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Zhang K, Law MCY, Nguyen TM, Tan YB, Wirawan M, Law YS, Jeong LS, Luo D. Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1. Cell Rep 2022; 40:111133. [PMID: 35905713 DOI: 10.1016/j.celrep.2022.111133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Many viruses encode RNA-modifying enzymes to edit the 5' end of viral RNA to mimic the cellular mRNA for effective protein translation, genome replication, and evasion of the host defense mechanisms. Alphavirus nsP1 synthesizes the 5' end Cap-0 structure of viral RNAs. However, the molecular basis of the capping process remains unclear. We determine high-resolution cryoelectron microscopy (cryo-EM) structures of Chikungunya virus nsP1 in complex with m7GTP/SAH, covalently attached m7GMP, and Cap-0 viral RNA. These structures reveal details of viral-RNA-capping reactions and uncover a sequence-specific virus RNA-recognition pattern that, in turn, regulates viral-RNA-capping efficiency to ensure optimal genome replication and subgenomic RNA transcription. This sequence-specific enzyme-RNA pairing is conserved across all alphaviruses.
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Affiliation(s)
- Kuo Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Michelle Cheok Yien Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Trinh Mai Nguyen
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Melissa Wirawan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yee-Song Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Lak Shin Jeong
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.
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Tan YB, Lello LS, Liu X, Law YS, Kang C, Lescar J, Zheng J, Merits A, Luo D. Crystal structures of alphavirus nonstructural protein 4 (nsP4) reveal an intrinsically dynamic RNA-dependent RNA polymerase fold. Nucleic Acids Res 2022; 50:1000-1016. [PMID: 35037043 PMCID: PMC8789068 DOI: 10.1093/nar/gkab1302] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Alphaviruses such as Ross River virus (RRV), chikungunya virus (CHIKV), Sindbis virus (SINV), and Venezuelan equine encephalitis virus (VEEV) are mosquito-borne pathogens that can cause arthritis or encephalitis diseases. Nonstructural protein 4 (nsP4) of alphaviruses possesses RNA-dependent RNA polymerase (RdRp) activity essential for viral RNA replication. No 3D structure has been available for nsP4 of any alphaviruses despite its importance for understanding alphaviral RNA replication and for the design of antiviral drugs. Here, we report crystal structures of the RdRp domain of nsP4 from both RRV and SINV determined at resolutions of 2.6 Å and 1.9 Å. The structure of the alphavirus RdRp domain appears most closely related to RdRps from pestiviruses, noroviruses, and picornaviruses. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) methods showed that in solution, nsP4 is highly dynamic with an intrinsically disordered N-terminal domain. Both full-length nsP4 and the RdRp domain were capable to catalyze RNA polymerization. Structure-guided mutagenesis using a trans-replicase system identified nsP4 regions critical for viral RNA replication.
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Affiliation(s)
- Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921
| | - Laura Sandra Lello
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Xin Liu
- Shanghai Institute of Materia Medica, China Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, China
| | - Yee-Song Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Rd, #05-01/06 Chromos, Singapore138670
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
| | - Jie Zheng
- Shanghai Institute of Materia Medica, China Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, China
| | - Andres Merits
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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Zhang R, Guan X, Yang M, Law YS, Voon CP, Yan J, Sun F, Lim BL. Overlapping Functions of the Paralogous Proteins AtPAP2 and AtPAP9 in Arabidopsis thaliana. Int J Mol Sci 2021; 22:7243. [PMID: 34298863 PMCID: PMC8303434 DOI: 10.3390/ijms22147243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2), which is anchored to the outer membranes of chloroplasts and mitochondria, affects carbon metabolism by modulating the import of some preproteins into chloroplasts and mitochondria. AtPAP9 bears a 72% amino acid sequence identity with AtPAP2, and both proteins carry a hydrophobic motif at their C-termini. Here, we show that AtPAP9 is a tail-anchored protein targeted to the outer membrane of chloroplasts. Yeast two-hybrid and bimolecular fluorescence complementation experiments demonstrated that both AtPAP9 and AtPAP2 bind to a small subunit of rubisco 1B (AtSSU1B) and a number of chloroplast proteins. Chloroplast import assays using [35S]-labeled AtSSU1B showed that like AtPAP2, AtPAP9 also plays a role in AtSSU1B import into chloroplasts. Based on these data, we propose that AtPAP9 and AtPAP2 perform overlapping roles in modulating the import of specific proteins into chloroplasts. Most plant genomes contain only one PAP-like sequence encoding a protein with a hydrophobic motif at the C-terminus. The presence of both AtPAP2 and AtPAP9 in the Arabidopsis genome may have arisen from genome duplication in Brassicaceae. Unlike AtPAP2 overexpression lines, the AtPAP9 overexpression lines did not exhibit early-bolting or high-seed-yield phenotypes. Their differential growth phenotypes could be due to the inability of AtPAP9 to be targeted to mitochondria, as the overexpression of AtPAP2 on mitochondria enhances the capacity of mitochondria to consume reducing equivalents.
