the case, they reflect regulatory relationships between control points of a given system and offer insights as read-outs of the concerted regulation of a myriad of biological processes. Here we review recent advances in understanding ultradian oscillations (period < 24h) in plant cells, with a special focus on single-cell oscillations. Ion channels are at the center stage due to their involvement in electrical/excitabile phenomena associated with oscillations and cell-cell communication. We highlight the importance of quantitative approaches to measure oscillations in appropriate physiological conditions, which are essential strategies to deal with the complexity of biological rhythms. Future development of optogenetics techniques in plants will further boost research on the role of membrane potential in oscillations and waves across multiple cell types.

NaCl affects photosynthetic and stomatal dynamics by osmotic effects and reduces photosynthetic capacity by ionic effects in tomato

NaCl stress affects stomatal behavior and photosynthesis by a combination of osmotic and ionic components, but it is unknown how these components affect stomatal and photosynthetic dynamics. Tomato (Solanum lycopersicum) plants were grown in a reference nutrient solution [control; electrical conductivity (EC)=2.3 dS m-1], a solution containing additional macronutrients (osmotic effect; EC=12.6 dS m-1), or a solution with additional 100 mM NaCl (osmotic and ionic effects; EC=12.8 dS m-1). Steady-state and dynamic photosynthesis, and leaf biochemistry, were characterized throughout leaf development. The osmotic effect decreased steady-state stomatal conductance while speeding up stomatal responses to light intensity shifts. After 19 d of treatment, photosynthetic induction was reduced by the osmotic effect, which was attributable to lower initial stomatal conductance due to faster stomatal closing under low light. Ionic effects of NaCl were barely observed in dynamic stomatal and photosynthetic behavior, but led to a reduction in leaf photosynthetic capacity, CO2 carboxylation rate, and stomatal conductance in old leaves after 26 d of treatment. With increasing leaf age, rates of light-triggered stomatal movement and photosynthetic induction decreased across treatments. We conclude that NaCl impacts dynamic stomatal and photosynthetic kinetics by osmotic effects and reduces photosynthetic capacity by ionic effects.

Green Light Partial Replacement of Red and Blue Light Improved Drought Tolerance by Regulating Water Use Efficiency in Cucumber Seedlings

Light is one of the most important environmental signals in plant growth, development, and stress response. Green light has been proved to enhance plant defense against biotic and/or abiotic stress. To illustrate the effects of green light partially replaced red light and blue light on the plant under drought condition, cucumber (Cucumis sativus L. cv. Xinchun No. 4) seedlings were treated with short-term drought stress and were concomitantly exposed to four treatments, which were set up by adjusting the relative amount of green light as 0 (RB), 25 (RBG25), 50 (RBG50), and 75 (RBG75) μmol m^-2 s^-1, respectively, with a total photosynthetic photon flux density of 250 μmol m^-2 s^-1 and a fixed red-to-blue ratio of 4:1. The results showed that compared with RB, RBG50 significantly increased shoot fresh weight (FW) and dry weight (DW), root DW, plant height, stem diameter, leaf area, and leaf dry mass per unit area (LMA) by 10.61, 7.69, 66.13, 6.22, 10.02, 4.10, and 12.41%, respectively. Also, the addition of green light significantly increased the root volume and root tip number. Moreover, green light partial replacement of red light and blue light increased total water content, especially free water content, improved leaf water status, and alleviated water loss in plants caused by drought stress. Also, the addition of green light increased net photosynthetic rate (P_n), reduced both stomata conductance (g_s) and transpiration rate (E), enhanced the intrinsic water-use efficiency (WUE) and instantaneous water-use efficiency (iWUE) of leaves, and increased the content of chlorophylls a and b. Green light substituting a proportion of blue and red light regulated stomatal aperture by significantly increasing abscisic acid (ABA) and γ-aminobutyric acid (GABA) content. In addition, the increase of GABA was resulted from the upregulation of Glutamate Decarboxylase 2 (CsGAD2). However, the relative electrolytic leakage and contents of malondialdehyde (MDA), superoxide anion ( O 2 - ), and hydrogen peroxide (H₂O₂) vigorously decreased as the intensity of green light was added to the spectrum under drought. Conclusively, green light partially replaced red light and blue light and improved drought tolerance of cucumber seedlings by upregulating the expression of CsGAD2 gene and promoting the synthesis of GABA. The increase in GABA content further downregulated the expression of aluminum-activated malate transporter 9 (CsALMT9) gene, induced stomata to close, improved water utilization, and alleviated damage caused by drought. This study highlights a role of green light in plant physiological processes. Moreover, analyzing the function of green light on improving drought tolerance of plants could open alternative avenues for improving plant stress resilience.

