The rise of the photosynthetic rate when light intensity increases is delayed in ndh gene-defective tobacco at high but not at low CO2 concentrations

Loss of plastid ndh genes in an autotrophic desert plant

Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.

Entropy Perspectives of Molecular and Evolutionary Biology

Attempts to find and quantify the supposed low entropy of organisms and its preservation are revised. The absolute entropy of the mixed components of non-living biomass (approximately −1.6 × 10³ J K⁻¹ L⁻¹) is the reference to which other entropy decreases would be ascribed to life. The compartmentation of metabolites and the departure from the equilibrium of metabolic reactions account for reductions in entropy of 1 and 40–50 J K⁻¹ L⁻¹, respectively, and, though small, are distinctive features of living tissues. DNA and proteins do not supply significant decreases in thermodynamic entropy, but their low informational entropy is relevant for life and its evolution. No other living feature contributes significantly to the low entropy associated with life. The photosynthetic conversion of radiant energy to biomass energy accounts for most entropy (2.8 × 10⁵ J K⁻¹ carbon kg⁻¹) produced by living beings. The comparatively very low entropy produced in other processes (approximately 4.8 × 10² J K⁻¹ L⁻¹ day⁻¹ in the human body) must be rapidly exported outside as heat to preserve low entropy decreases due to compartmentation and non-equilibrium metabolism. Enzymes and genes are described, whose control minimizes the rate of production of entropy and could explain selective pressures in biological evolution and the rapid proliferation of cancer cells.

On the Edge of Dispensability, the Chloroplast ndh Genes

The polypeptides encoded by the chloroplast ndh genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I. Except for Charophyceae (algae related to higher plants) and a few Prasinophyceae, all eukaryotic algae lack ndh genes. Among vascular plants, the ndh genes are absent in epiphytic and in some species scattered among different genera, families, and orders. The recent identification of many plants lacking plastid ndh genes allows comparison on phylogenetic trees and functional investigations of the ndh genes. The ndh genes protect Angiosperms under various terrestrial stresses, maintaining efficient photosynthesis. On the edge of dispensability, ndh genes provide a test for the natural selection of photosynthesis-related genes in evolution. Variable evolutionary environments place Angiosperms without ndh genes at risk of extinction and, probably, most extant ones may have lost ndh genes recently. Therefore, they are evolutionary endpoints in phylogenetic trees. The low number of sequenced plastid DNA and the long lifespan of some Gymnosperms lacking ndh genes challenge models about the role of ndh genes protecting against stress and promoting leaf senescence. Additional DNA sequencing in Gymnosperms and investigations into the molecular mechanisms of their response to stress will provide a unified model of the evolutionary and functional consequences of the lack of ndh genes.

The Complementary Roles of Chloroplast Cyclic Electron Transport and Mitochondrial Alternative Oxidase to Ensure Photosynthetic Performance

Chloroplasts use light energy and a linear electron transport (LET) pathway for the coupled generation of NADPH and ATP. It is widely accepted that the production ratio of ATP to NADPH is usually less than required to fulfill the energetic needs of the chloroplast. Left uncorrected, this would quickly result in an over-reduction of the stromal pyridine nucleotide pool (i.e., high NADPH/NADP⁺ ratio) and under-energization of the stromal adenine nucleotide pool (i.e., low ATP/ADP ratio). These imbalances could cause metabolic bottlenecks, as well as increased generation of damaging reactive oxygen species. Chloroplast cyclic electron transport (CET) and the chloroplast malate valve could each act to prevent stromal over-reduction, albeit in distinct ways. CET avoids the NADPH production associated with LET, while the malate valve consumes the NADPH associated with LET. CET could operate by one of two different pathways, depending upon the chloroplast ATP demand. The NADH dehydrogenase-like pathway yields a higher ATP return per electron flux than the pathway involving PROTON GRADIENT REGULATION5 (PGR5) and PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1 (PGRL1). Similarly, the malate valve could couple with one of two different mitochondrial electron transport pathways, depending upon the cytosolic ATP demand. The cytochrome pathway yields a higher ATP return per electron flux than the alternative oxidase (AOX) pathway. In both Arabidopsis thaliana and Chlamydomonas reinhardtii, PGR5/PGRL1 pathway mutants have increased amounts of AOX, suggesting complementary roles for these two lesser-ATP yielding mechanisms of preventing stromal over-reduction. These two pathways may become most relevant under environmental stress conditions that lower the ATP demands for carbon fixation and carbohydrate export.

