International Journal of Molecular Sciences

Editorial

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3 pages, 189 KiB

Open AccessEditorial

Photosynthetic Reactions: From Molecules to Function, and from Simple Models to Complex Systems

by Katarzyna B. Gieczewska, Beata Myśliwa-Kurdziel and Joanna Grzyb

Int. J. Mol. Sci. 2022, 23(19), 11180; https://doi.org/10.3390/ijms231911180 - 23 Sep 2022

Viewed by 973

Abstract

Photosynthesis is the basic process for life on Earth—and the one that has changed life history most drastically [...] Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

Research

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18 pages, 2601 KiB

Open AccessArticle

The Arabidopsis Accessions Selection Is Crucial: Insight from Photosynthetic Studies

by Joanna Wójtowicz and Katarzyna B. Gieczewska

Int. J. Mol. Sci. 2021, 22(18), 9866; https://doi.org/10.3390/ijms22189866 - 13 Sep 2021

Cited by 5 | Viewed by 2257

Abstract

Natural genetic variation in photosynthesis is strictly associated with the remarkable adaptive plasticity observed amongst Arabidopsis thaliana accessions derived from environmentally distinct regions. Exploration of the characteristic features of the photosynthetic machinery could reveal the regulatory mechanisms underlying those traits. In this study, [...] Read more.

Natural genetic variation in photosynthesis is strictly associated with the remarkable adaptive plasticity observed amongst Arabidopsis thaliana accessions derived from environmentally distinct regions. Exploration of the characteristic features of the photosynthetic machinery could reveal the regulatory mechanisms underlying those traits. In this study, we performed a detailed characterisation and comparison of photosynthesis performance and spectral properties of the photosynthetic apparatus in the following selected Arabidopsis thaliana accessions commonly used in laboratories as background lines: Col-0, Col-1, Col-2, Col-8, Ler-0, and Ws-2. The main focus was to distinguish the characteristic disparities for every accession in photosynthetic efficiency that could be accountable for their remarkable plasticity to adapt. The biophysical and biochemical analysis of the thylakoid membranes in control conditions revealed differences in lipid-to-protein contribution, Chlorophyll-to-Carotenoid ratio (Chl/Car), and xanthophyll cycle pigment distribution among accessions. We presented that such changes led to disparities in the arrangement of the Chlorophyll-Protein complexes, the PSI/PSII ratio, and the lateral mobility of the thylakoid membrane, with the most significant aberrations detected in the Ler-0 and Ws-2 accessions. We concluded that selecting an accession suitable for specific research on the photosynthetic process is essential for optimising the experiment. Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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21 pages, 5929 KiB

Open AccessArticle

Possible Steps of the Carboxylation of Ribulose-1,5-biphosphate from Intermediates: 2,3-Enediol versus 1,2-Enol

by Roman G. Fedunov and Victor A. Sokolov

Int. J. Mol. Sci. 2021, 22(18), 9749; https://doi.org/10.3390/ijms22189749 - 9 Sep 2021

Cited by 1 | Viewed by 1980

Abstract

Ribulose 1,5-bisphosphate (RuBP) undergoes enolization to initiate fixation of atmospheric carbon dioxide in the plant carbon cycle. The known model assumes the binding of RuBP to the Rubisco active site with the subsequent formation of 2,3-enediol (2,3,4-trihydroxypent-2-ene-1,5-diyl diphosphate). In the present study, it [...] Read more.

Ribulose 1,5-bisphosphate (RuBP) undergoes enolization to initiate fixation of atmospheric carbon dioxide in the plant carbon cycle. The known model assumes the binding of RuBP to the Rubisco active site with the subsequent formation of 2,3-enediol (2,3,4-trihydroxypent-2-ene-1,5-diyl diphosphate). In the present study, it is assumed that 1,2-enol (2,3,4-trihydroxypent-1-ene-1,5-diyl diphosphate) can be formed in the enolization step to initiate the carboxylation reaction. We have used Kohn–Sham density functional theory on WB97X-D3/Def2-TZVP levels to compare the reaction barriers in the two ways. We considered the pathways of carboxylation of 1/2-ene (mono/di)ol via the C1 and C2 carbons without taking into account the binding of RuBP to the magnesium ion. Calculations of Gibbs free energies confirm the equal probability of the formation of 2,3-enediol and 1,2-enol. Quantum–chemical modeling of enolization and carboxylation reactions supports the important role of the bridging water molecule and diphosphate groups, which provide proton transfer and lower reaction barriers. The results show that carbon dioxide fixation can occur without a magnesium ion, and binding with C1 can have a lower barrier (~12 kcal/mol) than with C2 (~23 kcal/mol). Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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16 pages, 5027 KiB