Systemic Signaling: A Role in Propelling Crop Yield

Food security has become a topic of great concern in many countries. Global food security depends heavily on agriculture that has access to proper resources and best practices to generate higher crop yields. Crops, as with other plants, have a variety of strategies to adapt their growth to external environments and internal needs. In plants, the distal organs are interconnected through the vascular system and intricate hierarchical signaling networks, to communicate and enhance survival within fluctuating environments. Photosynthesis and carbon allocation are fundamental to crop production and agricultural outputs. Despite tremendous progress achieved by analyzing local responses to environmental cues, and bioengineering of critical enzymatic processes, little is known about the regulatory mechanisms underlying carbon assimilation, allocation, and utilization. This review provides insights into vascular-based systemic regulation of photosynthesis and resource allocation, thereby opening the way for the engineering of source and sink activities to optimize the yield performance of major crops.

Towards improved dynamic photosynthesis in C3 crops by utilizing natural genetic variation

Under field environments, fluctuating light conditions induce dynamic photosynthesis, which affects carbon gain by crop plants. Elucidating the natural genetic variations among untapped germplasm resources and their underlying mechanisms can provide an effective strategy to improve dynamic photosynthesis and, ultimately, improve crop yields through molecular breeding approaches. In this review, we first overview two processes affecting dynamic photosynthesis, namely (i) biochemical processes associated with CO2 fixation and photoprotection and (ii) gas diffusion processes from the atmosphere to the chloroplast stroma. Next, we review the intra- and interspecific variations in dynamic photosynthesis in relation to each of these two processes. It is suggested that plant adaptations to different hydrological environments underlie natural genetic variation explained by gas diffusion through stomata. This emphasizes the importance of the coordination of photosynthetic and stomatal dynamics to optimize the balance between carbon gain and water use efficiency under field environments. Finally, we discuss future challenges in improving dynamic photosynthesis by utilizing natural genetic variation. The forward genetic approach supported by high-throughput phenotyping should be introduced to evaluate the effects of genetic and environmental factors and their interactions on the natural variation in dynamic photosynthesis.

Into the Shadows and Back into Sunlight: Photosynthesis in Fluctuating Light

Photosynthesis is an important remaining opportunity for further improvement in the genetic yield potential of our major crops. Measurement, analysis, and improvement of leaf CO₂ assimilation (A) have focused largely on photosynthetic rates under light-saturated steady-state conditions. However, in modern crop canopies of several leaf layers, light is rarely constant, and the majority of leaves experience marked light fluctuations throughout the day. It takes several minutes for photosynthesis to regain efficiency in both sun-shade and shade-sun transitions, costing a calculated 10-40% of potential crop CO₂ assimilation. Transgenic manipulations to accelerate the adjustment in sun-shade transitions have already shown a substantial productivity increase in field trials. Here, we explore means to further accelerate these adjustments and minimize these losses through transgenic manipulation, gene editing, and exploitation of natural variation. Measurement andanalysis of photosynthesis in sun-shade and shade-sun transitions are explained. Factors limiting speeds of adjustment and how they could be modified to effect improved efficiency are reviewed, specifically nonphotochemical quenching (NPQ), Rubisco activation, and stomatal responses.

Rapid stomatal closure contributes to higher water use efficiency in major C4 compared to C3 Poaceae crops

Understanding water use characteristics of C3 and C4 crops is important for food security under climate change. Here, we aimed to clarify how stomatal dynamics and water use efficiency (WUE) differ in fluctuating environments in major C3 and C4 crops. Under high and low nitrogen conditions, we evaluated stomatal morphology and kinetics of stomatal conductance (gs) at leaf and whole-plant levels in controlled fluctuating light environments in four C3 and five C4 Poaceae species. We developed a dynamic photosynthesis model, which incorporates C3 and C4 photosynthesis models that consider stomatal dynamics, to evaluate the contribution of rapid stomatal opening and closing to photosynthesis and WUE. C4 crops showed more rapid stomatal opening and closure than C3 crops, which could be explained by smaller stomatal size and higher stomatal density in plants grown at high nitrogen conditions. Our model analysis indicated that accelerating the speed of stomatal closure in C3 crops to the level of C4 crops could enhance WUE up to 16% by reducing unnecessary water loss during low light periods, whereas accelerating stomatal opening only minimally enhanced photosynthesis. The present results suggest that accelerating the speed of stomatal closure in major C3 crops to the level of major C4 crops is a potential breeding target for the realization of water-saving agriculture.

Appropriate time interval of PPFD measurement to estimate daily photosynthetic gain

Photosynthetic models sometimes incorporate meteorological elements typically recorded at a time interval of 10 min or 1 h. Because these data are calculated by averaging instantaneous values over time, short-term environmental fluctuations are concealed, which may affect outputs of the model. To assess an appropriate time interval of photosynthetic photon flux density (PPFD) measurement for accurate estimation of photosynthetic gain under open field conditions, we simulated the daily integral net photosynthetic gain using photosynthetic models with or without considering induction kinetics in response to changes in PPFD. Compared with the daily gain calculated from 60-min-interval PPFD data using a steady-state model that ignored the induction kinetics (i.e. a baseline gain), the gains simulated using higher-resolution PPFD data (10-s, 1-min, and 10-min intervals) and using a dynamic model that considered slow induction kinetics were both smaller by ~2%. The gain estimated by the slow dynamic model with 10-s-interval PPFD data was smaller than the baseline gain by more than 5% with a probability of 66%. Thus, the use of low-resolution PPFD data causes overestimation of daily photosynthetic gain in open fields. An appropriate time interval for PPFD measurement is 1 min or shorter to ensure accuracy of the estimates.

