1
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Dsouza L, Li X, Erić V, Huijser A, Jansen TLC, Holzwarth AR, Buda F, Bryant DA, Bahri S, Gupta KBSS, Sevink GJA, de Groot HJM. An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. Phys Chem Chem Phys 2024; 26:15856-15867. [PMID: 38546236 DOI: 10.1039/d4cp00221k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl c, compared to the wild type (WT). Nearly complete 13C chemical shift assignments were obtained from well-resolved homonuclear 13C-13C RFDR data. For proton assignments heteronuclear 13C-1H (hCH) data sets were collected at 1.2 GHz spinning at 60 kHz. The CHHC experiments revealed intermolecular correlations between 132/31, 132/32, and 121/31, with distance constraints of less than 5 Å. These constraints indicate the syn-anti parallel stacking motif for the aggregates. Fourier transform cryo-EM data reveal an axial repeat of 1.49 nm for the helical tubular aggregates, perpendicular to the inter-tube separation of 2.1 nm. This axial repeat is different from WT and is in line with BChl syn-anti stacks running essentially parallel to the tube axis. Such a packing mode is in agreement with the signature of the Qy band in circular dichroism (CD). Combining the experimental data with computational insight suggests that the packing for the light-harvesting function is similar between WT and bchQ, while the chirality within the chlorosomes is modestly but detectably affected by the reduced compositional heterogeneity in bchQ.
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Affiliation(s)
- Lolita Dsouza
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
| | - Xinmeng Li
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315, Oslo, Norway
| | - Vesna Erić
- Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
| | - Annemarie Huijser
- MESA+ Institute for Nanotechnology, University of Twente, 7500 AE, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands
| | - Alfred R Holzwarth
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
| | - Donald A Bryant
- Department for Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | | | - G J Agur Sevink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, The Netherlands.
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2
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Malina T, Bína D, Collins AM, Alster J, Pšenčík J. Efficient two-step excitation energy transfer in artificial light-harvesting antenna based on bacteriochlorophyll aggregates. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 254:112891. [PMID: 38555841 DOI: 10.1016/j.jphotobiol.2024.112891] [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: 11/27/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
Chlorosomes of green photosynthetic bacteria are large light-harvesting complexes enabling these organisms to survive at extremely low-light conditions. Bacteriochlorophylls found in chlorosomes self-organize and are ideal candidates for use in biomimetic light-harvesting in artificial photosynthesis and other applications for solar energy utilization. Here we report on the construction and characterization of an artificial antenna consisting of bacteriochlorophyll c co-aggregated with β-carotene, which is used to extend the light-harvesting spectral range, and bacteriochlorophyll a, which acts as a final acceptor for excitation energy. Efficient energy transfer between all three components was observed by means of fluorescence spectroscopy. The efficiency varies with the β-carotene content, which increases the average distance between the donor and acceptor in both energy transfer steps. The efficiency ranges from 89 to 37% for the transfer from β-carotene to bacteriochlorophyll c, and from 93 to 69% for the bacteriochlorophyll c to bacteriochlorophyll a step. A significant part of this study was dedicated to a development of methods for determination of energy transfer efficiency. These methods may be applied also for study of chlorosomes and other pigment complexes.
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Affiliation(s)
- Tomáš Malina
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic & Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Aaron M Collins
- Department of Environmental and Physical Sciences, Southern New Hampshire University, Manchester, NH, USA
| | - Jan Alster
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Jakub Pšenčík
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
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3
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Yakovlev AG, Taisova AS. Quenching of bacteriochlorophyll a triplet state by carotenoids in the chlorosome baseplate of green bacterium Chloroflexus aurantiacus. Phys Chem Chem Phys 2024; 26:8815-8823. [PMID: 38421198 DOI: 10.1039/d4cp00287c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
To capture weak light fluxes, green photosynthetic bacteria have unique structures - chlorosomes, consisting of 104-5 molecules of bacteriochlorophyll (BChl) c, d, e. Chlorosomes are attached to the cytoplasmic membrane through the baseplate, a paracrystalline protein structure containing BChl a and carotenoids (Car). The most important function of Car is the quenching of triplet states of BChl, which prevents the formation of singlet oxygen and thereby provides photoprotection. In our work, we studied the dynamics of the triplet states of BChl a and Car in the baseplate of Chloroflexus aurantiacus chlorosomes using picosecond differential spectroscopy. BChl a of the baseplate was excited into the Qy band at 810 nm, and the corresponding absorption changes were recorded in the range of 420-880 nm. It was found that the formation of the Car triplet state occurs in ∼1.3 ns, which is ∼3 times faster than the formation of this state in the peripheral antenna of C. aurantiacus according to literature data. The Car triplet state was recorded by the characteristic absorption band T1 → Tn at ∼550 nm. Simultaneously with the appearance of absorption T1 → Tn, there was a bleaching of the singlet absorption of Car in the region of 400-500 nm. Theoretical modeling made it possible to estimate the characteristic time of formation of the triplet state of BChl a as ∼0.5 ns. It is shown that the experimental data are well described by the sequential scheme of formation and quenching of the BChl a triplet state: BChl a* → BChl aT → CarT. Thus, carotenoids from green bacteria effectively protect the baseplate from possible damage by singlet oxygen.
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Affiliation(s)
- Andrei G Yakovlev
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory, Moscow 119991, Russian Federation.
| | - Alexandra S Taisova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory, Moscow 119991, Russian Federation.
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4
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Hisahara Y, Nakano T, Tamiaki H. Self-aggregation behavior of dimeric chlorophyll-a derivatives linked with ethynylene and m-phenylene moieties. Photochem Photobiol Sci 2023; 22:2329-2339. [PMID: 37464173 DOI: 10.1007/s43630-023-00454-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/29/2023] [Indexed: 07/20/2023]
Abstract
Chlorophyll(Chl)-a derivatives inserting an ethynylene-m-phenylene group between a zinc chlorin ring and a hydroxymethyl group, in which various substituents were introduced on the benzene spacer, were prepared as model compounds for the light-harvesting antennae (chlorosomes) of photosynthetic green bacteria. These compounds were synthesized from a C3-ethynylated Chl-a derivative via sequential Sonogashira cross-coupling reaction, and the effects of the substituents on the phenylene linker on their self-aggregation behaviors were investigated by electronic absorption, circular dichroism, and infrared absorption spectroscopic measurements. These studies exhibited that some compounds gave the disordered self-assemblies including several species; however, the zinc complex of the dimeric Chl-a derivative primarily allowed a single J-aggregate species in an aqueous Triton X-100 micellar solution. Additional control experiments revealed that its self-assembly was constructed through the hydrogen and coordination bonding involving the hydroxymethyl group on benzene ring, keto-carbonyl group at C13-position, and central zinc atom, and this is consistent with a conventional chlorosomal manner.