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Affiliation(s)
- Renshan Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
| | - Xiaoqian Guan
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
| | - Meijing Yang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
| | - Yee-Song Law
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
| | - Chia Pao Voon
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
| | - Junran Yan
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
| | - Feng Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; (R.Z.); (X.G.); (M.Y.); (Y.-S.L.); (C.P.V.); (J.Y.); (F.S.)
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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Xu Z, Zhang R, Yang M, Law YS, Sun F, Hon NL, Ngai SM, Lim BL. A Balance between the Activities of Chloroplasts and Mitochondria Is Crucial for Optimal Plant Growth. Antioxidants (Basel) 2021; 10:935. [PMID: 34207819 PMCID: PMC8228383 DOI: 10.3390/antiox10060935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/31/2021] [Accepted: 06/04/2021] [Indexed: 01/16/2023] Open
Abstract
Energy metabolism in plant cells requires a balance between the activities of chloroplasts and mitochondria, as they are the producers and consumers of carbohydrates and reducing equivalents, respectively. Recently, we showed that the overexpression of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2), a phosphatase dually anchored on the outer membranes of chloroplasts and mitochondria, can boost the plant growth and seed yield of Arabidopsis thaliana by coordinating the activities of both organelles. However, when AtPAP2 is solely overexpressed in chloroplasts, the growth-promoting effects are less optimal, indicating that active mitochondria are required for dissipating excess reducing equivalents from chloroplasts to maintain the optimal growth of plants. It is even more detrimental to plant productivity when AtPAP2 is solely overexpressed in mitochondria. Although these lines contain high level of adenosine triphosphate (ATP), they exhibit low leaf sucrose, low seed yield, and early senescence. These transgenic lines can be useful tools for studying how hyperactive chloroplasts or mitochondria affect the physiology of their counterparts and how they modify cellular metabolism and plant physiology.
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Affiliation(s)
- Zhou Xu
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Z.X.); (R.Z.); (M.Y.); (Y.-S.L.); (F.S.)
| | - Renshan Zhang
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Z.X.); (R.Z.); (M.Y.); (Y.-S.L.); (F.S.)
| | - Meijing Yang
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Z.X.); (R.Z.); (M.Y.); (Y.-S.L.); (F.S.)
| | - Yee-Song Law
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Z.X.); (R.Z.); (M.Y.); (Y.-S.L.); (F.S.)
| | - Feng Sun
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Z.X.); (R.Z.); (M.Y.); (Y.-S.L.); (F.S.)
| | - Ngai Lung Hon
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (N.L.H.); (S.M.N.)
| | - Sai Ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (N.L.H.); (S.M.N.)
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Z.X.); (R.Z.); (M.Y.); (Y.-S.L.); (F.S.)
