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Felčíková K, Hovan A, Polák M, Loginov DS, Holotová V, Díaz C, Kožár T, Lee O, Varhač R, Novák P, Bánó G, Sedlák E. Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer. Protein Sci 2024; 33:e4921. [PMID: 38501448 PMCID: PMC10949324 DOI: 10.1002/pro.4921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 03/20/2024]
Abstract
Flavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1 O2 ). However, its 1 O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase 1 O2 production efficiency GEPS, but at the same time weakened native FMN-protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategically placed cysteines (oxidation-prone amino acids) in the isoalloxazine-binding site due to significantly increased volume of the cysteinyl side residue(s). As a proof of concept, in three variants of the LOV2 domain of Avena sativa (AsLOV2), namely V416C, T418C, and V416C/T418C, the effective 1 O2 production strongly correlated with the efficiency of irradiation-induced FMN dissociation (wild type (WT) < V416C < T418C < V416C/T418C). This alternative approach enables us: (i) to overcome the low 1 O2 production efficiency of flavin-based GEPSs without affecting native isoalloxazine ring-protein interactions and (ii) to utilize AsLOV2, due to its inherent binding propensity to FMN, as a PS vehicle, which is released at a target by light irradiation.
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Affiliation(s)
- Kristína Felčíková
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Andrej Hovan
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Marek Polák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Dmitry S. Loginov
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Veronika Holotová
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Carlos Díaz
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - One‐Sun Lee
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Petr Novák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Gregor Bánó
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
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Adamec L, Plačková L, Doležal K. Characteristics of turion development in two aquatic carnivorous plants: Hormonal profiles, gas exchange and mineral nutrient content. Plant Direct 2024; 8:e558. [PMID: 38222932 PMCID: PMC10784648 DOI: 10.1002/pld3.558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/09/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Turions are vegetative, dormant, and storage overwintering organs formed in perennial aquatic plants in response to unfavorable ecological conditions and originate by extreme condensation of apical shoot segments. The contents of cytokinins, auxins, and abscisic acid were estimated in shoot apices of summer growing, rootless aquatic carnivorous plants, Aldrovanda vesiculosa and Utricularia australis, and in developing turions at three stages and full maturity to reveal hormonal patterns responsible for turion development. The hormones were analyzed in miniature turion samples using ultraperformance liquid chromatography coupled with triple quadrupole mass spectrometry. Photosynthetic measurements in young leaves also confirmed relatively high photosynthetic rates at later turion stages. The content of active cytokinin forms was almost stable in A. vesiculosa during turion development but markedly decreased in U. australis. In both species, auxin content culminated in the middle of turion development and then decreased again. The content of abscisic acid as the main inhibitory hormone was very low in growing plants in both species but rose greatly at first developmental stages and stayed very high in mature turions. The hormonal data indicate a great strength of developing turions within sink-source relationships and confirm the central role of abscisic acid in regulating the turion development.
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Affiliation(s)
- Lubomír Adamec
- Institute of BotanyCzech Academy of SciencesTřeboňCzech Republic
| | - Lenka Plačková
- Laboratory of Growth Regulators, Faculty of SciencePalacký UniversityOlomoucCRCzech Republic
- Institute of Experimental BotanyCzech Academy of SciencesPragueCzech Republic
| | - Karel Doležal
- Laboratory of Growth Regulators, Faculty of SciencePalacký UniversityOlomoucCRCzech Republic
- Institute of Experimental BotanyCzech Academy of SciencesPragueCzech Republic
- Department of Chemical Biology, Faculty of SciencePalacký UniversityOlomoucCzech Republic
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Valášek LS, Lukeš J, Paris Z. Stops making sense - For the people? Clin Transl Med 2023; 13:e1270. [PMID: 37203266 PMCID: PMC10196215 DOI: 10.1002/ctm2.1270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023] Open