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Affiliation(s)
- Yuma Hisahara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Takeo Nakano
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
- Department of Chemistry, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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5
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Frehan SK, Dsouza L, Li X, Eríc V, Jansen TLC, Mul G, Holzwarth AR, Buda F, Sevink GJA, de Groot HJM, Huijser A. Photon Energy-Dependent Ultrafast Exciton Transfer in Chlorosomes of Chlorobium tepidum and the Role of Supramolecular Dynamics. J Phys Chem B 2023; 127:7581-7589. [PMID: 37611240 PMCID: PMC10493955 DOI: 10.1021/acs.jpcb.3c05282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/09/2023] [Indexed: 08/25/2023]
Abstract
The antenna complex of green sulfur bacteria, the chlorosome, is one of the most efficient supramolecular systems for efficient long-range exciton transfer in nature. Femtosecond transient absorption experiments provide new insight into how vibrationally induced quantum overlap between exciton states supports highly efficient long-range exciton transfer in the chlorosome of Chlorobium tepidum. Our work shows that excitation energy is delocalized over the chlorosome in <1 ps at room temperature. The following exciton transfer to the baseplate occurs in ∼3 to 5 ps, in line with earlier work also performed at room temperature, but significantly faster than at the cryogenic temperatures used in previous studies. This difference can be attributed to the increased vibrational motion at room temperature. We observe a so far unknown impact of the excitation photon energy on the efficiency of this process. This dependency can be assigned to distinct optical domains due to structural disorder, combined with an exciton trapping channel competing with exciton transfer toward the baseplate. An oscillatory transient signal damped in <1 ps has the highest intensity in the case of the most efficient exciton transfer to the baseplate. These results agree well with an earlier computational finding of exciton transfer driven by low-frequency rotational motion of molecules in the chlorosome. Such an exciton transfer process belongs to the quantum coherent regime, for which the Förster theory for intermolecular exciton transfer does not apply. Our work hence strongly indicates that structural flexibility is important for efficient long-range exciton transfer in chlorosomes.
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Affiliation(s)
- Sean K. Frehan
- MESA+
Institute for Nanotechnology, University
of Twente, 7500 AE Enschede, The Netherlands
| | - Lolita Dsouza
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Xinmeng Li
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315 Oslo, Norway
| | - Vesna Eríc
- Zernike
Institute of Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute of Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Guido Mul
- MESA+
Institute for Nanotechnology, University
of Twente, 7500 AE Enschede, The Netherlands
| | - Alfred R. Holzwarth
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Francesco Buda
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Huub J. M. de Groot
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Annemarie Huijser
- MESA+
Institute for Nanotechnology, University
of Twente, 7500 AE Enschede, The Netherlands
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6
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Erić V, Castro JL, Li X, Dsouza L, Frehan SK, Huijser A, Holzwarth AR, Buda F, Sevink GJA, de Groot HJM, Jansen TLC. Ultrafast Anisotropy Decay Reveals Structure and Energy Transfer in Supramolecular Aggregates. J Phys Chem B 2023; 127:7487-7496. [PMID: 37594912 PMCID: PMC10476209 DOI: 10.1021/acs.jpcb.3c04719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/20/2023] [Indexed: 08/20/2023]
Abstract
Chlorosomes from green bacteria perform the most efficient light capture and energy transfer, as observed among natural light-harvesting antennae. Hence, their unique functional properties inspire developments in artificial light-harvesting and molecular optoelectronics. We examine two distinct organizations of the molecular building blocks as proposed in the literature, demonstrating how these organizations alter light capture and energy transfer, which can serve as a mechanism that the bacteria utilize to adapt to changes in light conditions. Spectral simulations of polarization-resolved two-dimensional electronic spectra unravel how changes in the helicity of chlorosomal aggregates alter energy transfer. We show that ultrafast anisotropy decay presents a spectral signature that reveals contrasting energy pathways in different chlorosomes.
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Affiliation(s)
- Vesna Erić
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Jorge Luis Castro
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Xinmeng Li
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Sælands vei 26, 0315 Oslo, Norway
| | - Lolita Dsouza
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Sean K. Frehan
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Annemarie Huijser
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Alfred R. Holzwarth
- Department
of Biophysical Chemistry, Max Planck Institute
for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim, Germany
| | - Francesco Buda
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Huub J. M. de Groot
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, 9747 AG Groningen, The Netherlands
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7
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Ishii T, Matsubara S, Tamiaki H. Ring-shaped self-assembly of a naphthalene-linked chlorophyll dimer. Chem Commun (Camb) 2023; 59:1967-1970. [PMID: 36723005 DOI: 10.1039/d2cc06368a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Light-harvesting antennas, for example the LH2 complex in purple bacteria, sophisticatedly align chlorophyll molecules in a cyclic fashion by using protein scaffolds. However, artificial preparation of the circular LH antenna model without any templates has not been reported. We demonstrated the construction of ring-shaped supramolecules by self-assembly of a semisynthetic chlorophyll dimer through a transformation from wavy fiber-like aggregates.
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Affiliation(s)
- Tatsuma Ishii
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
| | - Shogo Matsubara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan. .,Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Aichi, 466-8555, Japan.
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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8
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Erić V, Li X, Dsouza L, Frehan SK, Huijser A, Holzwarth AR, Buda F, Sevink GJA, de Groot HJM, Jansen TLC. Manifestation of Hydrogen Bonding and Exciton Delocalization on the Absorption and Two-Dimensional Electronic Spectra of Chlorosomes. J Phys Chem B 2023; 127:1097-1109. [PMID: 36696537 PMCID: PMC9923760 DOI: 10.1021/acs.jpcb.2c07143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chlorosomes are supramolecular aggregates that contain thousands of bacteriochlorophyll molecules. They perform the most efficient ultrafast excitation energy transfer of all natural light-harvesting complexes. Their broad absorption band optimizes light capture. In this study, we identify the microscopic sources of the disorder causing the spectral width and reveal how it affects the excited state properties and the optical response of the system. We combine molecular dynamics, quantum chemical calculations, and response function calculations to achieve this goal. The predicted linear and two-dimensional electronic spectra are found to compare well with experimental data reproducing all key spectral features. Our analysis of the microscopic model reveals the interplay of static and dynamic disorder from the molecular perspective. We find that hydrogen bonding motifs are essential for a correct description of the spectral line shape. Furthermore, we find that exciton delocalization over tens to hundreds of molecules is consistent with the two-dimensional electronic spectra.
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Affiliation(s)
- Vesna Erić
- University
of Groningen, Zernike Institute
for Advanced Materials, 9747
AG Groningen, The Netherlands
| | - Xinmeng Li
- Department
of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Sælands vei 26, 0315 Oslo, Norway
| | - Lolita Dsouza
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Sean K. Frehan
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Annemarie Huijser
- MESA+
Institute for Nanotechnology, University
of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - Alfred R. Holzwarth
- Department
of Biophysical Chemistry, Max Planck Institute
for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim, Germany
| | - Francesco Buda
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Huub J. M. de Groot
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Thomas L. C. Jansen
- University
of Groningen, Zernike Institute
for Advanced Materials, 9747
AG Groningen, The Netherlands,
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9
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Armstrong FA, Cheng B, Herold RA, Megarity CF, Siritanaratkul B. From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf. Chem Rev 2022; 123:5421-5458. [PMID: 36573907 PMCID: PMC10176485 DOI: 10.1021/acs.chemrev.2c00397] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP+ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.
