1
|
Tondepu SAG, Manova V, Vadivel D, Dondi D, Pagano A, Macovei A. MicroRNAs potentially targeting DDR-related genes are differentially expressed upon exposure to γ-rays during seed germination in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108771. [PMID: 38820913 DOI: 10.1016/j.plaphy.2024.108771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024]
Abstract
DNA damage response (DDR), a complex network of cellular pathways that cooperate to sense and repair DNA lesions, is regulated by several mechanisms, including microRNAs. As small, single-stranded RNA molecules, miRNAs post-transcriptionally regulate their target genes by mRNA cleavage or translation inhibition. Knowledge regarding miRNAs influence on DDR-associated genes is still scanty in plants. In this work, an in silico analysis was performed to identify putative miRNAs that could target DDR sensors, signal transducers and effector genes in wheat. Selected putative miRNA-gene pairs were tested in an experimental system where seeds from two wheat mutant lines were irradiated with 50 Gy and 300 Gy gamma(γ)-rays. To evaluate the effect of the treatments on wheat germination, phenotypic and molecular (DNA damage, ROS accumulation, gene/miRNA expression profile) analyses have been carried out. The results showed that in dry seeds ROS accumulated immediately after irradiation and decayed soon after while the negative impact on seedling growth was supported by enhanced accumulation of DNA damage. When a qRT-PCR analysis was performed, the selected miRNAs and DDR-related genes were differentially modulated by the γ-rays treatments in a dose-, time- and genotype-dependent manner. A significant negative correlation was observed between the expression of tae-miR5086 and the RAD50 gene, involved in double-strand break sensing and homologous recombination repair, one of the main processes that repairs DNA breaks induced by γ-rays. The results hereby reported can be relevant for wheat breeding programs and screening of the radiation response and tolerance of novel wheat varieties.
Collapse
Affiliation(s)
- Sri Amarnadh Gupta Tondepu
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Vasilissa Manova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences "Acad. G. Bonchev", Street Bldg. 21, 1113, Sofia, Bulgaria.
| | - Dhanalakshmi Vadivel
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Daniele Dondi
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Adolfo Ferrata 9, 27100, Pavia, Italy.
| |
Collapse
|
2
|
Evaluation of new low-valent computational models for the oxygen-evolving complex of photosystem II. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
3
|
Beal NJ, Corry TA, O'Malley PJ. A Comparison of Experimental and Broken Symmetry Density Functional Theory (BS-DFT) Calculated Electron Paramagnetic Resonance (EPR) Parameters for Intermediates Involved in the S 2 to S 3 State Transition of Nature's Oxygen Evolving Complex. J Phys Chem B 2018; 122:1394-1407. [PMID: 29300480 DOI: 10.1021/acs.jpcb.7b10843] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A broken symmetry density functional theory (BS-DFT) magnetic analysis of the S2, S2YZ•, and S3 states of Nature's oxygen evolving complex is performed for both the native Ca and Sr substituted forms. Good agreement with experiment is observed between the tyrosyl calculated g-tensor and 1H hyperfine couplings for the native Ca form. Changes in the hydrogen bonding environment of the tyrosyl radical in S2YZ• caused by Sr substitution lead to notable changes in the calculated g-tensor of the tyrosyl radical. Comparison of calculated and experimental 55Mn hyperfine couplings for the S3 state presently favors an open cubane form of the complex with an additional OH ligand coordinating to MnD. In Ca models, this additional ligation can arise by closed-cubane form deprotonation of the Ca ligand W3 in the S2YZ• state accompanied by spontaneous movement to the vacant Mn coordination site or by addition of an external OH group. For the Sr form, no spontaneous movement of W3 to the vacant Mn coordination site is observed in contrast to the native Ca form, a difference which may lead to the reduced catalytic activity of the Sr substituted form. BS-DFT studies on peroxo models of S3 as indicated by a recent X-ray free electron laser (XFEL) crystallography study give rise to a structural model compatible with experimental data and an S = 3 ground state compatible with EPR studies.
