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  1. Book ; Online: Assembly of the Photosystem II Membrane-Protein Complex of Oxygenic Photosynthesis

    Eaton-Rye, Roman SobotkaJulian J. / Eaton-Rye, Julian J. / Sobotka, Roman

    2017  

    Abstract: Photosystem II is a 700-kDa membrane-protein super-complex responsible for the light-driven splitting of water in oxygenic photosynthesis. The photosystem is comprised of two 350-kDa complexes each made of 20 different polypeptides and over 80 co-factors. ...

    Abstract Photosystem II is a 700-kDa membrane-protein super-complex responsible for the light-driven splitting of water in oxygenic photosynthesis. The photosystem is comprised of two 350-kDa complexes each made of 20 different polypeptides and over 80 co-factors. While there have been major advances in understanding the mature structure of this photosystem many key protein factors involved in the assembly of the complex do not appear in the holoenzyme. The mechanism for assembling this super-complex is a very active area of research with newly discovered assembly factors and subcomplexes requiring characterization. Additionally the ability to split water is inseparable from light-induced photodamage that arises from radicals and reactive O2 species generated by Photosystem II chemistry. Consequently, to sustain water splitting, a "self repair" cycle has evolved whereby damaged protein is removed and replaced so as to extend the working life of the complex.-

    Understanding how the biogenesis and repair processes are coordinated is among several important questions that remain to be answered. Other questions include: how and when are the inorganic cofactors inserted during the assembly and repair processes and how are the subcomplexes protected from photodamage during assembly? Evidence has also been obtained for Photosystem II biogenesis centers in cyanobacteria but do these also exist in plants? Do the molecular mechanisms associated with Photosystem II assembly shed fresh light on the assembly of other major energy-transducing complexes such as Photosystem I or the cytochrome b6/f complex or indeed other respiratory complexes? The contributions to this Frontiers in Plant Science Research Topic are likely to reveal new details applicable to the assembly of a range of membrane-protein complexes, including aspects of self-assembly and solar energy conversion that may be applied to artificial photosynthetic systems.-

    In addition, a deeper understanding of Photosystem II assembly - particularly in response to changing environmental conditions - will provide new knowledge underpinning photosynthetic yields which may contribute to improved food production and long-term food security
    Keywords Botany ; Science (General)
    Size 1 electronic resource (315 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020095937
    ISBN 9782889452330 ; 2889452336
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Fast Diffusion of the Unassembled PetC1-GFP Protein in the Cyanobacterial Thylakoid Membrane

    Radek Kaňa / Gábor Steinbach / Roman Sobotka / György Vámosi / Josef Komenda

    Life, Vol 11, Iss 15, p

    2021  Volume 15

    Abstract: Biological membranes were originally described as a fluid mosaic with uniform distribution of proteins and lipids. Later, heterogeneous membrane areas were found in many membrane systems including cyanobacterial thylakoids. In fact, cyanobacterial ... ...

    Abstract Biological membranes were originally described as a fluid mosaic with uniform distribution of proteins and lipids. Later, heterogeneous membrane areas were found in many membrane systems including cyanobacterial thylakoids. In fact, cyanobacterial pigment–protein complexes (photosystems, phycobilisomes) form a heterogeneous mosaic of thylakoid membrane microdomains (MDs) restricting protein mobility. The trafficking of membrane proteins is one of the key factors for long-term survival under stress conditions, for instance during exposure to photoinhibitory light conditions. However, the mobility of unbound ‘free’ proteins in thylakoid membrane is poorly characterized. In this work, we assessed the maximal diffusional ability of a small, unbound thylakoid membrane protein by semi-single molecule FCS (fluorescence correlation spectroscopy) method in the cyanobacterium Synechocystis sp. PCC6803. We utilized a GFP-tagged variant of the cytochrome b 6 f subunit PetC1 (PetC1-GFP), which was not assembled in the b 6 f complex due to the presence of the tag. Subsequent FCS measurements have identified a very fast diffusion of the PetC1-GFP protein in the thylakoid membrane (D = 0.14 − 2.95 µm 2 s −1 ). This means that the mobility of PetC1-GFP was comparable with that of free lipids and was 50–500 times higher in comparison to the mobility of proteins (e.g., IsiA, LHCII—light-harvesting complexes of PSII) naturally associated with larger thylakoid membrane complexes like photosystems. Our results thus demonstrate the ability of free thylakoid-membrane proteins to move very fast, revealing the crucial role of protein–protein interactions in the mobility restrictions for large thylakoid protein complexes.
    Keywords proteins mobility ; photosynthesis ; FCS ; thylakoids ; cyanobacteria ; Science ; Q
    Subject code 612 ; 571
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis

    Ziyu Zhao / Irene Vercellino / Jana Knoppová / Roman Sobotka / James W. Murray / Peter J. Nixon / Leonid A. Sazanov / Josef Komenda

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 11

    Abstract: Abstract Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 ... ...