Affiliation(s)
| | - Julius Lukeš
- Institute of ParasitologyBiology CentreCzech Academy of SciencesČeské Budějovice (Budweis)Czech Republic
- Faculty of SciencesUniversity of South BohemiaČeské Budějovice (Budweis)Czech Republic
| | - Zdeněk Paris
- Institute of ParasitologyBiology CentreCzech Academy of SciencesČeské Budějovice (Budweis)Czech Republic
- Faculty of SciencesUniversity of South BohemiaČeské Budějovice (Budweis)Czech Republic
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Genova M, Grycova L, Puttrich V, Magiera MM, Lansky Z, Janke C, Braun M. Tubulin polyglutamylation differentially regulates microtubule-interacting proteins. EMBO J 2023; 42:e112101. [PMID: 36636822 PMCID: PMC9975938 DOI: 10.15252/embj.2022112101] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Tubulin posttranslational modifications have been predicted to control cytoskeletal functions by coordinating the molecular interactions between microtubules and their associating proteins. A prominent tubulin modification in neurons is polyglutamylation, the deregulation of which causes neurodegeneration. Yet, the underlying molecular mechanisms have remained elusive. Here, using in-vitro reconstitution, we determine how polyglutamylation generated by the two predominant neuronal polyglutamylases, TTLL1 and TTLL7, specifically modulates the activities of three major microtubule interactors: the microtubule-associated protein Tau, the microtubule-severing enzyme katanin and the molecular motor kinesin-1. We demonstrate that the unique modification patterns generated by TTLL1 and TTLL7 differentially impact those three effector proteins, thus allowing for their selective regulation. Given that our experiments were performed with brain tubulin from mouse models in which physiological levels and patterns of polyglutamylation were altered by the genetic knockout of the main modifying enzymes, our quantitative measurements provide direct mechanistic insight into how polyglutamylation could selectively control microtubule interactions in neurons.
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Affiliation(s)
- Mariya Genova
- Institut Curie, Université PSL, CNRS UMR3348OrsayFrance
- Université Paris‐Saclay, CNRS UMR3348OrsayFrance
| | - Lenka Grycova
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
| | - Verena Puttrich
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
| | - Maria M Magiera
- Institut Curie, Université PSL, CNRS UMR3348OrsayFrance
- Université Paris‐Saclay, CNRS UMR3348OrsayFrance
| | - Zdenek Lansky
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348OrsayFrance
- Université Paris‐Saclay, CNRS UMR3348OrsayFrance
| | - Marcus Braun
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
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Procházková L, Matsuzaki R, Řezanka T, Nedbalová L, Remias D. The snow alga Chloromonas kaweckae sp. nov. (Volvocales, Chlorophyta) causes green surface blooms in the high tatras (Slovakia) and tolerates high irradiance. J Phycol 2023; 59:236-248. [PMID: 36461636 PMCID: PMC10946730 DOI: 10.1111/jpy.13307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Seasonally slowly melting mountain snowfields are populated by extremophilic microalgae. In alpine habitats, high-light sensitive, green phytoflagellates are usually observed in subsurface layers deeper in the snowpack under dim conditions, while robust orange to reddish cyst stages can be seen exposed on the surface. In this study, uncommon surface green snow was investigated in the High Tatra Mountains (Slovakia). The monospecific community found in the green surface bloom consisted of vegetative Chloromonas cells (Volvocales, Chlorophyta). Molecular data demonstrated that the field sample and the strain isolated and established from the bloom were conspecific, and they represent a new species, Chloromonas kaweckae sp. nov., which is described based on the morphology of the vegetative cells and asexual reproduction and on molecular analyses of the strain. Cells of C. kaweckae accumulated approximately 50% polyunsaturated fatty acids, which is advantageous at low temperatures. In addition, this new species performed active photosynthesis at temperatures close to the freezing point showed a light compensation point of 126 ± 22 μmol photons · m-2 · s-1 and some signs of photoinhibition at irradiances greater than 600 μmol photons · m-2 · s-1 . These data indicate that the photosynthetic apparatus of C. kaweckae could be regarded as adapted to relatively high light intensities, otherwise unusual for most flagellate stages of snow algae.