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Zhang K, Law YS, Law MCY, Tan YB, Wirawan M, Luo D. Structural insights into viral RNA capping and plasma membrane targeting by Chikungunya virus nonstructural protein 1. Cell Host Microbe 2021; 29:757-764.e3. [DOI: 10.1016/j.chom.2021.02.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 01/30/2023]
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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. Quant Plant Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Law YS, Ngan L, Yan J, Kwok LY, Sun Y, Cheng S, Schwenkert S, Lim BL. Multiple Kinases Can Phosphorylate the N-Terminal Sequences of Mitochondrial Proteins in Arabidopsis thaliana. Front Plant Sci 2018; 9:982. [PMID: 30042778 PMCID: PMC6048449 DOI: 10.3389/fpls.2018.00982] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/18/2018] [Indexed: 05/06/2023]
Abstract
Phosphorylation of the transit peptides of nuclear-encoded preprotein is a well-known regulatory process of protein import in plant chloroplasts. In the Arabidopsis Protein Phosphorylation Site Database, 103 out of 802 mitochondrial proteins were found to contain one or more experimentally proven phosphorylation sites in their first 60 amino acid residues. Analysis of the N-terminal sequences of selected mitochondrial preproteins and their homologs from 64 plant species showed high conservation among phosphorylation sites. The ability of kinases from various sources including leaf extract (LE), root extract (RE), wheat germ lysate (WGL), and STY kinases to phosphorylate N-terminal sequences of several respiratory chain proteins were examined by in vitro kinase assays. The three STY kinases were shown to phosphorylate the N-terminal sequences of some proteins we tested but exhibited different specificities. Interestingly, the N-terminal sequences of two mitochondrial ATP synthase beta subunit 1/3 (pF1β-1/3) could be phosphorylated by LE and RE but not by STY kinases, suggesting that there are uncharacterized presequence-phosphorylating kinases other than STY kinases present in RE and LE. Mitochondrial import studies showed that the import of RRL-synthesized pF1βs was impeded by the treatment of LE, and the addition of a short SSU transit peptide containing a phosphorylatable 14-3-3 binding site could enhance the import of LE-treated pF1βs. Our results suggested that the transit peptide of pSSU can compete with the presequences of pF1βs for an uncharacterized kinase(s) in leaf. Altogether, our data showed that phosphorylation of transit peptides/presequences are not uncommon for chloroplast-targeted and mitochondria-targeted proteins, albeit possibly differentially regulated.
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Affiliation(s)
- Yee-Song Law
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ling Ngan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Junran Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Lok Y. Kwok
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shifeng Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Serena Schwenkert
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Boon L. Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Boon L. Lim,
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Sun Y, Law YS, Cheng S, Lim BL. RNA editing of cytochrome c maturation transcripts is responsive to the energy status of leaf cells in Arabidopsis thaliana. Mitochondrion 2017; 35:23-34. [PMID: 28478183 DOI: 10.1016/j.mito.2017.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/24/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
Abstract
Overexpression of AtPAP2, a phosphatase located on the outer membranes of chloroplasts and mitochondria, leads to higher energy outputs from these organelles. AtPAP2 interacts with seven MORF proteins of the editosome complex. RNA-sequencing analysis showed that the editing degrees of most sites did not differ significantly between OE and WT, except some sites on the transcripts of several cytochrome c maturation (Ccm) genes. Western blotting of 2D BN-PAGE showed that the patterns of CcmFN1 polypeptides were different between the lines. We proposed that AtPAP2 may influence cytochrome c biogenesis by modulating RNA editing through its interaction with MORF proteins.
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Affiliation(s)
- Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yee-Song Law
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shifeng Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Wu Q, Tun HM, Law YS, Khafipour E, Shah NP. Common Distribution of gad Operon in Lactobacillus brevis and its GadA Contributes to Efficient GABA Synthesis toward Cytosolic Near-Neutral pH. Front Microbiol 2017; 8:206. [PMID: 28261168 PMCID: PMC5306213 DOI: 10.3389/fmicb.2017.00206] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/30/2017] [Indexed: 12/23/2022] Open
Abstract
Many strains of lactic acid bacteria (LAB) and bifidobacteria have exhibited strain-specific capacity to produce γ-aminobutyric acid (GABA) via their glutamic acid decarboxylase (GAD) system, which is one of amino acid-dependent acid resistance (AR) systems in bacteria. However, the linkage between bacterial AR and GABA production capacity has not been well established. Meanwhile, limited evidence has been provided to the global diversity of GABA-producing LAB and bifidobacteria, and their mechanisms of efficient GABA synthesis. In this study, genomic survey identified common distribution of gad operon-encoded GAD system in Lactobacillus brevis for its GABA production among varying species of LAB and bifidobacteria. Importantly, among four commonly distributed amino acid-dependent AR systems in Lb. brevis, its GAD system was a major contributor to maintain cytosolic pH homeostasis by consuming protons via GABA synthesis. This highlights that Lb. brevis applies GAD system as the main strategy against extracellular and intracellular acidification demonstrating its high capacity of GABA production. In addition, the abundant GadA retained its activity toward near-neutral pH (pH 5.5–6.5) of cytosolic acidity thus contributing to efficient GABA synthesis in Lb. brevis. This is the first global report illustrating species-specific characteristic and mechanism of efficient GABA synthesis in Lb. brevis.
