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Clausen U, Vital ST, Lambertus P, Gehler M, Scheve S, Wöhlbrand L, Rabus R. Catabolic Network of the Fermentative Gut Bacterium Phocaeicola vulgatus (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective. Microb Physiol 2024; 34:88-107. [PMID: 38262373 DOI: 10.1159/000536327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary-fiber-fueled, fermentative metabolism the microbial community as well as the host health. Moreover, the fermentative metabolism of P. vulgatus bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the P. vulgatus physiology. METHODS P. vulgatus was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics. RESULTS The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (gCDW/mmolS) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (mMATP/mMC) from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one sided (with rhamnose or fucose: mainly propane-1,2-diol). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to d-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, Sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected. CONCLUSIONS The present study provides insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols.
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Affiliation(s)
- Urte Clausen
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sören-Tobias Vital
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Pia Lambertus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Martina Gehler
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Nesterov SV, Yaguzhinsky LS. Directed proton transfer from F o to F 1 extends the multifaceted proton functions in ATP synthase. Biophys Rev 2023; 15:859-873. [PMID: 37975013 PMCID: PMC10643803 DOI: 10.1007/s12551-023-01132-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The role of protons in ATP synthase is typically considered to be energy storage in the form of an electrochemical potential, as well as an operating element proving rotation. However, this review emphasizes that protons also act as activators of conformational changes in F1 and as direct participants in phosphorylation reaction. The protons transferred through Fo do not immediately leave to the bulk aqueous phase, but instead provide for the formation of a pH gradient between acidifying Fo and alkalizing F1. It facilitates a directed inter-subunit proton transfer to F1, where they are used in the ATP synthesis reaction. This ensures that the enzyme activity is not limited by a lack of protons in the alkaline mitochondrial matrix or chloroplast stroma. Up to one hundred protons bind to the carboxyl groups of the F1 subunit, altering the electrical interactions between the amino acids of the enzyme. This removes the inhibition of ATP synthase caused by the electrostatic attraction of charged amino acids of the stator and rotor and also makes the enzyme more prone to conformational changes. Protonation occurs during ATP synthesis initiation and during phosphorylation, while deprotonation blocks the rotation inhibiting both synthesis and hydrolysis. Thus, protons participate in the functioning of all main components of ATP synthase molecular machine making it effectively a proton-driven electric machine. The review highlights the key role of protons as a coupling factor in ATP synthase with multifaceted functions, including charge and energy transport, torque generation, facilitation of conformational changes, and participation in the ATP synthesis reaction.
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Affiliation(s)
- Semen V. Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Lev S. Yaguzhinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Prakash O, Mostafa A, Im S, Song YC, Kang S, Kim DH. Enhanced anaerobic treatment of sulfate-rich wastewater by electrical voltage application. BIORESOURCE TECHNOLOGY 2023; 369:128430. [PMID: 36464001 DOI: 10.1016/j.biortech.2022.128430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Treatment of sulfate-rich wastewater with high methane recovery is a major concern due to sulfide inhibition. Here, an electrical voltage (EV) aims to enhance methanogenesis and sulfidogenesis to treat sulfate-rich wastewater. Two (control and EV-applied) reactors were operated with a gradual decrease in chemical oxygen demand (COD)/SO42- ratios (CSR). EV-applied reactor (EVR) demonstrated an increase of ∼30 % in methane production and ∼40 % in sulfate removal, compared to the control till CSR of 2.0. At CSR 1.0, the control failed, while EVR still exhibited a stable performance of 50 % COD-methane recovery. Microbial community results showed that the relative abundance of sulfate-reducing bacteria in EVR was 1.5 times higher than the control. Furthermore, higher relative abundance of dissimilatory sulfate reductase (>50 %) and Ni/Fe hydrogenase (x15) genes demonstrated an improved tolerance against H2S toxicity. This study highlights the importance of EV application by minimizing the byproduct inhibition in sulfate-rich wastewater.
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Affiliation(s)
- Om Prakash
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Alsayed Mostafa
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Seongwon Im
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Young-Chae Song
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Seoktae Kang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dong-Hoon Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea.