Adjustments of carbon allocation and stomatal dynamics by target localized strategies to increase crop productivity under changing climates

Increasing crop productivity to ensure food security for future generations is one of the greatest challenges in current plant research. This challenge is even greater due to global climate changes, as enhancing crop yields must occur against the backdrop of increasingly changing environments, particularly rising temperatures and water constraints. Global crop yield growth depends on an improved dynamic balance between carbon and water usage. Here we discuss different approaches that highlight the role of vascular tissue and guard cells in attempting to mitigate the carbon-water trade-off. We argue that crop engineering in the future will require the incorporation of a combination of improved traits. Since targeted gene modifications generally produce fewer undesirable pleiotropic effects than constitutive modifications, we envision that modifications of specific cell types, such as phloem companion cells and guard cells, represent an effective approach for adding beneficial gene modifications in the same plant. This approach will enable trait stacking to design future crops with both high yield and resilience to various climate change stresses.

Does Fluctuating Light Affect Crop Yield? A Focus on the Dynamic Photosynthesis of Two Soybean Varieties

In natural environments, plants are exposed to variable light conditions, but photosynthesis has been mainly studied at steady state and this might overestimate carbon (C) uptake at the canopy scale. To better elucidate the role of light fluctuations on canopy photosynthesis, we investigated how the chlorophyll content, and therefore the different absorbance of light, would affect the quantum yield in fluctuating light conditions. For this purpose, we grew a commercial variety (Eiko) and a chlorophyll deficient mutant (MinnGold) either in fluctuating (F) or non-fluctuating (NF) light conditions with sinusoidal changes in irradiance. Two different light treatments were also applied: a low light treatment (LL; max 650 μmol m^-2 s^-1) and a high light treatment (HL; max 1,000 μmol m^-2 s^-1). Canopy gas exchanges were continuously measured throughout the experiment. We found no differences in C uptake in LL treatment, either under F or NF. Light fluctuations were instead detrimental for the chlorophyll deficient mutant in HL conditions only, while the green variety seemed to be well-adapted to them. Varieties adapted to fluctuating light might be identified to target the molecular mechanisms responsible for such adaptations.

The plasma membrane aquaporin ZmPIP2;5 enhances the sensitivity of stomatal closure to water deficit

Increasing stomatal movement is beneficial to improve plant water use efficiency and drought resilience. Contradictory results indicate that aquaporins might regulate stomatal movement. Here, we tested whether the maize plasma membrane PIP2;5 aquaporin affects stomatal closure under water deficit, abscisic acid (ABA) or vapour pressure deficit (VPD) treatment in intact plants, detached leaves or peeled epidermis. Transpiration, stomatal conductance (g_s ) and aperture and reactive oxygen species (ROS) in stomatal complexes were studied in maize lines with increased or knocked down (KD) PIP2;5 gene expression. In well-watered conditions, the PIP2;5 overexpressing (OE) plants transpired more than wild types (WTs), while no significant difference in transpiration was observed between pip2;5 KD and WT. Upon mild water deficit or low ABA concentration treatments, transpiration and g_s decreased more in PIP2;5 OE lines and less in pip2;5 KD lines, in comparison with WTs. In the detached epidermis, ABA treatment induced faster stomatal closing in PIP2;5 OE lines compared to WTs, while pip2;5 KD stomata were ABA insensitive. These phenotypes were associated with guard cell ROS accumulation. Additionally, PIP2;5 is involved in the transpiration decrease observed under high VPD. These data indicate that maize PIP2;5 is a key actor increasing the sensitivity of stomatal closure to water deficit.

Effects of contrasting N supplies on leaf photosynthetic induction under fluctuating light in rice (Oryza sativa L.)

Nitrogen (N) is one of the most important nutrients for crop growth and yield formation, as it is an important constituent in a large amount of proteins, cell walls, and membranes related to photosynthesis. Recently, increasing studies have suggested the important roles of photosynthetic induction and stomatal movement under fluctuating light in regulating plant carbon assimilation and water use efficiency. How leaf N content affects photosynthetic induction remains uncertain. Here, we observed a significantly faster photosynthetic induction with the increasing supply of N under fluctuating light conditions. Photosynthetic induction was mainly limited by biochemical processes but not stomatal opening after a stepwise increase in irradiance across different N supplies. Higher N supply enhanced photosynthetic efficiency under constant and fluctuating light conditions but reduced leaf intrinsic water use efficiency (WUE_i ). This study is mainly focused on clarifying the crucial limitation of photosynthetic induction under different N treatments, which may facilitate the improvement of photosynthetic efficiency under complicated environments in the future.