Collapse
Affiliation(s)
- Nathan J Beal
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| | - Thomas A Corry
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| | - Patrick J O'Malley
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| |
Collapse
|
4
|
Morton J, Chrysina M, Craig VSJ, Akita F, Nakajima Y, Lubitz W, Cox N, Shen JR, Krausz E. Structured near-infrared Magnetic Circular Dichroism spectra of the Mn 4CaO 5 cluster of PSII in T. vulcanus are dominated by Mn(IV) d-d 'spin-flip' transitions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:88-98. [PMID: 29066392 DOI: 10.1016/j.bbabio.2017.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 01/13/2023]
Abstract
Photosystem II passes through four metastable S-states in catalysing light-driven water oxidation. Variable temperature variable field (VTVH) Magnetic Circular Dichroism (MCD) spectra in PSII of Thermosynochococcus (T.) vulcanus for each S-state are reported. These spectra, along with assignments, provide a new window into the electronic and magnetic structure of Mn4CaO5. VTVH MCD spectra taken in the S2 state provide a clear g=2, S=1/2 paramagnetic characteristic, which is entirely consistent with that known by EPR. The three features, seen as positive (+) at 749nm, negative (-) at 773nm and (+) at 808nm are assigned as 4A→2E spin-flips within the d3 configuration of the Mn(IV) centres present. This assignment is supported by comparison(s) to spin-flips seen in a range of Mn(IV) materials. S3 exhibits a more intense (-) MCD peak at 764nm and has a stronger MCD saturation characteristic. This S3 MCD saturation behaviour can be accurately modelled using parameters taken directly from analyses of EPR spectra. We see no evidence for Mn(III) d-d absorption in the near-IR of any S-state. We suggest that Mn(IV)-based absorption may be responsible for the well-known near-IR induced changes induced in S2 EPR spectra of T. vulcanus and not Mn(III)-based, as has been commonly assumed. Through an analysis of the nephelauxetic effect, the excitation energy of S-state dependent spin-flips seen may help identify coordination characteristics and changes at each Mn(IV). A prospectus as to what more detailed S-state dependent MCD studies promise to achieve is outlined.
Collapse
Affiliation(s)
- Jennifer Morton
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Maria Chrysina
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Vincent S J Craig
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Department of Biology, Faculty of Science, Okayama University, Okayama, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Department of Biology, Faculty of Science, Okayama University, Okayama, Japan
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, Australia; Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Department of Biology, Faculty of Science, Okayama University, Okayama, Japan
| | - Elmars Krausz
- Research School of Chemistry, Australian National University, Canberra, Australia.
| |
Collapse
|
5
|
Temperature dependence of the oxidation kinetics of TyrZ and TyrD in oxygen-evolving photosystem II complexes throughout the range from 320K to 5K. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1283-96. [DOI: 10.1016/j.bbabio.2015.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/10/2015] [Accepted: 07/15/2015] [Indexed: 11/21/2022]
|
6
|
Retegan M, Cox N, Lubitz W, Neese F, Pantazis DA. The first tyrosyl radical intermediate formed in the S2-S3 transition of photosystem II. Phys Chem Chem Phys 2015; 16:11901-10. [PMID: 24760184 DOI: 10.1039/c4cp00696h] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The EPR "split signals" represent key intermediates of the S-state cycle where the redox active D1-Tyr161 (YZ) has been oxidized by the reaction center of the photosystem II enzyme to its tyrosyl radical form, but the successive oxidation of the Mn4CaO5 cluster has not yet occurred (SiYZ˙). Here we focus on the S2YZ˙ state, which is formed en route to the final metastable state of the catalyst, the S3 state, the state which immediately precedes O-O bond formation. Quantum chemical calculations demonstrate that both isomeric forms of the S2 state, the open and closed cubane isomers, can form states with an oxidized YZ˙ residue without prior deprotonation of the Mn4CaO5 cluster. The two forms are expected to lie close in energy and retain the electronic structure and magnetic topology of the corresponding S2 state of the inorganic core. As expected, tyrosine oxidation results in a proton shift towards His190. Analysis of the electronic rearrangements that occur upon formation of the tyrosyl radical suggests that a likely next step in the catalytic cycle is the deprotonation of a terminal water ligand (W1) of the Mn4CaO5 cluster. Diamagnetic metal ion substitution is used in our calculations to obtain the molecular g-tensor of YZ˙. It is known that the gx value is a sensitive probe not only of the extent of the proton shift between the tyrosine-histidine pair, but also of the polarization environment of the tyrosine, especially about the phenolic oxygen. It is shown for PSII that this environment is determined by the Ca(2+) ion, which locates two water molecules about the phenoxyl oxygen, indirectly modulating the oxidation potential of YZ.