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Affiliation(s)
- Lenka Procházková
- Department of EcologyCharles University, Faculty of SciencePrague128 44Czech Republic
- The Czech Academy of Sciences, Institute of Botany, Centre for PhycologyDukelská 135379 82TřeboňCzech Republic
| | - Ryo Matsuzaki
- University of Tsukuba, Faculty of Life and Environmental Sciences1–1–1 TennodaiTsukubaIbaraki305–8572Japan
- National Institute for Environmental Studies, Biodiversity Division16‐2 OnogawaTsukubaIbaraki305‐8506Japan
| | - Tomáš Řezanka
- The Czech Academy of SciencesInstitute of MicrobiologyVídeňská 1083Prague142 20Czech Republic
| | - Linda Nedbalová
- Department of EcologyCharles University, Faculty of SciencePrague128 44Czech Republic
- The Czech Academy of Sciences, Institute of Botany, Centre for PhycologyDukelská 135379 82TřeboňCzech Republic
| | - Daniel Remias
- University of Applied Sciences Upper Austria, School of EngineeringStelzhamerstr. 23Wels4600Austria
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Smolinský R, Hiadlovská Z, Maršala Š, Škrabánek P, Škrobánek M, Martínková N. High predation risk decimates survival during the reproduction season. Ecol Evol 2022; 12:e9407. [PMID: 36262266 PMCID: PMC9576000 DOI: 10.1002/ece3.9407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/30/2022] Open
Abstract
Predators attack conspicuous prey phenotypes that are present in the environment. Male display behavior of conspicuous nuptial coloration becomes risky in the presence of a predator, and adult males face higher predation risk. High predation risk in one sex will lead to low survival and sex ratio bias in adult cohorts, unless the increased predation risk is compensated by higher escape rate.Here, we tested the hypothesis that sand lizards (Lacerta agilis) have sex-specific predation risk and escape rate. We expected the differences to manifest in changes in sex ratio with age, differences in frequency of tail autotomy, and in sex-specific survival rate.We developed a statistical model to estimate predation risk and escape rate, combining the observed sex ratio and frequency of tail autotomy with likelihood-based survival rate. Using Bayesian framework, we estimated the model parameters. We projected the date of the tail autotomy events from growth rates derived from capture-recapture data measurements.We found statistically stable sex ratio in age groups, equal frequency of tail regenerates between sexes, and similar survival rate. Predation risk is similar between sexes, and escape rate increases survival by about 5%. We found low survival rate and a low number of tail autotomy events in females during months when sand lizards mate and lay eggs, indicating high predator pressure throughout reproduction. Our data show that gravid females fail to escape predation.The risks of reproduction season in an ectotherm are a convolution of morphological changes (conspicuous coloration in males and body allometry changes in gravid females), behavior (nuptial displays), and environmental conditions which challenge lizard thermal performance. Performance of endotherm predators in cold spring months endangers gravid females more than displaying males in bright nuptial coloration.
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Affiliation(s)
- Radovan Smolinský
- Department of Biology, Faculty of EducationMasaryk UniversityBrnoCzech Republic
| | - Zuzana Hiadlovská
- Institute of Animal Physiology and GeneticsCzech Academy of SciencesBrnoCzech Republic
| | - Štěpán Maršala
- Institute of Automation and Computer ScienceBrno University of TechnologyBrnoCzech Republic
| | - Pavel Škrabánek
- Institute of Automation and Computer ScienceBrno University of TechnologyBrnoCzech Republic
| | - Michal Škrobánek
- Department of Biology, Faculty of EducationMasaryk UniversityBrnoCzech Republic
| | - Natália Martínková
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
- RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
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Shackleton RT, Vimercati G, Probert AF, Bacher S, Kull CA, Novoa A. Consensus and controversy in the discipline of invasion science. Conserv Biol 2022; 36:e13931. [PMID: 35561048 PMCID: PMC9805150 DOI: 10.1111/cobi.13931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Approaches, values, and perceptions in invasion science are highly dynamic, and like in other disciplines, views among different people can diverge. This has led to debate in the field specifically surrounding the core themes of values, management, impacts, and terminology. Considering these debates, we surveyed 698 scientists and practitioners globally to assess levels of polarization (opposing views) on core and contentious topics. The survey was distributed online (via Google Forms) and promoted through listservs and social media. Although there were generally high levels of consensus among respondents, there was some polarization (scores of ≥0.39 [top quartile]). Relating to values, there was high polarization regarding claims of invasive species denialism, whether invasive species contribute to biodiversity, and how biodiversity reporting should be conducted. With regard to management, there were polarized views on banning the commercial use of beneficial invasive species, the extent to which stakeholders' perceptions should influence management, whether invasive species use alone is an appropriate control strategy, and whether eradication of invasive plants is possible. For impacts, there was high polarization concerning whether invasive species drive or are a side effect of degradation and whether invasive species benefits are understated. For terminology, polarized views related to defining invasive species based only on spread, whether species can be labeled as invasive in their native ranges, and whether language used is too xenophobic. Factor and regression analysis revealed that views were particularly divergent between people working on different invasive taxa (plants and mammals) and in different disciplines (between biologists and social scientists), between academics and practitioners, and between world regions (between Africa and the Global North). Unlike in other studies, age and gender had a limited influence on response patterns. Better integration globally and between disciplines, taxa, and sectors (e.g., academic vs. practitioners) could help build broader understanding and consensus.