Plasmodesmata and their role in assimilate translocation

During multicellularization, plants evolved unique cell-cell connections, the plasmodesmata (PD). PD of angiosperms are complex cellular domains, embedded in the cell wall and consisting of multiple membranes and a large number of proteins. From the beginning, it had been assumed that PD provide passage for a wide range of molecules, from ions to metabolites and hormones, to RNAs and even proteins. In the context of assimilate allocation, it has been hypothesized that sucrose produced in mesophyll cells is transported via PD from cell to cell down a concentration gradient towards the phloem. Entry into the sieve element companion cell complex (SECCC) is then mediated on three potential routes, depending on the species and conditions, - either via diffusion across PD, after conversion to raffinose via PD using a polymer trap mechanism, or via a set of transporters which secrete sucrose from one cell and secondary active uptake into the SECCC. Multiple loading mechanisms can likely coexist. We here review the current knowledge regarding photoassimilate transport across PD between cells as a prerequisite for translocation from leaves to recipient organs, in particular roots and developing seeds. We summarize the state-of-the-art in protein composition, structure, transport mechanism and regulation of PD to apprehend their functions in carbohydrate allocation. Since many aspects of PD biology remain elusive, we highlight areas that require new approaches and technologies to advance our understanding of these enigmatic and important cell-cell connections.

Toolboxes for plant systems biology research

The terms 'systems' and 'synthetic biology' are often used together, with most scientists striding between the two fields rather than adhering to a single side. Often too, scientists want to understand a system to inform the design of gene circuits that could endow it with new functions. However, this does not need to be the progression of research, as synthetic constructs can help improve our understanding of a system. Here, we review synthetic biology tool kits with the potential to overcome pleiotropic effects, compensatory mechanisms, and redundancy in plants. Combined with -omics techniques, these tools could reveal novel insights on plant growth and development, an aim that has gained renewed urgency given the impact of climate change on crop productivity.

Optogenetic and Chemical Induction Systems for Regulation of Transgene Expression in Plants: Use in Basic and Applied Research

Continuous and ubiquitous expression of foreign genes sometimes results in harmful effects on the growth, development and metabolic activities of plants. Tissue-specific promoters help to overcome this disadvantage, but do not allow one to precisely control transgene expression over time. Thus, inducible transgene expression systems have obvious benefits. In plants, transcriptional regulation is usually driven by chemical agents under the control of chemically-inducible promoters. These systems are diverse, but usually contain two elements, the chimeric transcription factor and the reporter gene. The commonly used chemically-induced expression systems are tetracycline-, steroid-, insecticide-, copper-, and ethanol-regulated. Unlike chemical-inducible systems, optogenetic tools enable spatiotemporal, quantitative and reversible control over transgene expression with light, overcoming limitations of chemically-inducible systems. This review updates and summarizes optogenetic and chemical induction methods of transgene expression used in basic plant research and discusses their potential in field applications.

Metabolism-mediated mechanisms underpin the differential stomatal speediness regulation among ferns and angiosperms

Recent results suggest that metabolism-mediated stomatal closure mechanisms are important to regulate differentially the stomatal speediness between ferns and angiosperms. However, evidence directly linking mesophyll metabolism and the slower stomatal conductance (g_s ) in ferns is missing. Here, we investigated the effect of exogenous application of abscisic acid (ABA), sucrose and mannitol on stomatal kinetics and carried out a metabolic fingerprinting analysis of ferns and angiosperms leaves harvested throughout a diel course. Fern stomata did not respond to ABA in the time period analysed. No differences in the relative decrease in g_s was observed between ferns and the angiosperm following provision of sucrose or mannitol. However, ferns have slower g_s responses to these compounds than angiosperms. Metabolomics analysis highlights that ferns have a higher accumulation of secondary rather than primary metabolites throughout the diel course, with the opposite being observed in angiosperms. Our results indicate that metabolism-mediated stomatal closure mechanisms underpin the differential stomatal speediness regulation among ferns and angiosperms, in which the slower stomatal closure in ferns is associated with the lack of ABA-responsiveness, to a reduced capacity to respond to mesophyll-derived sucrose and to a higher carbon allocation toward secondary metabolism, which likely modulates both photosynthesis-g_s and growth-stress tolerance trade-offs.

What can mechanistic models tell us about guard cells, photosynthesis, and water use efficiency?

Stomatal pores facilitate gaseous exchange between the inner air spaces of the leaf and the atmosphere. The pores open to enable CO₂ entry for photosynthesis and close to reduce transpirational water loss. How stomata respond to the environment has long attracted interest in modeling as a tool to understand the consequences for the plant and for the ecosystem. Models that focus on stomatal conductance for gas exchange make intuitive sense, but such models need also to connect with the mechanics of the guard cells that regulate pore aperture if we are to understand the 'decisions made' by stomata, their impacts on the plant and on the global environment.

Optogenetic approaches in biotechnology and biomaterials

Advances in genetic engineering, combined with the development of optical technologies, have allowed optogenetics to broaden its area of possible applications in recent years. However, the application of optogenetic tools in industry, including biotechnology and the production of biomaterials, is still limited, because each practical task requires the engineering of a specific optogenetic system. In this review, we discuss recent advances in the use of optogenetic tools in the production of biofuels and valuable chemicals, the synthesis of biomedical and polymer materials, and plant agrobiology. We also offer a comprehensive analysis of the properties and industrial applicability of light-controlled and other smart biomaterials. These data allow us to outline the prospects for the future use of optogenetics in bioindustry.