Collapse
Affiliation(s)
- Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany.
| | | | | | | | | |
Collapse
|
7
|
Boussac A, Rappaport F, Brettel K, Sugiura M. Charge recombination in S(n)Tyr(Z)(•)Q(A)(-•) radical pairs in D1 protein variants of Photosystem II: long range electron transfer in the Marcus inverted region. J Phys Chem B 2013; 117:3308-14. [PMID: 23448315 DOI: 10.1021/jp400337j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charge recombination in the light-induced radical pair SnTyrZ(•)QA(-•) in Photosystem II (PSII) from Thermosynechococcus elongatus has been studied at cryogenic temperatures by time-resolved EPR for different configurations of PSII that are expected to affect the driving force of the reaction (oxidation states S0, S1, or S2 of the Mn4CaO5 cluster; PsbA1, PsbA2, or PsbA3 as D1 protein). The kinetics were independent of temperature in the studied range from 4.2 to 50 K and were not affected by exchange of H2O for D2O, consistent with single-step electron tunneling over the distance of ∼32 Å without any repopulation through Boltzmann equilibration of intermediates lying higher in energy. In PsbA1-PSII, the charge recombinations in the radical pairs SnTyrZ(•)QA(-•) (ket = 3.4 × 10(-3) s(-1) for S1) were slower than in PsbA3-PSII despite an expected lower driving force owing to a downshifted Em(QA/QA(-•)) in PsbA1-PSII. Conversely, the reaction was slower in the presence of S2 than in the presence of S1, despite an expected larger driving force due to an upshifted Em(TyrZ(•)/TyrZ) in S2. These observations indicate that the charge recombination occurs in the Marcus inverted region. Assuming that the driving force of the reaction (-ΔG(0) ≈ 1.2 eV at room temperature for S1) does not vary strongly with temperature, the data indicate an optimal electron transfer rate (for a hypothetical -ΔG(0) = λ) substantially faster than would be predicted from extrapolation of room temperature intraprotein ET rates over shorter distances. Possible origins of this deviation are discussed, including a possible enhancement of the electronic coupling of TyrZ(•) and QA(-•) by aromatic cofactors located in between. Observed similar S1TyrZ(•)QA(-•) charge recombinations in PsbA2-PSII and PsbA3-PSII predict that Em(QA/QA(-•)) in PsbA2-PSII is similar to that in PsbA3-PSII.
Collapse
Affiliation(s)
- Alain Boussac
- iBiTec-S, CNRS UMR 8221, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | | | | | | |
Collapse
|
8
|
Su JH, Cox N, Ames W, Pantazis DA, Rapatskiy L, Lohmiller T, Kulik LV, Dorlet P, Rutherford AW, Neese F, Boussac A, Lubitz W, Messinger J. The electronic structures of the S(2) states of the oxygen-evolving complexes of photosystem II in plants and cyanobacteria in the presence and absence of methanol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:829-40. [PMID: 21406177 DOI: 10.1016/j.bbabio.2011.03.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/02/2011] [Accepted: 03/04/2011] [Indexed: 01/25/2023]
Abstract
The electronic properties of the Mn(4)O(x)Ca cluster in the S(2) state of the oxygen-evolving complex (OEC) were studied using X- and Q-band EPR and Q-band (55)Mn-ENDOR using photosystem II preparations isolated from the thermophilic cyanobacterium T. elongatus and higher plants (spinach). The data presented here show that there is very little difference between the two species. Specifically it is shown that: (i) only small changes are seen in the fitted isotropic hyperfine values, suggesting that there is no significant difference in the overall spin distribution (electronic coupling scheme) between the two species; (ii) the inferred fine-structure tensor of the only Mn(III) ion in the cluster is of the same magnitude and geometry for both species types, suggesting that the Mn(III) ion has the same coordination sphere in both sample preparations; and (iii) the data from both species are consistent with only one structural model available in the literature, namely the Siegbahn structure [Siegbahn, P. E. M. Accounts Chem. Res.2009, 42, 1871-1880, Pantazis, D. A. et al., Phys. Chem. Chem. Phys.2009, 11, 6788-6798]. These measurements were made in the presence of methanol because it confers favorable magnetic relaxation properties to the cluster that facilitate pulse-EPR techniques. In the absence of methanol the separation of the ground state and the first excited state of the spin system is smaller. For cyanobacteria this effect is minor but in plant PS II it leads to a break-down of the S(T)=½ spin model of the S(2) state. This suggests that the methanol-OEC interaction is species dependent. It is proposed that the effect of small organic solvents on the electronic structure of the cluster is to change the coupling between the outer Mn (Mn(A)) and the other three Mn ions that form the trimeric part of the cluster (Mn(B), Mn(C), Mn(D)), by perturbing the linking bis-μ-oxo bridge. The flexibility of this bridging unit is discussed with regard to the mechanism of O-O bond formation.