Open AccessArticle

Insights into the Structure of Rubisco from Dinoflagellates-In Silico Studies

by Małgorzata Rydzy, Michał Tracz, Andrzej Szczepaniak and Joanna Grzyb

Int. J. Mol. Sci. 2021, 22(16), 8524; https://doi.org/10.3390/ijms22168524 - 7 Aug 2021

Cited by 3 | Viewed by 2886

Abstract

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is one of the best studied enzymes. It is crucial for photosynthesis, and thus for all of biosphere’s productivity. There are four isoforms of this enzyme, differing by amino acid sequence composition and quaternary structure. However, there is still a [...] Read more.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is one of the best studied enzymes. It is crucial for photosynthesis, and thus for all of biosphere’s productivity. There are four isoforms of this enzyme, differing by amino acid sequence composition and quaternary structure. However, there is still a group of organisms, dinoflagellates, single-cell eukaryotes, that are confirmed to possess Rubisco, but no successful purification of the enzyme of such origin, and hence a generation of a crystal structure was reported to date. Here, we are using in silico tools to generate the possible structure of Rubisco from a dinoflagellate representative, Symbiodinium sp. We selected two templates: Rubisco from Rhodospirillum rubrum and Rhodopseudomonas palustris. Both enzymes are the so-called form II Rubiscos, but the first is exclusively a homodimer, while the second one forms homo-hexamers. Obtained models show no differences in amino acids crucial for Rubisco activity. The variation was found at two closely located inserts in the C-terminal domain, of which one extends a helix and the other forms a loop. These inserts most probably do not play a direct role in the enzyme’s activity, but may be responsible for interaction with an unknown protein partner, possibly a regulator or a chaperone. Analysis of the possible oligomerization interface indicated that Symbiodinium sp. Rubisco most likely forms a trimer of homodimers, not just a homodimer. This hypothesis was empowered by calculation of binding energies. Additionally, we found that the protein of study is significantly richer in cysteine residues, which may be the cause for its activity loss shortly after cell lysis. Furthermore, we evaluated the influence of the loop insert, identified exclusively in the Symbiodinium sp. protein, on the functionality of the recombinantly expressed R. rubrum Rubisco. All these findings shed new light onto dinoflagellate Rubisco and may help in future obtainment of a native, active enzyme. Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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17 pages, 5431 KiB

Open AccessArticle

Photosynthetic Linear Electron Flow Drives CO₂ Assimilation in Maize Leaves

by Ginga Shimakawa and Chikahiro Miyake

Int. J. Mol. Sci. 2021, 22(9), 4894; https://doi.org/10.3390/ijms22094894 - 5 May 2021

Cited by 8 | Viewed by 2622

Abstract

Photosynthetic organisms commonly develop the strategy to keep the reaction center chlorophyll of photosystem I, P700, oxidized for preventing the generation of reactive oxygen species in excess light conditions. In photosynthesis of C₄ plants, CO₂ concentration is kept at higher levels [...] Read more.

Photosynthetic organisms commonly develop the strategy to keep the reaction center chlorophyll of photosystem I, P700, oxidized for preventing the generation of reactive oxygen species in excess light conditions. In photosynthesis of C₄ plants, CO₂ concentration is kept at higher levels around ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) by the cooperation of the mesophyll and bundle sheath cells, which enables them to assimilate CO₂ at higher rates to survive under drought stress. However, the regulatory mechanism of photosynthetic electron transport for P700 oxidation is still poorly understood in C₄ plants. Here, we assessed gas exchange, chlorophyll fluorescence, electrochromic shift, and near infrared absorbance in intact leaves of maize (a NADP-malic enzyme C₄ subtype species) in comparison with mustard, a C₃ plant. Instead of the alternative electron sink due to photorespiration in the C₃ plant, photosynthetic linear electron flow was strongly suppressed between photosystems I and II, dependent on the difference of proton concentration across the thylakoid membrane (ΔpH) in response to the suppression of CO₂ assimilation in maize. Linear relationships among CO₂ assimilation rate, linear electron flow, P700 oxidation, ΔpH, and the oxidation rate of ferredoxin suggested that the increase of ΔpH for P700 oxidation was caused by the regulation of proton conductance of chloroplast ATP synthase but not by promoting cyclic electron flow. At the scale of intact leaves, the ratio of PSI to PSII was estimated almost 1:1 in both C₃ and C₄ plants. Overall, the photosynthetic electron transport was regulated for P700 oxidation in maize through the same strategies as in C₃ plants only except for the capacity of photorespiration despite the structural and metabolic differences in photosynthesis between C₃ and C₄ plants. Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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18 pages, 4867 KiB