Dataset of short-term prediction of CO2 concentration based on a wireless sensor network

This CO₂ data is gathered from WSN (Wireless Sensor Network) sensors that is placed in some areas. To make this observation framework run effectively, examining the relationships between factors is required. We can utilize multiple wireless sensor devices. There are three parts of the system, including the sensor device, the sink node device, and the server. We use those devices to acquire data over a three-month period. In terms of the server infrastructure, we utilized an application server, a user interface server, and a database server to store our data. This study built a WSN framework for CO₂ observations. We investigate, analyze, and predict the level of CO₂, and the results have been collected. The Random Forest algorithm achieved a 0.82 R2 Score.

Chloroplast thioredoxin systems dynamically regulate photosynthesis in plants

Photosynthesis is a highly regulated process in photoautotrophic cells. The main goal of the regulation is to keep the basic photosynthetic reactions, i.e. capturing light energy, conversion into chemical energy and production of carbohydrates, in balance. The rationale behind the evolution of strong regulation mechanisms is to keep photosynthesis functional under all conditions encountered by sessile plants during their lifetimes. The regulatory mechanisms may, however, also impair photosynthetic efficiency by overriding the photosynthetic reactions in controlled environments like crop fields or bioreactors, where light energy could be used for production of sugars instead of dissipation as heat and down-regulation of carbon fixation. The plant chloroplast has a high number of regulatory proteins called thioredoxins (TRX), which control the function of chloroplasts from biogenesis and assembly of chloroplast machinery to light and carbon fixation reactions as well as photoprotective mechanisms. Here, we review the current knowledge of regulation of photosynthesis by chloroplast TRXs and assess the prospect of improving plant photosynthetic efficiency by modification of chloroplast thioredoxin systems.

Oxidation of P700 Ensures Robust Photosynthesis

In the light, photosynthetic cells can potentially suffer from oxidative damage derived from reactive oxygen species. Nevertheless, a variety of oxygenic photoautotrophs, including cyanobacteria, algae, and plants, manage their photosynthetic systems successfully. In the present article, we review previous research on how these photoautotrophs safely utilize light energy for photosynthesis without photo-oxidative damage to photosystem I (PSI). The reaction center chlorophyll of PSI, P700, is kept in an oxidized state in response to excess light, under high light and low CO2 conditions, to tune the light utilization and dissipate the excess photo-excitation energy in PSI. Oxidation of P700 is co-operatively regulated by a number of molecular mechanisms on both the electron donor and acceptor sides of PSI. The strategies to keep P700 oxidized are diverse among a variety of photoautotrophs, which are evolutionarily optimized for their ecological niche.

Regulation of cyclic electron flow by chloroplast NADPH-dependent thioredoxin system

Linear electron transport in the thylakoid membrane drives photosynthetic NADPH and ATP production, while cyclic electron flow (CEF) around photosystem I only promotes the translocation of protons from stroma to thylakoid lumen. The chloroplast NADH dehydrogenase-like complex (NDH) participates in one CEF route transferring electrons from ferredoxin back to the plastoquinone pool with concomitant proton pumping to the lumen. CEF has been proposed to balance the ratio of ATP/NADPH production and to control the redox poise particularly in fluctuating light conditions, but the mechanisms regulating the NDH complex remain unknown. We have investigated potential regulation of the CEF pathways by the chloroplast NADPH-thioredoxin reductase (NTRC) in vivo by using an Arabidopsis knockout line of NTRC as well as lines overexpressing NTRC. Here, we present biochemical and biophysical evidence showing that NTRC stimulates the activity of NDH-dependent CEF and is involved in the regulation of generation of proton motive force, thylakoid conductivity to protons, and redox balance between the thylakoid electron transfer chain and the stroma during changes in light conditions. Furthermore, protein-protein interaction assays suggest a putative thioredoxin-target site in close proximity to the ferredoxin-binding domain of NDH, thus providing a plausible mechanism for redox regulation of the NDH ferredoxin:plastoquinone oxidoreductase activity.