Drought stress reduces crop carbon gain due to delayed photosynthetic induction under fluctuating light conditions

Drought stress is a major limiting factor for crop growth and yield. Water availability in the field can cyclically change between drought and rewatering conditions, depending on precipitation patterns. Concurrently, light intensity under field conditions can fluctuate, inducing dynamic photosynthesis and transpiration during the crop growth period. The present study aimed to characterize carbon gain and water use in fluctuating light under drought and rewatering conditions in two major crops, namely rice and soybean. We conducted gas exchange measurements under fluctuating light conditions with rice and soybean plants exposed to drought treatment (9-13 days) imposed by withholding water and subsequent rewatering treatment (8-9 days). Drought stress significantly reduced the maximum CO₂ assimilation rate (A) in soybean but not in rice. Under drought conditions, A increased after a step increase in light and then gradually decreased in both crops, resulting in the significant reduction of steady-state A in rice and soybean. Moreover, drought stress delayed photosynthetic induction in both crops even when it had relatively small impact on maximum A. These results suggest that the drought effects on photosynthesis should be evaluated based on induction, maximum, and steady states. The delayed photosynthetic induction under drought owing to the reduced gas diffusional conductance via stomata resulted in a substantial loss of leaf carbon gain under fluctuating light conditions. Meanwhile, rewatering, after drought, completely recovered photosynthesis under fluctuating light in both crops. Therefore, the stability of photosynthetic induction can be a promising target to improve drought tolerance during crop breeding in the future.

Mesophyll conductance exerts a significant limitation on photosynthesis during light induction

Past studies have established mesophyll diffusion conductance to CO₂ (g_m ) as a variable and significant limitation to plant photosynthesis under steady-state conditions. However, the role of g_m in influencing photosynthesis (A) during the transient period of light induction is largely unknown. We combined gas exchange measurements with laser-enabled carbon isotope discrimination measurements to assess g_m during photosynthetic induction, using Arabidopsis as the measurement species. Our measurements revealed three key findings: (1) we found that the rate at which g_m approached steady state during induction was not necessarily faster than the induction rate of the carboxylation process, contradictory to what has been suggested in previous studies; (2) g_m displayed a strong and consistent coordination with A under both induction and steady-state settings, hinting that the mechanism driving g_m -A coupling does not require physiological stability as a prerequisite; and (3) photosynthetic limitation analysis of our data revealed that when integrated over the entire induction period, the relative limitation of A imposed by g_m can be as high as > 35%. The present study provides the first demonstration of the important role of g_m in limiting CO₂ assimilation during photosynthetic induction, thereby pointing to a need for more research attention to be devoted to g_m in future induction studies.

The bare necessities of plant K+ channel regulation

Potassium (K+) channels serve a wide range of functions in plants from mineral nutrition and osmotic balance to turgor generation for cell expansion and guard cell aperture control. Plant K+ channels are members of the superfamily of voltage-dependent K+ channels, or Kv channels, that include the Shaker channels first identified in fruit flies (Drosophila melanogaster). Kv channels have been studied in depth over the past half century and are the best-known of the voltage-dependent channels in plants. Like the Kv channels of animals, the plant Kv channels are regulated over timescales of milliseconds by conformational mechanisms that are commonly referred to as gating. Many aspects of gating are now well established, but these channels still hold some secrets, especially when it comes to the control of gating. How this control is achieved is especially important, as it holds substantial prospects for solutions to plant breeding with improved growth and water use efficiencies. Resolution of the structure for the KAT1 K+ channel, the first channel from plants to be crystallized, shows that many previous assumptions about how the channels function need now to be revisited. Here, I strip the plant Kv channels bare to understand how they work, how they are gated by voltage and, in some cases, by K+ itself, and how the gating of these channels can be regulated by the binding with other protein partners. Each of these features of plant Kv channels has important implications for plant physiology.

Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes

Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, a little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. Here, we used high-throughput thermal imaging to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum (Sorghum bicolor) accessions. Results from thermal imaging significantly correlated with photosynthetic gas exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with the greatest confidence, 77 were putative orthologs of Arabidopsis (Arabidopsis thaliana) genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.

Advances and prospects of rhodopsin-based optogenetics in plant research

Microbial rhodopsins have advanced optogenetics since the discovery of channelrhodopsins almost two decades ago. During this time an abundance of microbial rhodopsins has been discovered, engineered, and improved for studies in neuroscience and other animal research fields. Optogenetic applications in plant research, however, lagged largely behind. Starting with light-regulated gene expression, optogenetics has slowly expanded into plant research. The recently established all-trans retinal production in plants now enables the use of many microbial opsins, bringing extra opportunities to plant research. In this review, we summarize the recent advances of rhodopsin-based plant optogenetics and provide a perspective for future use, combined with fluorescent sensors to monitor physiological parameters.