Open AccessArticle

Single-Walled Carbon Nanotubes Modify Leaf Micromorphology, Chloroplast Ultrastructure and Photosynthetic Activity of Pea Plants

by Violeta Velikova, Nia Petrova, László Kovács, Asya Petrova, Dimitrina Koleva, Tsonko Tsonev, Stefka Taneva, Petar Petrov and Sashka Krumova

Int. J. Mol. Sci. 2021, 22(9), 4878; https://doi.org/10.3390/ijms22094878 - 5 May 2021

Cited by 25 | Viewed by 3084

Abstract

Single-walled carbon nanotubes (SWCNTs) emerge as promising novel carbon-based nanoparticles for use in biomedicine, pharmacology and precision agriculture. They were shown to penetrate cell walls and membranes and to physically interact and exchange electrons with photosynthetic complexes in vitro. Here, for the first [...] Read more.

Single-walled carbon nanotubes (SWCNTs) emerge as promising novel carbon-based nanoparticles for use in biomedicine, pharmacology and precision agriculture. They were shown to penetrate cell walls and membranes and to physically interact and exchange electrons with photosynthetic complexes in vitro. Here, for the first time, we studied the concentration-dependent effect of foliar application of copolymer-grafted SWCNTs on the structural and functional characteristics of intact pea plants. The lowest used concentration of 10 mg L⁻¹ did not cause any harmful effects on the studied leaf characteristics, while abundant epicuticular wax generation on both leaf surfaces was observed after 300 mg L⁻¹ treatment. Swelling of both the granal and the stromal regions of thylakoid membranes was detected after application of 100 mg L⁻¹ and was most pronounced after 300 mg L⁻¹. Higher SWCNT doses lead to impaired photosynthesis in terms of lower proton motive force generation, slower generation of non-photochemical quenching and reduced zeaxanthin content; however, the photosystem II function was largely preserved. Our results clearly indicate that SWCNTs affect the photosynthetic apparatus in a concentration-dependent manner. Low doses (10 mg L⁻¹) of SWCNTs appear to be a safe suitable object for future development of nanocarriers for substances that are beneficial for plant growth. Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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22 pages, 5775 KiB

Open AccessArticle

The Role of Selected Wavelengths of Light in the Activity of Photosystem II in Gloeobacter violaceus

by Monika Kula-Maximenko, Kamil Jan Zieliński and Ireneusz Ślesak

Int. J. Mol. Sci. 2021, 22(8), 4021; https://doi.org/10.3390/ijms22084021 - 13 Apr 2021

Cited by 7 | Viewed by 2704

Abstract

Gloeobacter violaceus is a cyanobacteria species with a lack of thylakoids, while photosynthetic antennas, i.e., phycobilisomes (PBSs), photosystem II (PSII), and I (PSI), are located in the cytoplasmic membrane. We verified the hypothesis that blue–red (BR) light supplemented with a far-red (FR), ultraviolet [...] Read more.

Gloeobacter violaceus is a cyanobacteria species with a lack of thylakoids, while photosynthetic antennas, i.e., phycobilisomes (PBSs), photosystem II (PSII), and I (PSI), are located in the cytoplasmic membrane. We verified the hypothesis that blue–red (BR) light supplemented with a far-red (FR), ultraviolet A (UVA), and green (G) light can affect the photosynthetic electron transport chain in PSII and explain the differences in the growth of the G. violaceus culture. The cyanobacteria were cultured under different light conditions. The largest increase in G. violaceus biomass was observed only under BR + FR and BR + G light. Moreover, the shape of the G. violaceus cells was modified by the spectrum with the addition of G light. Furthermore, it was found that both the spectral composition of light and age of the cyanobacterial culture affect the different content of phycobiliproteins in the photosynthetic antennas (PBS). Most likely, in cells grown under light conditions with the addition of FR and G light, the average antenna size increased due to the inactivation of some reaction centers in PSII. Moreover, the role of PSI and gloeorhodopsin as supplementary sources of metabolic energy in the G. violaceus growth is discussed. Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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Review