    Abstract Abstract Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.
    Keywords Science ; Q
    Subject code 540
    Language English
    Publishing date 2023-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Author Correction

    Petra Skotnicová / Hristina Staleva-Musto / Valentyna Kuznetsova / David Bína / Minna M. Konert / Shan Lu / Tomáš Polívka / Roman Sobotka

    Nature Communications, Vol 13, Iss 1, Pp 1-

    Plant LHC-like proteins show robust folding and static non-photochemical quenching

    2022  Volume 1

    Keywords Science ; Q
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Cyanobacterial high-light-inducible proteins — Protectors of chlorophyll–protein synthesis and assembly

    Komenda, Josef / Roman Sobotka

    Biochimica et biophysica acta. 2016 Mar., v. 1857, no. 3

    2016  

    Abstract: Cyanobacteria contain a family of genes encoding one-helix high-light-inducible proteins (Hlips) that are homologous to light harvesting chlorophyll a/b-binding proteins of plants and algae. Based on various experimental approaches used for their study, ... ...

    Abstract Cyanobacteria contain a family of genes encoding one-helix high-light-inducible proteins (Hlips) that are homologous to light harvesting chlorophyll a/b-binding proteins of plants and algae. Based on various experimental approaches used for their study, a spectrum of functions that includes regulation of chlorophyll biosynthesis, transient chlorophyll binding, quenching of singlet oxygen and non-photochemical quenching of absorbed energy is ascribed to Hlips. However, these functions had not been supported by conclusive experimental evidence until recently when it became clear that Hlips are able to quench absorbed light energy and assist during terminal step(s) of the chlorophyll biosynthesis and early stages of Photosystem II assembly. In this review we summarize and discuss the present knowledge about Hlips and provide a model of how individual members of the Hlip family operate during the biogenesis of chlorophyll–proteins, namely Photosystem II. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
    Keywords Cyanobacteria ; algae ; bacteria ; biogenesis ; biosynthesis ; chlorophyll ; energy ; genes ; models ; photosystem II ; proteins ; singlet oxygen
    Language English
    Dates of publication 2016-03
    Size p. 288-295.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282711-6
    ISSN 0005-2728 ; 0304-4173
    ISSN 0005-2728 ; 0304-4173
    DOI 10.1016/j.bbabio.2015.08.011
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Plant LHC-like proteins show robust folding and static non-photochemical quenching

    Petra Skotnicová / Hristina Staleva-Musto / Valentyna Kuznetsova / David Bína / Minna M. Konert / Shan Lu / Tomáš Polívka / Roman Sobotka

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Plant light harvesting complex (LHC)‐like proteins protect the photosynthetic machinery from excess light. Here the authors show that plant LHC‐like dimers are stabilized by associated pigments and can quench chlorophyll fluorescence via direct energy ... ...

    Abstract Plant light harvesting complex (LHC)‐like proteins protect the photosynthetic machinery from excess light. Here the authors show that plant LHC‐like dimers are stabilized by associated pigments and can quench chlorophyll fluorescence via direct energy transfer from chlorophyll to zeaxanthin.
    Keywords Science ; Q
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov.

    Ivo Sedláček / Pavla Holochová / Hans-Jürgen Busse / Vendula Koublová / Stanislava Králová / Pavel Švec / Roman Sobotka / Eva Staňková / Jan Pilný / Ondrej Šedo / Jana Smolíková / Karel Sedlář

    Microorganisms, Vol 10, Iss 4, p

    2022  Volume 704

    Abstract: A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were ... ...

    Abstract A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyr B and lep A genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia . The closest relatives of the reference strain P8398 T were Massilia atriviolacea , Massilia violaceinigra , Massilia rubra , Massilia mucilaginosa , Massilia aquatica , Massilia frigida , Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyr B and lep A sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398 T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398 T (= CCM 8941 T = LMG 32108 T ).
    Keywords Massilia ; violacein ; psychrophilic ; description ; whole-genome sequencing ; Antarctica ; Biology (General) ; QH301-705.5
    Subject code 333
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Non-photochemical quenching in cryptophyte alga Rhodomonas salina is located in chlorophyll a/c antennae.