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Affiliation(s)
- Fraser A. Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Beichen Cheng
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ryan A. Herold
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Clare F. Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Bhavin Siritanaratkul
- Stephenson Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZF, United Kingdom
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10
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Fukaya N, Ogi S, Sotome H, Fujimoto KJ, Yanai T, Bäumer N, Fernández G, Miyasaka H, Yamaguchi S. Impact of Hydrophobic/Hydrophilic Balance on Aggregation Pathways, Morphologies, and Excited-State Dynamics of Amphiphilic Diketopyrrolopyrrole Dyes in Aqueous Media. J Am Chem Soc 2022; 144:22479-22492. [PMID: 36459436 DOI: 10.1021/jacs.2c07299] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We report the thermodynamic and kinetic aqueous self-assembly of a series of amide-functionalized dithienyldiketopyrrolopyrroles (TDPPs) that bear various hydrophilic oligoethylene glycol (OEG) and hydrophobic alkyl chains. Spectroscopic and microscopic studies showed that the TDPP-based amphiphiles with an octyl group form sheet-like aggregates with J-type exciton coupling. The effect of the alkyl chains on the aggregated structure and the internal molecular orientation was examined via computational studies combining MD simulations and TD-DFT calculations. Furthermore, solvent and thermal denaturation experiments provided a state diagram that indicates the formation of unexpected nanoparticles during the self-assembly into nanosheets when longer OEG side chains are introduced. A kinetic analysis revealed that the nanoparticles were obtained selectively as an on-pathway intermediate state toward the formation of thermodynamically controlled nanosheets. The metastable aggregates were used for seed-initiated supramolecular assembly, which allowed establishing control over the assembly kinetics and the aggregate size. The sheet-like aggregates prepared using the seeding method exhibited coherent vibration in the excited state, indicating a well-ordered orientation of the TDPP units. These results underline the significance of fine tuning of the hydrophobic/hydrophilic balance in the molecular design to kinetically control the assembly of amphiphilic π-conjugated molecules into two-dimensional nanostructures in aqueous media.
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Affiliation(s)
- Natsumi Fukaya
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan
| | - Soichiro Ogi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan.,Integrated Research Consortium on Chemical Science (IRCCS), Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan
| | - Hikaru Sotome
- Division of Frontier Materials Science and Center for Advanced Interdisciplinary Research, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka560-8531, Japan
| | - Kazuhiro J Fujimoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan.,Integrated Research Consortium on Chemical Science (IRCCS), Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan.,Integrated Research Consortium on Chemical Science (IRCCS), Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan
| | - Nils Bäumer
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149Münster, Germany
| | - Gustavo Fernández
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149Münster, Germany
| | - Hiroshi Miyasaka
- Division of Frontier Materials Science and Center for Advanced Interdisciplinary Research, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka560-8531, Japan
| | - Shigehiro Yamaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan.,Integrated Research Consortium on Chemical Science (IRCCS), Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo, Chikusa, Nagoya464-8602, Japan
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11
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Yakovlev AG, Taisova AS, Fetisova ZG. Dynamic Stark effect in β and γ carotenes induced by photoexcitation of bacteriochlorophyll c in chlorosomes from Chloroflexus aurantiacus. PHOTOSYNTHESIS RESEARCH 2022; 154:291-302. [PMID: 36115930 DOI: 10.1007/s11120-022-00942-7] [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: 01/19/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Chlorosomes of green bacteria can be considered as a prototype of future artificial light-harvesting devices due to their unique property of self-assembly of a large number of bacteriochlorophyll (BChl) c/d/e molecules into compact aggregates. The presence of carotenoids (Cars) in chlorosomes is very important for photoprotection, light harvesting and structure stabilization. In this work, we studied for the first time the electrochromic band shift (Stark effect) in Cars of the phototrophic filamentous green bacterium Chloroflexus (Cfx.) aurantiacus induced by fs light excitation of the main pigment, BChl c. The high accuracy of the spectral measurements permitted us to extract a small wavy spectral feature, which, obviously, can be associated with the dynamic shift of the Car absorption band. A global analysis of spectroscopy data and theoretical modeling of absorption spectra showed that near 60% of Cars exhibited a red Stark shift of ~ 25 cm-1 and the remaining 40% exhibited a blue shift. We interpreted this finding as evidence of various orientations of Car in chlorosomes. We estimated the average value of the light-induced electric field strength in the place of Car molecules as ~ 106 V/cm and the average distance between Car and the neighboring BChl c as ~ 10 Å. We concluded that the dynamics of the Car electrochromic band shift mainly reflected the dynamics of exciton migration through the chlorosome toward the baseplate within ~ 1 ps. Our work has unambiguously shown that Cars are sensitive indicators of light-induced internal electric fields in chlorosomes.
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Affiliation(s)
- Andrei G Yakovlev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russian Federation.
| | - Alexandra S Taisova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russian Federation
| | - Zoya G Fetisova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russian Federation
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12
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Atahan-Evrenk S. Theoretical Study of the Structure and Binding Energies of Dimers of Zn(II)-Porphyrin Derivatives. J Phys Chem A 2022; 126:7102-7109. [PMID: 36194887 PMCID: PMC9574925 DOI: 10.1021/acs.jpca.2c03692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zinc-complexed porphyrin and chlorophyll derivatives form functional aggregates with remarkable photophysical and optoelectronic properties. Understanding the type and strength of intermolecular interactions between these molecules is essential for designing new materials with desired morphology and functionality. The dimer interactions of a molecular set composed of porphyrin derivatives obtained by substitutional changes starting from free-base porphyrin is studied. It is found that the B97M-rV/def2-TZVP level of theory provides a good compromise between the accuracy and cost to get the dimer geometries and interaction energies (IEs). The neglect of the relaxation energy due to the change in the monomer configurations upon complex formation causes a more significant error than the basis set superposition error. The metal complexation increases the binding energy by about -6 to -8 kcal/mol, and the introduction of keto and hydroxy groups further stabilizes the dimers by about -20 kcal/mol. Although the saturation of one of the pyrrol double bonds does not change the IE, the addition of R groups increases it.
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Affiliation(s)
- Sule Atahan-Evrenk
- Faculty of Medicine, TOBB University of Economics and Technology, Sogutozu Cd No. 43 Sogutozu, Ankara06560, Turkey
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13
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Zhou X, Lin S, Yan H. Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine. J Nanobiotechnology 2022; 20:257. [PMID: 35658974 PMCID: PMC9164479 DOI: 10.1186/s12951-022-01449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.