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Affiliation(s)
- Qinglong Wu
- School of Biological Sciences, The University of Hong Kong Hong Kong, Hong Kong
| | - Hein Min Tun
- Department of Animal Science, University of Manitoba Winnipeg, MB, Canada
| | - Yee-Song Law
- School of Biological Sciences, The University of Hong Kong Hong Kong, Hong Kong
| | - Ehsan Khafipour
- Department of Animal Science, University of ManitobaWinnipeg, MB, Canada; Department of Medical Microbiology, University of ManitobaWinnipeg, MB, Canada
| | - Nagendra P Shah
- School of Biological Sciences, The University of Hong KongHong Kong, Hong Kong; Victoria UniversityMelbourne, VIC, Australia
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Abstract
Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) is the only phosphatase that is dual-targeted to both chloroplasts and mitochondria. Like Toc33/34 of the TOC and Tom 20 of the TOM, AtPAP2 is anchored to the outer membranes of chloroplasts and mitochondria via a hydrophobic C-terminal motif. AtPAP2 on the mitochondria was previously shown to recognize the presequences of several nuclear-encoded mitochondrial proteins and modulate the import of pMORF3 into the mitochondria. Here we show that AtPAP2 binds to the small subunit of Rubisco (pSSU) and that chloroplast import experiments demonstrated that pSSU was imported less efficiently into pap2 chloroplasts than into wild-type chloroplasts. We propose that AtPAP2 is an outer membrane-bound phosphatase receptor that facilitates the import of selected proteins into chloroplasts.
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Affiliation(s)
- Renshan Zhang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xiaoqian Guan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Feng Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shuai Chen
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Kam Bo Wong
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- CONTACT Boon Leong LIM
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Law YS, Zhang R, Guan X, Cheng S, Sun F, Duncan O, Murcha MW, Whelan J, Lim BL. Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis. Plant Physiol 2015; 169:1344-55. [PMID: 26304849 PMCID: PMC4587475 DOI: 10.1104/pp.15.01115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/21/2015] [Indexed: 05/18/2023]
Abstract
The nucleus-encoded mitochondria-targeted proteins, multiple organellar RNA editing factors (MORF3, MORF5, and MORF6), interact with Arabidopsis (Arabidopsis thaliana) PURPLE ACID PHOSPHATASE2 (AtPAP2) located on the chloroplast and mitochondrial outer membranes in a presequence-dependent manner. Phosphorylation of the presequence of the precursor MORF3 (pMORF3) by endogenous kinases in wheat germ translation lysate, leaf extracts, or STY kinases, but not in rabbit reticulocyte translation lysate, resulted in the inhibition of protein import into mitochondria. This inhibition of import could be overcome by altering threonine/serine residues to alanine on the presequence, thus preventing phosphorylation. Phosphorylated pMORF3, but not the phosphorylation-deficient pMORF3, can form a complex with 14-3-3 proteins and HEAT SHOCK PROTEIN70. The phosphorylation-deficient mutant of pMORF3 also displayed faster rates of import when translated in wheat germ lysates. Mitochondria isolated from plants with altered amounts of AtPAP2 displayed altered protein import kinetics. The import rate of pMORF3 synthesized in wheat germ translation lysate into pap2 mitochondria was slower than that into wild-type mitochondria, and this rate disparity was not seen for pMORF3 synthesized in rabbit reticulocyte translation lysate, the latter translation lysate largely deficient in kinase activity. Taken together, these results support a role for the phosphorylation and dephosphorylation of pMORF3 during the import into plant mitochondria. These results suggest that kinases, possibly STY kinases, and AtPAP2 are involved in the import of protein into both mitochondria and chloroplasts and provide a mechanism by which the import of proteins into both organelles may be coordinated.
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Affiliation(s)
- Yee-Song Law
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - Renshan Zhang
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - Xiaoqian Guan
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - Shifeng Cheng
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - Feng Sun
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - Owen Duncan
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - Monika W Murcha
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - James Whelan
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China (Y.-S.L., R.Z., X.G., S.C., F.S., B.L.L.);Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia (O.D., M.W.M.);Department of Animal, Plant, and Soil Science, School of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia (J.W.); andState Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China (B.L.L.)