A distinct giant coat protein complex II vesicle population in Arabidopsis thaliana

Plants live as sessile organisms with large-scale gene duplication events and subsequent paralogue divergence during evolution. Notably, plant paralogues are expressed tissue-specifically and fine-tuned by phytohormones during various developmental processes. The coat protein complex II (COPII) is a highly conserved vesiculation machinery mediating protein transport from the endoplasmic reticulum to the Golgi apparatus in eukaryotes¹. Intriguingly, Arabidopsis COPII paralogues greatly outnumber those in yeast and mammals^2-6. However, the functional diversity and underlying mechanism of distinct COPII paralogues in regulating protein endoplasmic reticulum export and coping with various adverse environmental stresses are poorly understood. Here we characterize a novel population of COPII vesicles produced in response to abscisic acid, a key phytohormone regulating abiotic stress responses in plants. These hormone-induced giant COPII vesicles are regulated by an Arabidopsis-specific COPII paralogue and carry stress-related channels/transporters for alleviating stresses. This study thus provides a new mechanism underlying abscisic acid-induced stress responses via the giant COPII vesicles and answers a long-standing question on the evolutionary significance of gene duplications in Arabidopsis.

Functional modulation of an aquaporin to intensify photosynthesis and abrogate bacterial virulence in rice

Plant aquaporins are a recently noted biological resource with a great potential to improve crop growth and defense traits. Here, we report the functional modulation of the rice (Oryza sativa) aquaporin OsPIP1;3 to enhance rice photosynthesis and grain production and to control bacterial blight and leaf streak, the most devastating worldwide bacterial diseases in the crop. We characterize OsPIP1;3 as a physiologically relevant CO₂ -transporting facilitator, which supports 30% of rice photosynthesis on average. This role is nullified by interaction of OsPIP1;3 with the bacterial protein Hpa1, an essential component of the Type III translocon that supports translocation of the bacterial Type III effectors PthXo1 and TALi into rice cells to induce leaf blight and streak, respectively. Hpa1 binding shifts OsPIP1;3 from CO₂ transport to effector translocation, aggravates bacterial virulence, and blocks rice photosynthesis. On the contrary, the external application of isolated Hpa1 to rice plants effectively prevents OsPIP1;3 from interaction with Hpa1 secreted by the bacteria that are infecting the plants. Blockage of the OsPIP1;3-Hpa1 interaction reverts OsPIP1;3 from effector translocation to CO₂ transport, abrogates bacterial virulence, and meanwhile induces defense responses in rice. These beneficial effects can combine to enhance photosynthesis by 29-30%, reduce bacterial disease by 58-75%, and increase grain yield by 11-34% in different rice varieties investigated in small-scale field trials conducted during the past years. Our results suggest that crop productivity and immunity can be coordinated by modulating the physiological and pathological functions of a single aquaporin to break the growth-defense tradeoff barrier.

Expression Pattern and Functional Analyses of Arabidopsis Guard Cell-Enriched GDSL Lipases

There are more than 100 GDSL lipases in Arabidopsis, but only a few members have been functionally investigated. Moreover, no reports have ever given a comprehensive analysis of GDSLs in stomatal biology. Here, we systematically investigated the expression patterns of 19 putative Guard-cell-enriched GDSL Lipases (GGLs) at various developmental stages and in response to hormone and abiotic stress treatments. Gene expression analyses showed that these GGLs had diverse expression patterns. Fifteen GGLs were highly expressed in guard cells, with seven preferentially in guard cells. Most GGLs were localized in endoplasmic reticulum, and some were also localized in lipid droplets and nucleus. Some closely homologous GGLs exhibited similar expression patterns at various tissues and in response to hormone and abiotic stresses, or similar subcellular localization, suggesting the correlation of expression pattern and biological function, and the functional redundancy of GGLs in plant development and environmental adaptations. Further phenotypic identification of ggl mutants revealed that GGL7, GGL14, GGL22, and GGL26 played unique and redundant roles in stomatal dynamics, stomatal density and morphology, and plant water relation. The present study provides unique resources for functional insights into these GGLs to control stomatal dynamics and development, plant growth, and adaptation to the environment.

GABA: A Key Player in Drought Stress Resistance in Plants

γ-aminobutyric acid (GABA) is a non-protein amino acid involved in various physiological processes; it aids in the protection of plants against abiotic stresses, such as drought, heavy metals, and salinity. GABA tends to have a protective effect against drought stress in plants by increasing osmolytes and leaf turgor and reducing oxidative damage via antioxidant regulation. Guard cell GABA production is essential, as it may provide the benefits of reducing stomatal opening and transpiration and controlling the release of tonoplast-localized anion transporter, thus resulting in increased water-use efficiency and drought tolerance. We summarized a number of scientific reports on the role and mechanism of GABA-induced drought tolerance in plants. We also discussed existing insights regarding GABA’s metabolic and signaling functions used to increase plant tolerance to drought stress.