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Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Su Lin
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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14
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Shoji S, Stepanenko V, Würthner F, Tamiaki H. Self-assembly of a zinc bacteriochlorophyll- d analog with a lipophilic tertiary amide group in the 17-substituent. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sunao Shoji
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC) & Bavarian Polymer Institute (BPI), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Vladimir Stepanenko
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC) & Bavarian Polymer Institute (BPI), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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15
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Zhou X, Liu H, Djutanta F, Satyabola D, Jiang S, Qi X, Yu L, Lin S, Hariadi RF, Liu Y, Woodbury NW, Yan H. DNA-templated programmable excitonic wires for micron-scale exciton transport. Chem 2022. [DOI: 10.1016/j.chempr.2022.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Ai J, Guo J, Li Y, Zhong X, Lv Y, Li J, Yang A. The diversity of microbes and prediction of their functions in karst caves under the influence of human tourism activities-a case study of Zhijin Cave in Southwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:25858-25868. [PMID: 34854002 DOI: 10.1007/s11356-021-17783-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms, sensitive to the surrounding environment changes, show how the cave environment can be impacted by human activities. Zhijin Cave, featured with the most well-developed karst landform in China, has been open to tourists for more than 30 years. This study explored the microbial diversity in a karst cave and the impacts of tourism activities on the microbial communities and the community structures of bacteria and archaea in three niches in Zhijin Cave, including the mixture of bacteria and cyanobacteria on the rock wall, the aquatic sediments, and the surface sediments, using 16S rRNA high-throughput sequencing technology. It was found that Actinobacteriota and Proteobacteria were the dominant bacteria in the cave and Crenarchaeota and Thermoplasmatota were the dominant archaea. The correlation between microorganisms and environmental variables in the cave showed that archaea were more affected by pH and ORP than bacteria and F-, Cl-, NO3-, and SO42- were all positively relevant to the distribution of most bacteria and archaea in the cave. PICRUSt's prediction of microbial functions also indicated that abundance of the bacteria's functions was higher than that of the archaea. The intention of this study was to improve the understanding, development, and protection of microbial resources in caves.
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Affiliation(s)
- Jia Ai
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Jianeng Guo
- Management Office of Zhijin Cave Scenic Area, Bijie, 552100, Guizhou, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China.
| | - Xiong Zhong
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Yang Lv
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
| | - Aijiang Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
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17
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Li X, Buda F, de Groot HJ, Sevink GJA. The role of chirality and plastic crystallinity in the optical and mechanical properties of chlorosomes. iScience 2022; 25:103618. [PMID: 35005556 PMCID: PMC8719020 DOI: 10.1016/j.isci.2021.103618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/15/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
The most efficient light-harvesting antennae found in nature, chlorosomes, are molecular tubular aggregates (TMAs) assembled by pigments without protein scaffolds. Here, we discuss a classification of chlorosomes as a unique tubular plastic crystal and we attribute the robust energy transfer in chlorosomes to this unique nature. To systematically study the role of supramolecular tube chirality by molecular simulation, a role that has remained unresolved, we share a protocol for generating realistic tubes at atomic resolution. We find that both the optical and the mechanical behavior are strongly dependent on chirality. The optical-chirality relation enables a direct interpretation of experimental spectra in terms of overall tube chirality. The mechanical response shows that the overall chirality regulates the hardness of the tube and provides a new characteristic for relating chlorosomes to distinct chirality. Our protocol also applies to other TMA systems and will inspire other systematic studies beyond lattice models. Classifies chlorosomes in terms of a tubular plastic crystal phase Clarifies the unique strategy of chlorosomes for harvesting and transporting energy Presents a protocol for building atom-resolved helical tube structures Maps tube chirality directly to measurable optical and mechanical responses
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Affiliation(s)
- Xinmeng Li
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, P.O.Box 1033, Blindern, Oslo, 0315 Oslo, Norway
- Corresponding author
| | - Francesco Buda
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
| | - Huub J.M. de Groot
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
| | - G. J. Agur Sevink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, South Holland, the Netherlands
- Corresponding author
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18
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Jun S, Yang C, Choi S, Isaji M, Tamiaki H, Ihee H, Kim J. Exciton delocalization length in chlorosomes investigated by lineshape dynamics of two-dimensional electronic spectra. Phys Chem Chem Phys 2021; 23:24111-24117. [PMID: 34498018 DOI: 10.1039/d1cp03413h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chlorosome, a photosynthetic light-harvesting complex found in green sulfur bacteria, is an aggregate of self-assembled pigments and is optimized for efficient light harvesting and energy transfer under dim-light conditions. In this highly-disordered aggregate, the absorption and transfer of photoexcitation energy are governed by the degree of disorder. To describe the disorder, the number of molecules forming excitons, which is termed exciton delocalization length (EDL), is a relevant parameter because the EDL sensitively changes with the disorder of the constituent molecules. In this work, we determined the EDL in chlorosomes using two-dimensional electronic spectroscopy (2D-ES). Since spectral features correlated with EDL are spread out in the two-dimensional (2D) electronic spectra, we were able to determine the EDL accurately without the effects of homogeneous and inhomogeneous line broadening. In particular, by taking advantage of the multi-dimensionality and the time evolution of 2D spectra, we not only determined the excitation frequency dependence of EDL but also monitored the temporal change of EDL. We found that the EDL is ∼7 at 77 K and ∼6 at 298 K and increases with the excitation frequency, with the maximum located well above the maximum of the absorption spectrum of chlorosomes. The spectral profile of EDL changes rapidly within 100 fs and becomes flat over time due to dephasing of initial exciton coherence. From the coherent oscillations superimposed on the decay of EDL, it was learned that high-frequency phonons are more activated at 298 K than at 77 K.
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Affiliation(s)
- Sunhong Jun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seungjoo Choi
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea.
| | - Megumi Isaji
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea.
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19
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Kunsel T, Günther LM, Köhler J, Jansen TLC, Knoester J. Probing size variations of molecular aggregates inside chlorosomes using single-object spectroscopy. J Chem Phys 2021; 155:124310. [PMID: 34598584 DOI: 10.1063/5.0061529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We theoretically investigate the possibility to use single-object spectroscopy to probe size variations of the bacteriochlorophyll aggregates inside chlorosomes. Chlorosomes are the light-harvesting organelles of green sulfur and non-sulfur bacteria. They are known to be the most efficient light-harvesting systems in nature. Key to this efficiency is the organization of bacteriochlorophyll molecules in large self-assembled aggregates that define the secondary structure inside the chlorosomes. Many studies have been reported to elucidate the morphology of these aggregates and the molecular packing inside them. It is widely believed that tubular aggregates play an important role. Because the size (radius and length) of these aggregates affects the optical and excitation energy transport properties, it is of interest to be able to probe these quantities inside chlorosomes. We show that a combination of single-chlorosome linear polarization resolved spectroscopy and single-chlorosome circular dichroism spectroscopy may be used to access the typical size of the tubular aggregates within a chlorosome and, thus, probe possible variations between individual chlorosomes that may result, for instance, from different stages in growth or different growth conditions.
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Affiliation(s)
- T Kunsel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - L M Günther
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstraße 30, D-95440 Bayreuth, Germany
| | - J Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstraße 30, D-95440 Bayreuth, Germany
| | - T L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - J Knoester
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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20
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Kun Á. The major evolutionary transitions and codes of life. Biosystems 2021; 210:104548. [PMID: 34547424 DOI: 10.1016/j.biosystems.2021.104548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022]
Abstract
Major evolutionary transitions as well as the evolution of codes of life are key elements in macroevolution which are characterized by increase in complexity Major evolutionary transitions ensues by a transition in individuality and by the evolution of a novel mode of using, transmitting or storing information. Here is where codes of life enter the picture: they are arbitrary mappings between different (mostly) molecular species. This flexibility allows information to be employed in a variety of ways, which can fuel evolutionary innovation. The collation of the list of major evolutionary transitions and the list of codes of life show a clear pattern: codes evolved prior to a major evolutionary transition and then played roles in the transition and/or in the transformation of the new individual. The evolution of a new code of life is in itself not a major evolutionary transition but allow major evolutionary transitions to happen. This could help us to identify new organic codes.