The cancer Warburg effect may be a testable example of the minimum entropy production rate principle

Cancer cells consume more glucose by glycolytic fermentation to lactate than by respiration, a characteristic known as the Warburg effect. In contrast with the 36 moles of ATP produced by respiration, fermentation produces two moles of ATP per mole of glucose consumed, which poses a puzzle with regard to the function of the Warburg effect. The production of free energy (ΔG), enthalpy (ΔH), and entropy (ΔS) per mole linearly varies with the fraction (x) of glucose consumed by fermentation that is frequently estimated around 0.9. Hence, calculation shows that, in respect to pure respiration, the predominant fermentative metabolism decreases around 10% the production of entropy per mole of glucose consumed in cancer cells. We hypothesize that increased fermentation could allow cancer cells to accomplish the Prigogine theorem of the trend to minimize the rate of production of entropy. According to the theorem, open cellular systems near the steady state could evolve to minimize the rates of entropy production that may be reached by modified replicating cells producing entropy at a low rate. Remarkably, at CO₂ concentrations above 930 ppm, glucose respiration produces less entropy than fermentation, which suggests experimental tests to validate the hypothesis of minimization of the rate of entropy production through the Warburg effect.

Effects of high CO2 levels on dynamic photosynthesis: carbon gain, mechanisms, and environmental interactions

Understanding the photosynthetic responses of terrestrial plants to environments with high levels of CO2 is essential to address the ecological effects of elevated atmospheric CO2. Most photosynthetic models used for global carbon issues are based on steady-state photosynthesis, whereby photosynthesis is measured under constant environmental conditions; however, terrestrial plant photosynthesis under natural conditions is highly dynamic, and photosynthetic rates change in response to rapid changes in environmental factors. To predict future contributions of photosynthesis to the global carbon cycle, it is necessary to understand the dynamic nature of photosynthesis in relation to high CO2 levels. In this review, we summarize the current body of knowledge on the photosynthetic response to changes in light intensity under experimentally elevated CO2 conditions. We found that short-term exposure to high CO2 enhances photosynthetic rate, reduces photosynthetic induction time, and reduces post-illumination CO2 burst, resulting in increased leaf carbon gain during dynamic photosynthesis. However, long-term exposure to high CO2 during plant growth has varying effects on dynamic photosynthesis. High levels of CO2 increase the carbon gain in photosynthetic induction in some species, but have no significant effects in other species. Some studies have shown that high CO2 levels reduce the biochemical limitation on RuBP regeneration and Rubisco activation during photosynthetic induction, whereas the effects of high levels of CO2 on stomatal conductance differ among species. Few studies have examined the influence of environmental factors on effects of high levels of CO2 on dynamic photosynthesis. We identified several knowledge gaps that should be addressed to aid future predictions of photosynthesis in high-CO2 environments.

Partially dissecting the steady-state electron fluxes in Photosystem I in wild-type and pgr5 and ndh mutants of Arabidopsis

Cyclic electron flux (CEF) around Photosystem I (PS I) is difficult to quantify. We obtained the linear electron flux (LEFO2) through both photosystems and the total electron flux through PS I (ETR1) in Arabidopsis in CO2-enriched air. ΔFlux = ETR1 - LEFO2 is an upper estimate of CEF, which consists of two components, an antimycin A-sensitive, PGR5 (proton gradient regulation 5 protein)-dependent component and an insensitive component facilitated by a chloroplastic nicotinamide adenine dinucleotide dehydrogenase-like complex (NDH). Using wild type as well as pgr5 and ndh mutants, we observed that (1) 40% of the absorbed light was partitioned to PS I; (2) at high irradiance a substantial antimycin A-sensitive CEF occurred in the wild type and the ndh mutant; (3) at low irradiance a sizable antimycin A-sensitive CEF occurred in the wild type but not in the ndh mutant, suggesting an enhancing effect of NDH in low light; and (4) in the pgr5 mutant, and the wild type and ndh mutant treated with antimycin A, a residual ΔFlux existed at high irradiance, attributable to charge recombination and/or pseudo-cyclic electron flow. Therefore, in low-light-acclimated plants exposed to high light, ΔFlux has contributions from various paths of electron flow through PS I.