Guard cell endomembrane Ca2+-ATPases underpin a 'carbon memory' of photosynthetic assimilation that impacts on water-use efficiency

Stomata of most plants close to preserve water when the demand for CO₂ by photosynthesis is reduced. Stomatal responses are slow compared with photosynthesis, and this kinetic difference erodes assimilation and water-use efficiency under fluctuating light. Despite a deep knowledge of guard cells that regulate the stoma, efforts to enhance stomatal kinetics are limited by our understanding of its control by foliar CO₂. Guided by mechanistic modelling that incorporates foliar CO₂ diffusion and mesophyll photosynthesis, here we uncover a central role for endomembrane Ca²⁺ stores in guard cell responsiveness to fluctuating light and CO₂. Modelling predicted and experiments demonstrated a delay in Ca²⁺ cycling that was enhanced by endomembrane Ca²⁺-ATPase mutants, altering stomatal conductance and reducing assimilation and water-use efficiency. Our findings illustrate the power of modelling to bridge the gap from the guard cell to whole-plant photosynthesis, and they demonstrate an unforeseen latency, or 'carbon memory', of guard cells that affects stomatal dynamics, photosynthesis and water-use efficiency.

Optogenetic control of the guard cell membrane potential and stomatal movement by the light-gated anion channel GtACR1

Guard cells control the aperture of plant stomata, which are crucial for global fluxes of CO₂ and water. In turn, guard cell anion channels are seen as key players for stomatal closure, but is activation of these channels sufficient to limit plant water loss? To answer this open question, we used an optogenetic approach based on the light-gated anion channelrhodopsin 1 (GtACR1). In tobacco guard cells that express GtACR1, blue- and green-light pulses elicit Cl^- and NO₃ ^- currents of -1 to -2 nA. The anion currents depolarize the plasma membrane by 60 to 80 mV, which causes opening of voltage-gated K⁺ channels and the extrusion of K⁺ As a result, continuous stimulation with green light leads to loss of guard cell turgor and closure of stomata at conditions that provoke stomatal opening in wild type. GtACR1 optogenetics thus provides unequivocal evidence that opening of anion channels is sufficient to close stomata.

Natural Variation in Crops: Realized Understanding, Continuing Promise

Crops feed the world's population and shape human civilization. The improvement of crop productivity has been ongoing for almost 10,000 years and has evolved from an experience-based to a knowledge-driven practice over the past three decades. Natural alleles and their reshuffling are long-standing genetic changes that affect how crops respond to various environmental conditions and agricultural practices. Decoding the genetic basis of natural variation is central to understanding crop evolution and, in turn, improving crop breeding. Here, we review current advances in the approaches used to map the causal alleles of natural variation, provide refined insights into the genetics and evolution of natural variation, and outline how this knowledge promises to drive the development of sustainable agriculture under the dome of emerging technologies.

The impact of slow stomatal kinetics on photosynthesis and water use efficiency under fluctuating light

Dynamic light conditions require continuous adjustments of stomatal aperture. The kinetics of stomatal conductance (gs) is hypothesized to be key to plant productivity and water use efficiency (WUE). Using step-changes in light intensity, we studied the diversity of light-induced gs kinetics in relation to stomatal anatomy in five banana genotypes (Musa spp.) and modeled the impact of both diffusional and biochemical limitations on photosynthesis (A). The dominant A limiting factor was the diffusional limitation associated with gs kinetics. All genotypes exhibited a strong limitation of A by gs, indicating a priority for water saving. Moreover, significant genotypic differences in gs kinetics and gs limitations of A were observed. For two contrasting genotypes, the impact of differential gs kinetics was further investigated under realistic diurnally fluctuating light conditions and at the whole-plant level. Genotype-specific stomatal kinetics observed at the leaf level was corroborated at whole-plant level by transpiration dynamics, validating that genotype-specific responses are still maintained despite differences in gs control at different locations in the leaf and across leaves. However, under diurnally fluctuating light conditions the impact of gs speediness on A and intrinsic (iWUE) depended on time of day. During the afternoon there was a setback in kinetics: absolute gs and gs responses to light were damped, strongly limiting A and impacting diurnal iWUE. We conclude the impact of differential gs kinetics depended on target light intensity, magnitude of change, gs prior to the change in light intensity, and particularly time of day.

Plant electrical signals: A multidisciplinary challenge

Plant electrical signals, an early event in the plant-stimulus interaction, rapidly transmit information generated by the stimulus to other organs, and even the whole plant, to promote the corresponding response and trigger a regulatory cascade. In recent years, many promising state-of-the-art technologies applicable to study plant electrophysiology have emerged. Research focused on expression of genes associated with electrical signals has also proliferated. We propose that it is appropriate for plant electrical signals to be considered in the form of a "plant electrophysiological phenotype". This review synthesizes research on plant electrical signals from a novel, interdisciplinary perspective, which is needed to improve the efficient aggregation and use of plant electrical signal data and to expedite interpretation of plant electrical signals.