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Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Parmenides Foundation, Kirchplatz 1, D-82049, Pullach, Germany; Institute of Evolution, Centre for Ecological Research, Konkoly-Thege Miklós út 29-33, H-1121, Budapest, Hungary; MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, H-1117, Budapest, Hungary; Institute for Advanced Studies Kőszeg, Chernel utca 14, H-9730, Kőszeg, Hungary; Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Pázmány Péter sétány 1/C, H-1117, Budapest, Hungary.
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21
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Yakovlev AG, Taisova AS, Fetisova ZG. Femtosecond excited-state dynamics in chlorosomal carotenoids of the photosynthetic bacterium Chloroflexus aurantiacus revealed by near infrared pump-probe spectroscopy. Phys Chem Chem Phys 2021; 23:12761-12770. [PMID: 34042141 DOI: 10.1039/d1cp00927c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In photosynthetic green bacteria, chlorosomes provide light harvesting with high efficiency. Chlorosomal carotenoids (Cars) participate in light harvesting together with the main pigment, bacteriochlorophyll (BChl) c/d/e. In the present work, we studied the excited-state dynamics in Cars from Chloroflexus (Cfx.) aurantiacus chlorosomes by near infrared pump-probe spectroscopy with 25 fs temporal resolution at room temperature. The S2 state of Cars was excited at a wavelength of ∼520 nm, and the absorption changes were probed at 860-1000 nm where the excited state absorption (ESA) of the Cars S2 state occurred. Global analysis of the spectroscopy data revealed an ultrafast (∼15 fs) and large (>130 nm) red shift of the S2 ESA spectrum together with the well-known S2 → S1 IC (∼190 fs) and Cars → BChl c EET (∼120 fs). The S2 lifetime was found to be ∼74 fs. Our findings are in line with earlier results on the excited-state dynamics in Cars in vitro. To explain the extremely fast S2 dynamics, we have tentatively proposed two alternative schemes. The first scheme assumed the formation of a vibrational wavepacket in the S2 state, the motion of which caused a dynamical red shift of the S2 ESA spectrum. The second scheme assumed the presence of two potential minima in the S2 state and incoherent energy transfer between them.
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Affiliation(s)
- Andrei G Yakovlev
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory, 119991, Moscow, Russian Federation.
| | - Alexandra S Taisova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory, 119991, Moscow, Russian Federation.
| | - Zoya G Fetisova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory, 119991, Moscow, Russian Federation.
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22
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Abstract
Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.
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23
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Matsubara S, Tamiaki H. Supramolecular Nanofibers Constructed by Hydrogen Bonding of Chlorophyll Dimer. CHEM LETT 2021. [DOI: 10.1246/cl.210026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shogo Matsubara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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24
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Malina T, Koehorst R, Bína D, Pšenčík J, van Amerongen H. Superradiance of bacteriochlorophyll c aggregates in chlorosomes of green photosynthetic bacteria. Sci Rep 2021; 11:8354. [PMID: 33863954 PMCID: PMC8052352 DOI: 10.1038/s41598-021-87664-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/01/2021] [Indexed: 01/18/2023] Open
Abstract
Chlorosomes are the main light-harvesting complexes of green photosynthetic bacteria that are adapted to a phototrophic life at low-light conditions. They contain a large number of bacteriochlorophyll c, d, or e molecules organized in self-assembling aggregates. Tight packing of the pigments results in strong excitonic interactions between the monomers, which leads to a redshift of the absorption spectra and excitation delocalization. Due to the large amount of disorder present in chlorosomes, the extent of delocalization is limited and further decreases in time after excitation. In this work we address the question whether the excitonic interactions between the bacteriochlorophyll c molecules are strong enough to maintain some extent of delocalization even after exciton relaxation. That would manifest itself by collective spontaneous emission, so-called superradiance. We show that despite a very low fluorescence quantum yield and short excited state lifetime, both caused by the aggregation, chlorosomes indeed exhibit superradiance. The emission occurs from states delocalized over at least two molecules. In other words, the dipole strength of the emissive states is larger than for a bacteriochlorophyll c monomer. This represents an important functional mechanism increasing the probability of excitation energy transfer that is vital at low-light conditions. Similar behaviour was observed also in one type of artificial aggregates, and this may be beneficial for their potential use in artificial photosynthesis.
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Affiliation(s)
- Tomáš Malina
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Rob Koehorst
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands.,MicroSpectroscopy Research Facility, Wageningen University, Wageningen, The Netherlands
| | - David Bína
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.,Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Jakub Pšenčík
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands.,MicroSpectroscopy Research Facility, Wageningen University, Wageningen, The Netherlands
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25
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Kawai S, Martinez JN, Lichtenberg M, Trampe E, Kühl M, Tank M, Haruta S, Nishihara A, Hanada S, Thiel V. In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat. Microorganisms 2021; 9:microorganisms9030652. [PMID: 33801086 PMCID: PMC8004040 DOI: 10.3390/microorganisms9030652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
- Correspondence: (S.K.); (V.T.)
| | - Joval N. Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Department of Natural Sciences, College of Arts and Sciences, University of St. La Salle, Bacolod City, Negros Occidental 6100, Philippines
| | - Mads Lichtenberg
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Erik Trampe
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Michael Kühl
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Correspondence: (S.K.); (V.T.)
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Wang Z, Suo B, Yin S, Zou W. Quantum Chemical Simulation of the Qy Absorption Spectrum of Zn Chlorin Aggregates for Artificial Photosynthesis. Molecules 2021; 26:1086. [PMID: 33669551 PMCID: PMC7922025 DOI: 10.3390/molecules26041086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
Zn chlorin (Znchl) is easy to synthesize and has similar optical properties to those of bacteriochlorophyll c in the nature, which is expected to be used as a light-harvesting antenna system in artificial photosynthesis. In order to further explore the optical characteristics of Znchl, various sizes of a parallel layered Znchl-aggregate model and the THF-Znchl explicit solvent monomer model were constructed in this study, and their Qy excited state properties were simulated by using time-dependent density functional theory (TDDFT) and exciton theory. For the Znchl monomer, with a combination of the explicit solvent model and the implicit solvation model based on density (SMD), the calculated Qy excitation energy agreed very well with the experimental one. The Znchl aggregates may be simplified to a Zn36 model to reproduce the experimental Qy absorption spectrum by the Förster coupling theory. The proposed Znchl aggregate model provides a good foundation for the future exploration of other properties of Znchl and simulations of artificial light-harvesting antennas. The results also indicate that J-aggregrates along z-direction, due to intermolecular coordination bonds, are the dominant factor in extending the Qy band of Znchl into the near infrared region.