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Wu Q, Law YS, Shah NP. Dairy Streptococcus thermophilus improves cell viability of Lactobacillus brevis NPS-QW-145 and its γ-aminobutyric acid biosynthesis ability in milk. Sci Rep 2015; 5:12885. [PMID: 26245488 PMCID: PMC4526857 DOI: 10.1038/srep12885] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/06/2015] [Indexed: 11/13/2022] Open
Abstract
Most high γ-aminobutyric acid (GABA) producers are Lactobacillus brevis of plant origin, which may be not able to ferment milk well due to its poor proteolytic nature as evidenced by the absence of genes encoding extracellular proteinases in its genome. In the present study, two glutamic acid decarboxylase (GAD) genes, gadA and gadB, were found in high GABA-producing L. brevis NPS-QW-145. Co-culturing of this organism with conventional dairy starters was carried out to manufacture GABA-rich fermented milk. It was observed that all the selected strains of Streptococcus thermophilus, but not Lactobacillus delbrueckii subsp. bulgaricus, improved the viability of L. brevis NPS-QW-145 in milk. Only certain strains of S. thermophilus improved the gadA mRNA level in L. brevis NPS-QW-145, thus enhanced GABA biosynthesis by the latter. These results suggest that certain S. thermophilus strains are highly recommended to co-culture with high GABA producer for manufacturing GABA-rich fermented milk.
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Affiliation(s)
- Qinglong Wu
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yee-Song Law
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Nagendra P Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
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Law YS, Gudimella R, Song BK, Ratnam W, Harikrishna JA. Molecular characterization and comparative sequence analysis of defense-related gene, Oryza rufipogon receptor-like protein kinase 1. Int J Mol Sci 2012; 13:9343-9362. [PMID: 22942769 PMCID: PMC3430300 DOI: 10.3390/ijms13079343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/06/2012] [Accepted: 07/06/2012] [Indexed: 11/16/2022] Open
Abstract
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression.
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Affiliation(s)
- Yee-Song Law
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia; E-Mails: (Y.-S.L.); (R.G.)
| | - Ranganath Gudimella
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia; E-Mails: (Y.-S.L.); (R.G.)
| | - Beng-Kah Song
- School of Science, Monash University Sunway Campus, Jalan Lagoon Selatan, Bandar Sunway, Selangor 46150, Malaysia; E-Mail:
| | - Wickneswari Ratnam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia; E-Mail:
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia; E-Mails: (Y.-S.L.); (R.G.)
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Sivakumar P, Law YS, Ho CL, Harikrishna JA. High frequency plant regeneration from mature seed of elite, recalcitrant Malaysian indica rice ( Oryza sativa L.) CV. MR 219. Acta Biol Hung 2010; 61:313-21. [PMID: 20724277 DOI: 10.1556/abiol.61.2010.3.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An efficient in vitro plant regeneration system was established for elite, recalcitrant Malaysian indica rice, Oryza sativa L. CV. MR 219 using mature seeds as explant on Murashige and Skoog and Chu N6 media containing 2,4-dichlorophenoxy acetic acid and kinetin either alone or in different combinations. L-proline, casein hydrolysate and L-glutamine were added to callus induction media for enhancement of embryogenic callus induction. The highest frequency of friable callus induction (84%) was observed in N6 medium containing 2.5 mg l(-1) 2,4-dichlorophenoxy acetic acid, 0.2 mg l(-1) kinetin, 2.5 mg l(-1) L-proline, 300 mg l(-1) casein hydrolysate, 20 mg l(-1) L-glutamine and 30 g l(-1) sucrose under culture in continuous lighting conditions. The maximum regeneration frequency (71%) was observed, when 30-day-old N6 friable calli were cultured on MS medium supplemented with 3 mg l(-1) 6-benzyl aminopurine, 1 mg l(-1) naphthalene acetic acid, 2.5 mg l(-1) L-proline, 300 mg l(-1) casein hydrolysate and 3% maltose. Developed shoots were rooted in half strength MS medium supplemented with 2% sucrose and were successfully transplanted to soil with 95% survival. This protocol may be used for other recalcitrant indica rice genotypes and to transfer desirable genes in to Malaysian indica rice cultivar MR219 for crop improvement.
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Affiliation(s)
- P Sivakumar
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
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