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Turina P. Modulation of the H+/ATP coupling ratio by ADP and ATP as a possible regulatory feature in the F-type ATP synthases. Front Mol Biosci 2022; 9:1023031. [PMID: 36275634 PMCID: PMC9583940 DOI: 10.3389/fmolb.2022.1023031] [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] [Received: 08/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
F-type ATP synthases are transmembrane enzymes, which play a central role in the metabolism of all aerobic and photosynthetic cells and organisms, being the major source of their ATP synthesis. Catalysis occurs via a rotary mechanism, in which the free energy of a transmembrane electrochemical ion gradient is converted into the free energy of ATP phosphorylation from ADP and Pi, and vice versa. An ADP, tightly bound to one of the three catalytic sites on the stator head, is associated with catalysis inhibition, which is relieved by the transmembrane proton gradient and by ATP. By preventing wasteful ATP hydrolysis in times of low osmotic energy and low ATP/ADP ratio, such inhibition constitutes a classical regulatory feedback effect, likely to be an integral component of in vivo regulation. The present miniview focuses on an additional putative regulatory phenomenon, which has drawn so far little attention, consisting in a substrate-induced tuning of the H+/ATP coupling ratio during catalysis, which might represent an additional key to energy homeostasis in the cell. Experimental pieces of evidence in support of such a phenomenon are reviewed.
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Lapashina AS, Kashko ND, Zubareva VM, Galkina KV, Markova OV, Knorre DA, Feniouk BA. Attenuated ADP-inhibition of F OF 1 ATPase mitigates manifestations of mitochondrial dysfunction in yeast. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148544. [PMID: 35331734 DOI: 10.1016/j.bbabio.2022.148544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Proton-translocating FOF1 ATP synthase (F-ATPase) couples ATP synthesis or hydrolysis to transmembrane proton transport in bacteria, chloroplasts, and mitochondria. The primary function of the mitochondrial FOF1 is ATP synthesis driven by protonmotive force (pmf) generated by the respiratory chain. However, when pmf is low or absent (e.g. during anoxia), FOF1 consumes ATP and functions as a proton-pumping ATPase. Several regulatory mechanisms suppress the ATPase activity of FOF1 at low pmf. In yeast mitochondria they include special inhibitory proteins Inh1p and Stf1p, and non-competitive inhibition of ATP hydrolysis by MgADP (ADP-inhibition). Presumably, these mechanisms help the cell to preserve the ATP pool upon membrane de-energization. However, no direct evidence was presented to support this hypothesis so far. Here we report that a point mutation Q263L in subunit beta of Saccharomyces cerevisiae ATP synthase significantly attenuated ADP-inhibition of the enzyme without major effect on the rate of ATP production by mitochondria. The mutation also decreased the sensitivity of the enzyme ATPase activity to azide. Similar effects of the corresponding mutations were observed in earlier studies in bacterial enzymes. This observation indicates that the molecular mechanism of ADP-inhibition is probably the same in mitochondrial and in bacterial FOF1. The mutant yeast strain had lower growth rate and had a longer lag period preceding exponential growth phase when starved cells were transferred to fresh growth medium. However, upon the loss of mitochondrial DNA (ρ0) the βQ263L mutation effect was reversed: the βQ263L ρ0 mutant grew faster than the wild-type ρ0 yeast. The results suggest that ADP-inhibition might play a role in prevention of wasteful ATP hydrolysis in the mitochondrial matrix.
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Affiliation(s)
- Anna S Lapashina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia; Sechenov First Moscow State Medical University, Department of Biological Chemistry, Moscow, Russia
| | - Nataliia D Kashko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Valeria M Zubareva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Kseniia V Galkina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V Markova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Knorre
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Boris A Feniouk
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
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A review on lactoferrin as a proton pump inhibitor. Int J Biol Macromol 2022; 202:309-317. [PMID: 35038474 DOI: 10.1016/j.ijbiomac.2022.01.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022]
Abstract
Lactoferrin (Lf) is a versatile natural milk-derived protein that exhibits multiple interesting biological activities. Since it is safe for human administration and currently manufactured using low cost and well-established large-scale processes, the Lf scientific community has been devoted at dissecting its mechanisms of action towards its more rational and efficient use for various applications. Emerging literature has identified proton pumping ATPases as molecular targets of Lf in different cellular models linked to distinct activities of this natural protein. Information on this subject has not been systematically analysed before, hence herein we review the current state of art on the effect of Lf on proton pumping ATPases. Though structurally different, we propose that Lf holds a proton pump inhibitor (PPI)-like activity based on the functional resemblance with the classical inhibitors of the stomach H+/K+-ATPase. The downstream events and outcomes of the PPI-like activity of Lf, as well as its impact for the development of improved Lf applications are also discussed.