Synthetic biology as driver for the biologization of materials sciences

Materials in nature have fascinating properties that serve as a continuous source of inspiration for materials scientists. Accordingly, bio-mimetic and bio-inspired approaches have yielded remarkable structural and functional materials for a plethora of applications. Despite these advances, many properties of natural materials remain challenging or yet impossible to incorporate into synthetic materials. Natural materials are produced by living cells, which sense and process environmental cues and conditions by means of signaling and genetic programs, thereby controlling the biosynthesis, remodeling, functionalization, or degradation of the natural material. In this context, synthetic biology offers unique opportunities in materials sciences by providing direct access to the rational engineering of how a cell senses and processes environmental information and translates them into the properties and functions of materials. Here, we identify and review two main directions by which synthetic biology can be harnessed to provide new impulses for the biologization of the materials sciences: first, the engineering of cells to produce precursors for the subsequent synthesis of materials. This includes materials that are otherwise produced from petrochemical resources, but also materials where the bio-produced substances contribute unique properties and functions not existing in traditional materials. Second, engineered living materials that are formed or assembled by cells or in which cells contribute specific functions while remaining an integral part of the living composite material. We finally provide a perspective of future scientific directions of this promising area of research and discuss science policy that would be required to support research and development in this field.

Mesophyll-derived sugars are positive regulators of light-driven stomatal opening

Guard cell membrane ion transport and metabolism are deeply interconnected, and their coordinated regulation is integral to stomatal opening. Whereas ion transport is exceptionally well understood, how guard cell metabolism influences stomatal movements is less well known. Organic metabolites, such as malate and sugars, fulfill several functions in guard cells during stomatal opening as allosteric activators, counter-ions, energy source and osmolytes. However, their origin and exact fate remain debated. Recent work revealed that the guard cell carbon pool regulating stomatal function and plant growth is mostly of mesophyll origin, highlighting a tight correlation between mesophyll and guard cell metabolism. This review discusses latest research into guard cell carbon metabolism and its impact on stomatal function and whole plant physiology.

Sucrose Utilization for Improved Crop Yields: A Review Article

Photosynthetic carbon converted to sucrose is vital for plant growth. Sucrose acts as a signaling molecule and a primary energy source that coordinates the source and sink development. Alteration in source-sink balance halts the physiological and developmental processes of plants, since plant growth is mostly triggered when the primary assimilates in the source leaf balance with the metabolic needs of the heterotrophic sinks. To measure up with the sink organ's metabolic needs, the improvement of photosynthetic carbon to synthesis sucrose, its remobilization, and utilization at the sink level becomes imperative. However, environmental cues that influence sucrose balance within these plant organs, limiting positive yield prospects, have also been a rising issue over the past few decades. Thus, this review discusses strategies to improve photosynthetic carbon assimilation, the pathways actively involved in the transport of sucrose from source to sink organs, and their utilization at the sink organ. We further emphasize the impact of various environmental cues on sucrose transport and utilization, and the strategic yield improvement approaches under such conditions.

Membrane voltage as a dynamic platform for spatiotemporal signaling, physiological, and developmental regulation

Membrane voltage arises from the transport of ions through ion-translocating ATPases, ion-coupled transport of solutes, and ion channels, and is an integral part of the bioenergetic "currency" of the membrane. The dynamics of membrane voltage-so-called action, systemic, and variation potentials-have also led to a recognition of their contributions to signal transduction, both within cells and across tissues. Here, we review the origins of our understanding of membrane voltage and its place as a central element in regulating transport and signal transmission. We stress the importance of understanding voltage as a common intermediate that acts both as a driving force for transport-an electrical "substrate"-and as a product of charge flux across the membrane, thereby interconnecting all charge-carrying transport across the membrane. The voltage interconnection is vital to signaling via second messengers that rely on ion flux, including cytosolic free Ca2+, H+, and the synthesis of reactive oxygen species generated by integral membrane, respiratory burst oxidases. These characteristics inform on the ways in which long-distance voltage signals and voltage oscillations give rise to unique gene expression patterns and influence physiological, developmental, and adaptive responses such as systemic acquired resistance to pathogens and to insect herbivory.

A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation

Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.

A Holistic Approach to Study Photosynthetic Acclimation Responses of Plants to Fluctuating Light

Plants in natural environments receive light through sunflecks, the duration and distribution of these being highly variable across the day. Consequently, plants need to adjust their photosynthetic processes to avoid photoinhibition and maximize yield. Changes in the composition of the photosynthetic apparatus in response to sustained changes in the environment are referred to as photosynthetic acclimation, a process that involves changes in protein content and composition. Considering this definition, acclimation differs from regulation, which involves processes that alter the activity of individual proteins over short-time periods, without changing the abundance of those proteins. The interconnection and overlapping of the short- and long-term photosynthetic responses, which can occur simultaneously or/and sequentially over time, make the study of long-term acclimation to fluctuating light in plants challenging. In this review we identify short-term responses of plants to fluctuating light that could act as sensors and signals for acclimation responses, with the aim of understanding how plants integrate environmental fluctuations over time and tailor their responses accordingly. Mathematical modeling has the potential to integrate physiological processes over different timescales and to help disentangle short-term regulatory responses from long-term acclimation responses. We review existing mathematical modeling techniques for studying photosynthetic responses to fluctuating light and propose new methods for addressing the topic from a holistic point of view.