Collapse
Affiliation(s)
- Ji-Hu Su
- Max-Planck-Institut für Bioanorganische Chemie, D-45470 Mülheim an der Ruhr, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Effects of formate binding on the quinone–iron electron acceptor complex of photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:216-26. [DOI: 10.1016/j.bbabio.2010.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/01/2010] [Accepted: 10/25/2010] [Indexed: 11/21/2022]
|
10
|
Havelius KGV, Su JH, Han G, Mamedov F, Ho FM, Styring S. The formation of the split EPR signal from the S(3) state of Photosystem II does not involve primary charge separation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:11-21. [PMID: 20863810 DOI: 10.1016/j.bbabio.2010.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 09/14/2010] [Accepted: 09/15/2010] [Indexed: 11/16/2022]
Abstract
Metalloradical EPR signals have been found in intact Photosystem II at cryogenic temperatures. They reflect the light-driven formation of the tyrosine Z radical (Y(Z)) in magnetic interaction with the CaMn(4) cluster in a particular S state. These so-called split EPR signals, induced at cryogenic temperatures, provide means to study the otherwise transient Y(Z) and to probe the S states with EPR spectroscopy. In the S(0) and S(1) states, the respective split signals are induced by illumination of the sample in the visible light range only. In the S(3) state the split EPR signal is induced irrespective of illumination wavelength within the entire 415-900nm range (visible and near-IR region) [Su, J. H., Havelius, K. G. V., Ho, F. M., Han, G., Mamedov, F., and Styring, S. (2007) Biochemistry 46, 10703-10712]. An important question is whether a single mechanism can explain the induction of the Split S(3) signal across the entire wavelength range or whether wavelength-dependent mechanisms are required. In this paper we confirm that the Y(Z) radical formation in the S(1) state, reflected in the Split S(1) signal, is driven by P680-centered charge separation. The situation in the S(3) state is different. In Photosystem II centers with pre-reduced quinone A (Q(A)), where the P680-centered charge separation is blocked, the Split S(3) EPR signal could still be induced in the majority of the Photosystem II centers using both visible and NIR (830nm) light. This shows that P680-centered charge separation is not involved. The amount of oxidized electron donors and reduced electron acceptors (Q(A)(-)) was well correlated after visible light illumination at cryogenic temperatures in the S(1) state. This was not the case in the S(3) state, where the Split S(3) EPR signal was formed in the majority of the centers in a pathway other than P680-centered charge separation. Instead, we propose that one mechanism exists over the entire wavelength interval to drive the formation of the Split S(3) signal. The origin for this, probably involving excitation of one of the Mn ions in the CaMn(4) cluster in Photosystem II, is discussed.
Collapse
Affiliation(s)
- Kajsa G V Havelius
- Molecular Biomimetrics, Department of Photochemistry and Molecular Sciences, Uppsala University, The Angström Laboratory, Uppsala, Sweden
| | | | | | | | | | | |
Collapse
|
11
|
Cox N, Ogata H, Stolle P, Reijerse E, Auling G, Lubitz W. A Tyrosyl−Dimanganese Coupled Spin System is the Native Metalloradical Cofactor of the R2F Subunit of the Ribonucleotide Reductase of Corynebacterium ammoniagenes. J Am Chem Soc 2010; 132:11197-213. [DOI: 10.1021/ja1036995] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholas Cox
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim (Ruhr), Germany, and Institut für Mikrobiologie, Leibniz Universität Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | - Hideaki Ogata
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim (Ruhr), Germany, and Institut für Mikrobiologie, Leibniz Universität Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | - Patrick Stolle
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim (Ruhr), Germany, and Institut für Mikrobiologie, Leibniz Universität Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | - Edward Reijerse
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim (Ruhr), Germany, and Institut für Mikrobiologie, Leibniz Universität Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | - Georg Auling
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim (Ruhr), Germany, and Institut für Mikrobiologie, Leibniz Universität Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim (Ruhr), Germany, and Institut für Mikrobiologie, Leibniz Universität Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| |
Collapse
|