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15 pages, 1906 KiB

Open AccessReview

How Light Reactions of Photosynthesis in C4 Plants Are Optimized and Protected under High Light Conditions

by Wioleta Wasilewska-Dębowska, Maksymilian Zienkiewicz and Anna Drozak

Int. J. Mol. Sci. 2022, 23(7), 3626; https://doi.org/10.3390/ijms23073626 - 26 Mar 2022

Cited by 8 | Viewed by 5962

Abstract

Most C4 plants that naturally occur in tropical or subtropical climates, in high light environments, had to evolve a series of adaptations of photosynthesis that allowed them to grow under these conditions. In this review, we summarize mechanisms that ensure the balancing of [...] Read more.

Most C4 plants that naturally occur in tropical or subtropical climates, in high light environments, had to evolve a series of adaptations of photosynthesis that allowed them to grow under these conditions. In this review, we summarize mechanisms that ensure the balancing of energy distribution, counteract photoinhibition, and allow the dissipation of excess light energy. They secure effective electron transport in light reactions of photosynthesis, which will lead to the production of NADPH and ATP. Furthermore, a higher content of the cyclic electron transport components and an increase in ATP production are observed, which is necessary for the metabolism of C4 for effective assimilation of CO₂. Most of the data are provided by studies of the genus Flaveria, where species belonging to different metabolic subtypes and intermediate forms between C3 and C4 are present. All described mechanisms that function in mesophyll and bundle sheath chloroplasts, into which photosynthetic reactions are divided, may differ in metabolic subtypes as a result of the different organization of thylakoid membranes, as well as the different demand for ATP and NADPH. This indicates that C4 plants have plasticity in the utilization of pathways in which efficient use and dissipation of excitation energy are realized. Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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23 pages, 2211 KiB

Open AccessReview

Antioxidant and Signaling Role of Plastid-Derived Isoprenoid Quinones and Chromanols

by Beatrycze Nowicka, Agnieszka Trela-Makowej, Dariusz Latowski, Kazimierz Strzalka and Renata Szymańska

Int. J. Mol. Sci. 2021, 22(6), 2950; https://doi.org/10.3390/ijms22062950 - 14 Mar 2021

Cited by 16 | Viewed by 3406

Abstract

Plant prenyllipids, especially isoprenoid chromanols and quinols, are very efficient low-molecular-weight lipophilic antioxidants, protecting membranes and storage lipids from reactive oxygen species (ROS). ROS are byproducts of aerobic metabolism that can damage cell components, they are also known to play a role in [...] Read more.

Plant prenyllipids, especially isoprenoid chromanols and quinols, are very efficient low-molecular-weight lipophilic antioxidants, protecting membranes and storage lipids from reactive oxygen species (ROS). ROS are byproducts of aerobic metabolism that can damage cell components, they are also known to play a role in signaling. Plants are particularly prone to oxidative damage because oxygenic photosynthesis results in O₂ formation in their green tissues. In addition, the photosynthetic electron transfer chain is an important source of ROS. Therefore, chloroplasts are the main site of ROS generation in plant cells during the light reactions of photosynthesis, and plastidic antioxidants are crucial to prevent oxidative stress, which occurs when plants are exposed to various types of stress factors, both biotic and abiotic. The increase in antioxidant content during stress acclimation is a common phenomenon. In the present review, we describe the mechanisms of ROS (singlet oxygen, superoxide, hydrogen peroxide and hydroxyl radical) production in chloroplasts in general and during exposure to abiotic stress factors, such as high light, low temperature, drought and salinity. We highlight the dual role of their presence: negative (i.e., lipid peroxidation, pigment and protein oxidation) and positive (i.e., contribution in redox-based physiological processes). Then we provide a summary of current knowledge concerning plastidic prenyllipid antioxidants belonging to isoprenoid chromanols and quinols, as well as their structure, occurrence, biosynthesis and function both in ROS detoxification and signaling. Full article

(This article belongs to the Special Issue Photosynthetic Reactions: From Molecules to Function, from Simple Models to Complex System)

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