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Affiliation(s)
- Zhimo Wang
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China;
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China;
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710062, China;
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China;
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Utilization of blue-green light by chlorosomes from the photosynthetic bacterium Chloroflexus aurantiacus: Ultrafast excitation energy conversion and transfer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148396. [PMID: 33581107 DOI: 10.1016/j.bbabio.2021.148396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/14/2023]
Abstract
Chlorosomes of photosynthetic green bacteria are unique molecular assemblies providing efficient light harvesting followed by multi-step transfer of excitation energy to reaction centers. In each chlorosome, 104-105 bacteriochlorophyll (BChl) c/d/e molecules are organized by self-assembly into high-ordered aggregates. We studied the early-time dynamics of the excitation energy flow and energy conversion in chlorosomes isolated from Chloroflexus (Cfx.) aurantiacus bacteria by pump-probe spectroscopy with 30-fs temporal resolution at room temperature. Both the S2 state of carotenoids (Cars) and the Soret states of BChl c were excited at ~490 nm, and absorption changes were probed at 400-900 nm. A global analysis of spectroscopy data revealed that the excitation energy transfer (EET) from Cars to BChl c aggregates occurred within ~100 fs, and the Soret → Q energy conversion in BChl c occurred faster within ~40 fs. This conclusion was confirmed by a detailed comparison of the early exciton dynamics in chlorosomes with different content of Cars. These processes are accompanied by excitonic and vibrational relaxation within 100-270 fs. The well-known EET from BChl c to the baseplate BChl a proceeded on a ps time-scale. We showed that the S1 state of Cars does not participate in EET. We discussed the possible presence (or absence) of an intermediate state that might mediates the Soret → Qy internal conversion in chlorosomal BChl c. We discussed a possible relationship between the observed exciton dynamics and the structural heterogeneity of chlorosomes.
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Günther LM, Knoester J, Köhler J. Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes. Molecules 2021; 26:899. [PMID: 33572047 PMCID: PMC7914687 DOI: 10.3390/molecules26040899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.
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Affiliation(s)
- Lisa M. Günther
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany;
| | - Jasper Knoester
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands;
| | - Jürgen Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany;
- Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
- Bavarian Polymer Institute, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
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Harada J, Mizoguchi T, Kinoshita Y, Yamamoto K, Tamiaki H. Over-expression of the C82-methyltransferase BchQ in mutant strains of the green sulfur bacterium Chlorobaculum limnaeum for synthesis of C8-hyper-alkylated chlorosomal pigments. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Yakovlev AG, Taisova AS, Fetisova ZG. Q-band hyperchromism and B-band hypochromism of bacteriochlorophyll c as a tool for investigation of the oligomeric structure of chlorosomes of the green photosynthetic bacterium Chloroflexus aurantiacus. PHOTOSYNTHESIS RESEARCH 2020; 146:95-108. [PMID: 31939070 DOI: 10.1007/s11120-019-00707-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Chlorosomes of green photosynthetic bacteria are the most amazing example of long-range ordered natural light-harvesting antennae. Chlorosomes are the largest among all known photosynthetic light-harvesting structures (~ 104-105 pigments in the aggregated state). The chlorosomal bacteriochlorophyll (BChl) c/d/e molecules are organized via self-assembly and do not require proteins to provide a scaffold for efficient light harvesting. Despite numerous investigations, a consensus regarding the spatial structure of chlorosomal antennae has not yet been reached. In the present work, we studied hyperchromism/hypochromism in the chlorosomal BChl c Q/B absorption bands of the green photosynthetic bacterium Chloroflexus (Cfx.) aurantiacus. The chlorosomes were isolated from cells grown under different light intensities and therefore, as we discovered earlier, they had different sizes of both BChl c antennae and their unit building blocks. We have shown experimentally that the Q-/B-band hyperchromism/hypochromism is proportional to the size of the chlorosomal antenna. We explained theoretically these findings in terms of excitonic intensity borrowing between the Q and B bands for the J-/H-aggregates of the BChls. The theory developed by Gülen (Photosynth Res 87:205-214, 2006) showed the dependence of the Q-/B-band hyperchromism/hypochromism on the structure of the aggregates. For the model of exciton-coupled BChl c linear chains within a unit building block, the theory predicted an increase in the hyperchromism/hypochromism with the increase in the number of molecules per chain and a decrease in it with the increase in the number of chains. It was previously shown that this model ensured a good fit with spectroscopy experiments and approximated the BChl c low packing density in vivo. The presented experimental and theoretical studies of the Q-/B-band hyperchromism/hypochromism permitted us to conclude that the unit building block of Cfx. aurantiacus chlorosomes comprises of several short BChl c chains.This conclusion is in accordance with previous linear and nonlinear spectroscopy studies on Cfx. aurantiacus chlorosomes.
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Affiliation(s)
- Andrei G Yakovlev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, Russian Federation, 119991.
| | - Alexandra S Taisova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, Russian Federation, 119991
| | - Zoya G Fetisova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, Russian Federation, 119991.
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Supramolecular chlorophyll aggregates inspired from specific light-harvesting antenna “chlorosome”: Static nanostructure, dynamic construction process, and versatile application. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2020.100385] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Madigan MT, Kempher ML, Bender KS, Jung DO, Sattley WM, Lindemann SR, Konopka AE, Dohnalkova AC, Fredrickson JK. A green sulfur bacterium from epsomitic Hot Lake, Washington, USA. Can J Microbiol 2020; 67:332-341. [PMID: 33136441 DOI: 10.1139/cjm-2020-0462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hot Lake is a small heliothermal and hypersaline lake in far north-central Washington State (USA) and is limnologically unusual because MgSO4 rather than NaCl is the dominant salt. In late summer, the Hot Lake metalimnion becomes distinctly green from blooms of planktonic phototrophs. In a study undertaken over 60 years ago, these blooms were predicted to include green sulfur bacteria, but no cultures were obtained. We sampled Hot Lake and established enrichment cultures for phototrophic sulfur bacteria in MgSO4-rich sulfidic media. Most enrichments turned green or red within 2 weeks, and from green-colored enrichments, pure cultures of a lobed green sulfur bacterium (phylum Chlorobi) were isolated. Phylogenetic analyses showed the organism to be a species of the prosthecate green sulfur bacterium Prosthecochloris. Cultures of this Hot Lake phototroph were halophilic and tolerated high levels of sulfide and MgSO4. In addition, unlike all recognized species of Prosthecochloris, the Hot Lake isolates grew at temperatures up to 45 °C, indicating an adaptation to the warm summer temperatures of the lake. Photoautotrophy by Hot Lake green sulfur bacteria may contribute dissolved organic matter to anoxic zones of the lake, and their diazotrophic capacity may provide a key source of bioavailable nitrogen, as well.