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Galkina KV, Zubareva VM, Kashko ND, Lapashina AS, Markova OV, Feniouk BA, Knorre DA. Heterogeneity of Starved Yeast Cells in IF1 Levels Suggests the Role of This Protein in vivo. Front Microbiol 2022; 13:816622. [PMID: 35401495 PMCID: PMC8984185 DOI: 10.3389/fmicb.2022.816622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
In mitochondria, a small protein IF1 suppresses the hydrolytic activity of ATP synthase and presumably prevents excessive ATP hydrolysis under conditions of energy deprivation. In yeast Saccharomyces cerevisiae, IF1 homologs are encoded by two paralogous genes: INH1 and STF1. INH1 expression is known to aggravate the deleterious effects of mitochondrial DNA (mtDNA) depletion. Surprisingly, no beneficial effects of INH1 and STF1 were documented for yeast so far, and the functions of INH1 and STF1 in wild type cells are unclear. Here, we put forward a hypothesis that INH1 and STF1 bring advantage during the fast start of proliferation after reentry into exponential growth from post-diauxic or stationary phases. We found that yeast cells increase the concentration of both proteins in the post-diauxic phase. Post-diauxic phase yeast cells formed two subpopulations distinct in Inh1p and Stf1p concentrations. Upon exit from the post-diauxic phase cells with high level of Inh1-GFP started growing earlier than cells devoid of Inh1-GFP. However, double deletion of INH1 and STF1 did not increase the lag period necessary for stationary phase yeast cells to start growing after reinoculation into the fresh medium. These results point to a redundancy of the mechanisms preventing uncontrolled ATP hydrolysis during energy deprivation.
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Affiliation(s)
- Kseniia V. Galkina
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Valeria M. Zubareva
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Nataliia D. Kashko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna S. Lapashina
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Department of Biological Chemistry, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Olga V. Markova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris A. Feniouk
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A. Knorre
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Dmitry A. Knorre,
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Voon CP, Law YS, Guan X, Lim SL, Xu Z, Chu WT, Zhang R, Sun F, Labs M, Leister D, Pribil M, Hronková M, Kubásek J, Cui Y, Jiang L, Tsuyama M, Gardeström P, Tikkanen M, Lim BL. Modulating the activities of chloroplasts and mitochondria promotes adenosine triphosphate production and plant growth. QUANTITATIVE PLANT BIOLOGY 2021; 2:e7. [PMID: 37077204 PMCID: PMC10095973 DOI: 10.1017/qpb.2021.7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 05/03/2023]
Abstract
Efficient photosynthesis requires a balance of ATP and NADPH production/consumption in chloroplasts, and the exportation of reducing equivalents from chloroplasts is important for balancing stromal ATP/NADPH ratio. Here, we showed that the overexpression of purple acid phosphatase 2 on the outer membranes of chloroplasts and mitochondria can streamline the production and consumption of reducing equivalents in these two organelles, respectively. A higher capacity of consumption of reducing equivalents in mitochondria can indirectly help chloroplasts to balance the ATP/NADPH ratio in stroma and recycle NADP+, the electron acceptors of the linear electron flow (LEF). A higher rate of ATP and NADPH production from the LEF, a higher capacity of carbon fixation by the Calvin-Benson-Bassham (CBB) cycle and a greater consumption of NADH in mitochondria enhance photosynthesis in the chloroplasts, ATP production in the mitochondria and sucrose synthesis in the cytosol and eventually boost plant growth and seed yields in the overexpression lines.
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Affiliation(s)
- Chia P. Voon
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Yee-Song Law
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Xiaoqian Guan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Shey-Li Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Zhou Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Wing-Tung Chu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Renshan Zhang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Feng Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
| | - Mathias Labs
- Plant Molecular Biology, Department of Biology, Ludwig-Maximilians-University Munich (LMU), Munich, Germany
| | - Dario Leister
- Plant Molecular Biology, Department of Biology, Ludwig-Maximilians-University Munich (LMU), Munich, Germany
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie Hronková
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Jiří Kubásek
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Yong Cui
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
| | - Michito Tsuyama
- Department of Agriculture, Kyushu University, Fukuoka, Japan
| | - Per Gardeström
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Mikko Tikkanen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Turku, Finland
| | - Boon L. Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, China
- School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, China
- Author for correspondence: B. L. Lim, E-mail:
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