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Affiliation(s)
- Ross T. Shackleton
- Swiss Federal Institute for Forest Snow and Landscape Research WSLBirmensdorfSwitzerland
- Centre for Invasion Biology, Department of Botany and ZoologyStellenbosch UniversityStellenboschSouth Africa
- Institute of Geography and SustainabilityUniversity of LausanneLausanneSwitzerland
| | - Giovanni Vimercati
- Department of Biology, Unit Ecology and EvolutionUniversity of FribourgFribourgSwitzerland
| | - Anna F. Probert
- Department of Biology, Unit Ecology and EvolutionUniversity of FribourgFribourgSwitzerland
| | - Sven Bacher
- Department of Biology, Unit Ecology and EvolutionUniversity of FribourgFribourgSwitzerland
| | - Christian A. Kull
- Institute of Geography and SustainabilityUniversity of LausanneLausanneSwitzerland
| | - Ana Novoa
- Department of Invasion EcologyInstitute of Botany, Czech Academy of SciencesPrůhoniceCzech Republic
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Bugmann H, Seidl R, Hartig F, Bohn F, Brůna J, Cailleret M, François L, Heinke J, Henrot A, Hickler T, Hülsmann L, Huth A, Jacquemin I, Kollas C, Lasch‐Born P, Lexer MJ, Merganič J, Merganičová K, Mette T, Miranda BR, Nadal‐Sala D, Rammer W, Rammig A, Reineking B, Roedig E, Sabaté S, Steinkamp J, Suckow F, Vacchiano G, Wild J, Xu C, Reyer CPO. Tree mortality submodels drive simulated long-term forest dynamics: assessing 15 models from the stand to global scale. Ecosphere 2019; 10:e02616. [PMID: 34853712 PMCID: PMC8609442 DOI: 10.1002/ecs2.2616] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 12/28/2018] [Indexed: 01/08/2023] Open
Abstract
Models are pivotal for assessing future forest dynamics under the impacts of changing climate and management practices, incorporating representations of tree growth, mortality, and regeneration. Quantitative studies on the importance of mortality submodels are scarce. We evaluated 15 dynamic vegetation models (DVMs) regarding their sensitivity to different formulations of tree mortality under different degrees of climate change. The set of models comprised eight DVMs at the stand scale, three at the landscape scale, and four typically applied at the continental to global scale. Some incorporate empirically derived mortality models, and others are based on experimental data, whereas still others are based on theoretical reasoning. Each DVM was run with at least two alternative mortality submodels. Model behavior was evaluated against empirical time series data, and then, the models were subjected to different scenarios of climate change. Most DVMs matched empirical data quite well, irrespective of the mortality submodel that was used. However, mortality submodels that performed in a very similar manner against past data often led to sharply different trajectories of forest dynamics under future climate change. Most DVMs featured high sensitivity to the mortality submodel, with deviations of basal area and stem numbers on the order of 10-40% per century under current climate and 20-170% under climate change. The sensitivity of a given DVM to scenarios of climate change, however, was typically lower by a factor of two to three. We conclude that (1) mortality is one of the most uncertain processes when it comes to assessing forest response to climate change, and (2) more data and a better process understanding of tree mortality are needed to improve the robustness of simulated future forest dynamics. Our study highlights that comparing several alternative mortality formulations in DVMs provides valuable insights into the effects of process uncertainties on simulated future forest dynamics.
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