    Radek Kaňa / Eva Kotabová / Roman Sobotka / Ondřej Prášil

    PLoS ONE, Vol 7, Iss 1, p e

    2012  Volume 29700

    Abstract: Photosynthesis uses light as a source of energy but its excess can result in production of harmful oxygen radicals. To avoid any resulting damage, phototrophic organisms can employ a process known as non-photochemical quenching (NPQ), where excess light ... ...

    Abstract Photosynthesis uses light as a source of energy but its excess can result in production of harmful oxygen radicals. To avoid any resulting damage, phototrophic organisms can employ a process known as non-photochemical quenching (NPQ), where excess light energy is safely dissipated as heat. The mechanism(s) of NPQ vary among different phototrophs. Here, we describe a new type of NPQ in the organism Rhodomonas salina, an alga belonging to the cryptophytes, part of the chromalveolate supergroup. Cryptophytes are exceptional among photosynthetic chromalveolates as they use both chlorophyll a/c proteins and phycobiliproteins for light harvesting. All our data demonstrates that NPQ in cryptophytes differs significantly from other chromalveolates - e.g. diatoms and it is also unique in comparison to NPQ in green algae and in higher plants: (1) there is no light induced xanthophyll cycle; (2) NPQ resembles the fast and flexible energetic quenching (qE) of higher plants, including its fast recovery; (3) a direct antennae protonation is involved in NPQ, similar to that found in higher plants. Further, fluorescence spectroscopy and biochemical characterization of isolated photosynthetic complexes suggest that NPQ in R. salina occurs in the chlorophyll a/c antennae but not in phycobiliproteins. All these results demonstrate that NPQ in cryptophytes represents a novel class of effective and flexible non-photochemical quenching.
    Keywords Medicine ; R ; Science ; Q
    Subject code 580
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Magnesium Stable Isotope Fractionation on a Cellular Level Explored by Cyanobacteria and Black Fungi with Implications for Higher Plants

    Rasesh Pokharel / Ruben Gerrits / J. A. Schuessler / P. Frings / Roman Sobotka / Anna A. Gorbushina / F. von Blanckenburg

    Environmental Science and Technology

    2018  

    Publishing country de
    Document type Article ; Online
    DOI 10.1021/acs.est.8b02238
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Magnesium Stable Isotope Fractionation on a Cellular Level Explored by Cyanobacteria and Black Fungi with Implications for Higher Plants

    Pokharel, Rasesh / Ruben Gerrits / Jan A. Schuessler / Patrick J. Frings / Roman Sobotka / Anna A. Gorbushina / Friedhelm von Blanckenburg

    Environmental science & technology. 2018 Oct. 15, v. 52, no. 21

    2018  

    Abstract: In a controlled growth experiment we found that the cyanobacterium Nostoc punctiforme has a bulk cell ²⁶Mg/²⁴Mg ratio (expressed as δ²⁶Mg) that is −0.27‰ lower than the growth solution at a pH of ca. 5.9. This contrasts with a recently published δ²⁶Mg ... ...

    Abstract In a controlled growth experiment we found that the cyanobacterium Nostoc punctiforme has a bulk cell ²⁶Mg/²⁴Mg ratio (expressed as δ²⁶Mg) that is −0.27‰ lower than the growth solution at a pH of ca. 5.9. This contrasts with a recently published δ²⁶Mg value that was 0.65‰ higher than growth solution for the black fungus Knufia petricola at similar laboratory conditions, interpreted to reflect loss of ²⁴Mg during cell growth. By a mass balance model constrained by δ²⁶Mg in chlorophyll extract we inferred the δ²⁶ Mg value of the main Mg compartments in a cyanobacteria cell: free cytosolic Mg (−2.64‰), chlorophyll (1.85‰), and the nonchlorophyll-bonded Mg compartments like ATP and ribosomes (−0.64‰). The lower δ²⁶Mg found in Nostoc punctiforme would thus result from the absence of significant Mg efflux during cell growth in combination with either (a) discrimination against ²⁶Mg during uptake by desolvation of Mg or transport across protein channels or (b) discrimination against ²⁴Mg in the membrane transporter during efflux. The model predicts the preferential incorporation of ²⁶Mg in cells and plant organs low in Mg and the absence of isotope fractionation in those high in Mg, corroborated by a compilation of Mg isotope ratios from fungi, bacteria, and higher plants.
    Keywords Nostoc punctiforme ; adenosine triphosphate ; bacteria ; cell growth ; chlorophyll ; fungi ; isotope fractionation ; magnesium ; models ; pH ; plant organs ; ribosomes ; stable isotopes
    Language English
    Dates of publication 2018-1015
    Size p. 12216-12224.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5851
    DOI 10.1021/acs.est.8b02238
    Database NAL-Catalogue (AGRICOLA)

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