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Affiliation(s)
- Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
| | - Megan L Kempher
- Department of Microbiology and Plant Sciences, University of Oklahoma, Norman, OK 73019, USA
| | - Kelly S Bender
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
| | - Deborah O Jung
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
| | - W Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN 46953, USA
| | - Stephen R Lindemann
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Allan E Konopka
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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Šebelík V, West R, Trsková EK, Kaňa R, Polívka T. Energy transfer pathways in the CAC light-harvesting complex of Rhodomonas salina. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148280. [PMID: 32717221 DOI: 10.1016/j.bbabio.2020.148280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 11/30/2022]
Abstract
Photosynthetic organisms had to evolve diverse mechanisms of light-harvesting to supply photosynthetic apparatus with enough energy. Cryptophytes represent one of the groups of photosynthetic organisms combining external and internal antenna systems. They contain one type of immobile phycobiliprotein located at the lumenal side of the thylakoid membrane, together with membrane-bound chlorophyll a/c antenna (CAC). Here we employ femtosecond transient absorption spectroscopy to study energy transfer pathways in the CAC proteins of cryptophyte Rhodomonas salina. The major CAC carotenoid, alloxanthin, is a cryptophyte-specific carotenoid, and it is the only naturally-occurring carotenoid with two triple bonds in its structure. In order to explore the energy transfer pathways within the CAC complex, three excitation wavelengths (505, 590, and 640 nm) were chosen to excite pigments in the CAC antenna. The excitation of Chl c at either 590 or 640 nm proves efficient energy transfer between Chl c and Chl a. The excitation of alloxanthin at 505 nm shows an active pathway from the S2 state with efficiency around 50%, feeding both Chl a and Chl c with approximately 1:1 branching ratio, yet, the S1-route is rather inefficient. The 57 ps energy transfer time to Chl a gives ~25% efficiency of the S1 channel. The low efficiency of the S1 route renders the overall carotenoid-Chl energy transfer efficiency low, pointing to the regulatory role of alloxanthin in the CAC antenna.
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Affiliation(s)
- Václav Šebelík
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Robert West
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Eliška Kuthanová Trsková
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic; Institute of Microbiology, Centre ALGATECH, Czech Academy of Sciences, Třeboň, Czech Republic
| | - Radek Kaňa
- Institute of Microbiology, Centre ALGATECH, Czech Academy of Sciences, Třeboň, Czech Republic
| | - Tomáš Polívka
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic.
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Wörmer L, Gajendra N, Schubotz F, Matys ED, Evans TW, Summons RE, Hinrichs KU. A micrometer-scale snapshot on phototroph spatial distributions: mass spectrometry imaging of microbial mats in Octopus Spring, Yellowstone National Park. GEOBIOLOGY 2020; 18:742-759. [PMID: 32936514 DOI: 10.1111/gbi.12411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial mats from alkaline hot springs in the Yellowstone National Park are ideal natural laboratories to study photosynthetic life under extreme conditions, as well as the nuanced interactions of oxygenic and anoxygenic phototrophs. They represent distinctive examples of chlorophototroph (i.e., chlorophyll or bacteriochlorophyll-based phototroph) diversity, and several novel phototrophs have been first described in these systems, all confined in space, coexisting and competing for niches defined by parameters such as light, oxygen, or temperature. In a novel approach, we employed mass spectrometry imaging of chloropigments, quinones, and intact polar lipids (IPLs) to describe the spatial distribution of different groups of chlorophototrophs along the ~ 1 cm thick microbial mat at 75 µm resolution and in the top ~ 1.5 mm green part of the mat at 25 µm resolution. We observed a fine-tuned sequence of oxygenic and anoxygenic chlorophototrophs with distinctive biomarker signatures populating the microbial mat. The transition of oxic to anoxic conditions is characterized by an accumulation of biomarkers indicative of anoxygenic phototrophy. It is also identified as a clear boundary for different species and ecotypes, which adjust their biomarker inventory, particularly the interplay of quinones and chloropigments, to prevailing conditions. Colocalization of the different biomarker groups led to the identification of characteristic IPL signatures and indicates that glycosidic diether glycerolipids are diagnostic for anoxygenic phototrophs in this mat system. The zoom-in into the upper green part further reveals how oxygenic and anoxygenic phototrophs share this microenvironment and informs on subtle, microscale adjustments in lipid composition of Synechococcus spp.
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Affiliation(s)
- Lars Wörmer
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Niroshan Gajendra
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florence Schubotz
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Emily D Matys
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas W Evans
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
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Kunsel T, Löhner A, Mayo JJ, Köhler J, Jansen TLC, Knoester J. Unraveling intra-aggregate structural disorder using single-molecule spectroscopy. J Chem Phys 2020; 153:134304. [PMID: 33032400 DOI: 10.1063/5.0023551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Structural disorder within self-assembled molecular aggregates may have strong effects on their optical functionality. Such disorder, however, is hard to explore using standard ensemble measurements. In this paper, we report on the characterization of intra-aggregate structural disorder through a linewidth analysis of fluorescence excitation experiments on individual zinc-chlorin (ZnChl) nanotubular molecular aggregates. Recent experiments suggest an anomaly in the linewidths of the two absorption bands that dominate the spectra: the higher-energy bands on average show a smaller linewidth than the lower-energy bands. This anomaly is explored in this paper by analyzing and modeling the correlation of the two linewidths for each aggregate. We exploit a Frenkel exciton model to show that the experimentally observed correlation of linewidths and other statistical properties of the single-aggregate spectra can be explained from small variations of the molecular orientations within individual aggregates.
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Affiliation(s)
- T Kunsel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - A Löhner
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstraße 30, 94557 Bayreuth, Germany
| | - J J Mayo
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - J Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, Universitätsstraße 30, 94557 Bayreuth, Germany
| | - T L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - J Knoester
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Silori Y, Chawla S, De AK. Unravelling the Role of Water in Ultrafast Excited-State Relaxation Dynamics within Nano-Architectures of Chlorophyll a. Chemphyschem 2020; 21:1908-1917. [PMID: 32619067 DOI: 10.1002/cphc.202000487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/01/2020] [Indexed: 11/06/2022]
Abstract
Water plays a pivotal role in structural stability of supramolecular pigment assemblies designed for natural light harvesting (for example, chlorosome antenna complex) as well as their artificial analogs. However, the dynamic role of water in the context of excite-state relaxation has not been explored till date, which we report here. Using femtosecond transient absorption spectroscopy, we investigate the excited-state dynamics of two types of nano-scale assemblies of chlorophyll a with different structural motifs, rod-shaped and micellar assemblies, that depend on the water content. We show how water participates in excess energy dissipation by vibrational cooling of the non-thermally populated Qy band at different rates in different types of clusters but exhibits no polar solvation dynamics. For the micelles, we observe a bifurcation of stimulated emission line shape, whereas a positive-to-negative switching of differential absorption is observed for the rods; both these observations are correlated with their specific structural aspects. Density functional theory calculations reveal two possible stable ground state geometries of dimers, accounting for the bifurcation of line shape in micelles. Thus, our study elucidates water-mediated structure-function relationship within these pigment assemblies.
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Affiliation(s)
- Yogita Silori
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab, 140 306, India
| | - Sakshi Chawla
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab, 140 306, India
| | - Arijit K De
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab, 140 306, India
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Kishi M, Nakamura Y, Tamiaki H. Effect of additional hydroxy group on self-aggregation of synthetic zinc bacteriochlorophyll-c analogs. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Katayama A, Tamiaki H. Stereoselective self-aggregation of zinc bacteriochlorophyll-d analogs possessing an O-substituted oxime moiety at the 13-position. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Greening C, Lithgow T. Formation and function of bacterial organelles. Nat Rev Microbiol 2020; 18:677-689. [PMID: 32710089 DOI: 10.1038/s41579-020-0413-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 01/28/2023]
Abstract
Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by a lipid bilayer (such as thylakoids, magnetosomes and anammoxosomes), whereas others are defined by a lipid monolayer (such as lipid bodies), a proteinaceous coat (such as carboxysomes) or have a phase-defined boundary (such as nucleolus-like compartments). These diverse organelles have various metabolic and physiological functions, facilitating adaptation to different environments and driving the evolution of cellular complexity. This Review highlights that, despite the diversity of reported organelles, some unifying concepts underlie their formation, structure and function. Bacteria have fundamental mechanisms of organelle formation, through which conserved processes can form distinct organelles in different species depending on the proteins recruited to the luminal space and the boundary of the organelle. These complex subcellular compartments provide evolutionary advantages as well as enabling metabolic specialization, biogeochemical processes and biotechnological advances. Growing evidence suggests that the presence of organelles is the rule, rather than the exception, in bacterial cells.
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Affiliation(s)
- Chris Greening
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.
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Takeda T, Katayama A, Kinoshita Y, Tamiaki H. Synthesis of zinc 13-oxime-functionalized chlorophyll-a derivatives and their (131E/Z)-dependent self-aggregation. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Fernandez L, Peura S, Eiler A, Linz AM, McMahon KD, Bertilsson S. Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake. Front Microbiol 2020; 11:1500. [PMID: 32714313 PMCID: PMC7341956 DOI: 10.3389/fmicb.2020.01500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/09/2020] [Indexed: 12/28/2022] Open
Abstract
Aquatic N-fixation is generally associated with the growth and mass development of Cyanobacteria in nitrogen-deprived photic zones. However, sequenced genomes and environmental surveys suggest active aquatic N-fixation also by many non-cyanobacterial groups. Here, we revealed the seasonal variation and genomic diversity of potential N-fixers in a humic bog lake using metagenomic data and nif gene clusters analysis. Groups with diazotrophic operons were functionally divergent and included Cholorobi, Geobacter, Desulfobacterales, Methylococcales, and Acidobacteria. In addition to nifH (a gene that encodes the dinitrogenase reductase component of the molybdenum nitrogenase), we also identified sequences corresponding to vanadium and iron-only nitrogenase genes. Within the Chlorobi population, the nitrogenase (nifH) cluster was included in a well-structured retrotransposon. Furthermore, the presence of light-harvesting photosynthesis genes implies that anoxygenic photosynthesis may fuel nitrogen fixation under the prevailing low-irradiance conditions. The presence of rnf genes (related to the expression of H+/Na+-translocating ferredoxin: NAD+ oxidoreductase) in Methylococcales and Desulfobacterales suggests that other energy-generating processes may drive the costly N-fixation in the absence of photosynthesis. The highly reducing environment of the anoxic bottom layer of Trout Bog Lake may thus also provide a suitable niche for active N-fixers and primary producers. While future studies on the activity of these potential N-fixers are needed to clarify their role in freshwater nitrogen cycling, the metagenomic data presented here enabled an initial characterization of previously overlooked diazotrophs in freshwater biomes.
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Affiliation(s)
- Leyden Fernandez
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alexander Eiler
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | - Alexandra M. Linz
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin–Madison, Madison, WI, United States
| | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin–Madison, Madison, WI, United States
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Nakano T, Tamiaki H. Self-Aggregation abilities of synthetic bacteriochlorophyll-d analogs bearing a propargyl- or benzyl-type alcohol. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Schade B, Singh AK, Wycisk V, Cuellar‐Camacho JL, von Berlepsch H, Haag R, Böttcher C. Stereochemistry-Controlled Supramolecular Architectures of New Tetrahydroxy-Functionalised Amphiphilic Carbocyanine Dyes. Chemistry 2020; 26:6919-6934. [PMID: 32027069 PMCID: PMC7317399 DOI: 10.1002/chem.201905745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 11/28/2022]
Abstract
The syntheses of novel amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine (TBC) dye derivatives with aminopropanediol head groups, which only differ in stereochemistry (chiral enantiomers, meso form and conformer), are reported. For the achiral meso form, a new synthetic route towards asymmetric cyanine dyes was established. All compounds form J aggregates in water, the optical properties of which were characterised by means of spectroscopic methods. The supramolecular structure of the aggregates is investigated by means of cryo-transmission electron microscopy, cryo-electron tomography and AFM, revealing extended sheet-like aggregates for chiral enantiomers and nanotubes for the mesomer, respectively, whereas the conformer forms predominately needle-like crystals. The experiments demonstrate that the aggregation behaviour of compounds can be controlled solely by head group stereochemistry, which in the case of enantiomers enables the formation of extended hydrogen-bond chains by the hydroxyl functionalities. In case of the achiral meso form, however, such chains turned out to be sterically excluded.
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Affiliation(s)
- Boris Schade
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Abhishek Kumar Singh
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Virginia Wycisk
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Jose Luis Cuellar‐Camacho
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Hans von Berlepsch
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Rainer Haag
- Institut für Chemie und BiochemieOrganische ChemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Christoph Böttcher
- Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMolInstitut für Chemie und BiochemieFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
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Li X, Buda F, de Groot HJM, Sevink GJA. Dynamic Disorder Drives Exciton Transfer in Tubular Chlorosomal Assemblies. J Phys Chem B 2020; 124:4026-4035. [PMID: 32343578 PMCID: PMC7246976 DOI: 10.1021/acs.jpcb.0c00441] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chlorosomes stand out for their highly efficient excitation energy transfer (EET) in extreme low light conditions. Yet, little is known about the EET when a chlorosome is excited to a pure state that is an eigenstate of the exciton Hamiltonian. In this work, we consider the dynamic disorder in the intermolecular electronic coupling explicitly by calculating the electronic coupling terms in the Hamiltonian using nuclear coordinates that are taken from molecular dynamics simulation trajectories. We show that this dynamic disorder is capable of driving the evolution of the exciton, being a stationary state of the initial Hamiltonian. In particular, long-distance excitation energy transfer between domains of high exciton population and oscillatory behavior of the population in the site basis are observed, in line with two-dimensional electronic spectroscopy studies. We also found that in the high exciton population domains, their population variation is correlated with their overall coupling strength. Analysis in a reference state basis shows that such dynamic disorder, originating from thermal energy, creates a fluctuating landscape for the exciton and promotes the EET process. We propose such dynamic disorder as an important microscopic origin for the high efficient EET widely observed in different types of chlorosomes, bioinspired tubular aggregates, or other light-harvesting complexes.
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Affiliation(s)
- Xinmeng Li
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Francesco Buda
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Huub J M de Groot
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - G J Agur Sevink
- Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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46
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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47
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Nakano T, Tamiaki H. Synthesis and Self‐Aggregation of Chlorophyll‐
a
Derivatives with Ethynylene and Phenylene Groups Inserted Between the Hydroxymethyl Group and the Chlorin π‐Skeleton. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Takeo Nakano
- Graduate School of Life SciencesRitsumeikan University Kusatsu Shiga 525-8577 Japan
| | - Hitoshi Tamiaki
- Graduate School of Life SciencesRitsumeikan University Kusatsu Shiga 525-8577 Japan
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48
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49
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Katayama A, Tamiaki H. Synthesis of zinc bacteriochlorophyll-d analogs bearing an alkoxyimino group at the 131-position and their self-aggregation in an aqueous micelle solution. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2019.151386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Triplet state quenching of bacteriochlorophyll c aggregates in a protein-free environment of a chlorosome interior. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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