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Lu P, Sui M, Zhang M, Wang M, Kamiya T, Okamoto K, Itoh H, Okuda S, Suzuki M, Asakura T, Fujiwara T, Nagata K. Rosmarinic Acid and Sodium Citrate Have a Synergistic Bacteriostatic Effect against Vibrio Species by Inhibiting Iron Uptake. Int J Mol Sci 2021; 22:13010. [PMID: 34884815 PMCID: PMC8657459 DOI: 10.3390/ijms222313010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND New strategies are needed to combat multidrug-resistant bacteria. The restriction of iron uptake by bacteria is a promising way to inhibit their growth. We aimed to suppress the growth of Vibrio bacterial species by inhibiting their ferric ion-binding protein (FbpA) using food components. METHODS Twenty spices were selected for the screening of FbpA inhibitors. The candidate was applied to antibacterial tests, and the mechanism was further studied. RESULTS An active compound, rosmarinic acid (RA), was screened out. RA binds competitively and more tightly than Fe3+ to VmFbpA, the FbpA from V. metschnikovii, with apparent KD values of 8 μM vs. 17 μM. Moreover, RA can inhibit the growth of V. metschnikovii to one-third of the control at 1000 μM. Interestingly, sodium citrate (SC) enhances the growth inhibition effect of RA, although SC only does not inhibit the growth. The combination of RA/SC completely inhibits the growth of not only V. metschnikovii at 100/100 μM but also the vibriosis-causative pathogens V. vulnificus and V. parahaemolyticus, at 100/100 and 1000/100 μM, respectively. However, RA/SC does not affect the growth of Escherichia coli. CONCLUSIONS RA/SC is a potential bacteriostatic agent against Vibrio species while causing little damage to indigenous gastrointestinal bacteria.
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Affiliation(s)
- Peng Lu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Miaomiao Sui
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Mimin Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Mengyao Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Takehiro Kamiya
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Ken Okamoto
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Hideaki Itoh
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Suguru Okuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Tomiko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (M.S.); (M.Z.); (M.W.); (T.K.); (K.O.); (H.I.); (S.O.); (M.S.); (T.A.); (T.F.)
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Gazara RK, Moharana KC, Bellieny-Rabelo D, Venancio TM. Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants. PLANT MOLECULAR BIOLOGY 2018; 97:435-449. [PMID: 29956113 DOI: 10.1007/s11103-018-0750-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/14/2018] [Indexed: 05/13/2023]
Abstract
Here we uncover the major evolutionary events shaping the evolution of the GID1 family of gibberellin receptors in land plants at the sequence, structure and gene expression levels. Gibberellic acid (gibberellin, GA) controls key developmental processes in the life cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 54 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support for a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots that provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (which typically have low GA levels). Taken together, our results indicate that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.
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Affiliation(s)
- Rajesh K Gazara
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego 2000/P5/217, Parque Califórnia, Campos dos Goytacazes, RJ, CEP: 28013-602, Brazil
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego 2000/P5/217, Parque Califórnia, Campos dos Goytacazes, RJ, CEP: 28013-602, Brazil
| | - Daniel Bellieny-Rabelo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego 2000/P5/217, Parque Califórnia, Campos dos Goytacazes, RJ, CEP: 28013-602, Brazil
- Department of Microbiology and Plant Pathology, University of Pretoria, Lunnon Road, Pretoria, 0028, South Africa
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego 2000/P5/217, Parque Califórnia, Campos dos Goytacazes, RJ, CEP: 28013-602, Brazil.
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Li D, Du S, Tan W, Duan H. Computational insight into the structure-activity relationship of novel N-substituted phthalimides with gibberellin-like activity. J Mol Model 2015; 21:271. [PMID: 26412055 DOI: 10.1007/s00894-015-2817-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 09/07/2015] [Indexed: 02/01/2023]
Abstract
N-substituted phthalimides (NSPs) that show multiple gibberellin (GA)-like effects on the growth and development of higher plants have been reported. These NSPs may represent a potential alternative to commercial GAs. Therefore, in this work, molecular docking and molecular dynamics simulations were used to explore the mode of interaction between some NSPs and the GA receptor GID1A in order to clarify the relationship between structure and GA-like activity in the NSPs. The results obtained demonstrate that both a multiple-hydrogen-bond network and a "hat-shaped" hydrophobic interaction play important roles in the binding of the NSPs to GID1A. The carbonyl group of a phthalimide fragment in the NSPs acted in a similar manner to the pharmacophore group 6-COOH in GAs, forming multiple-hydrogen-bond interactions with residues Ser191 and Tyr322 in the binding domain of GID1A. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to further study the 3D quantitative structure-activity relationship (3D-QSAR) of the NSPs. It was confirmed that the GA-like activity of these NSPs is strongly linked to a few H-bond donor and acceptor field contributions of the NSPs to the H-bond interactions with GID1A. Five new NSP molecules D1-D5 were designed using the binding domain of GID1A and then docked into the receptor. D1 and D4 were shown to have good docking scores due to enhanced hydrophobic contact. We hope that these results will provide useful guidance in the rational design of new NSPs.
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Affiliation(s)
- Dongling Li
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China, 100193
| | - Shaoqing Du
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China, 100193
| | - Weiming Tan
- Engineering Research Center of Plant Growth Regulators, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China, 100193
| | - Hongxia Duan
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China, 100193.
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de Saint Germain A, Bonhomme S, Boyer FD, Rameau C. Novel insights into strigolactone distribution and signalling. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:583-9. [PMID: 23830996 DOI: 10.1016/j.pbi.2013.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 05/07/2023]
Abstract
Strigolactones (SLs), a group of small carotenoid-derived molecules, were first known for their function in the rhizosphere in both symbiotic and parasitic interactions. Most of the progress for deciphering SL biosynthesis and signalling pathways comes from the use of high branching mutants identified in several species demonstrating that SLs also play a hormonal role in plant development. How SLs are perceived by the different organisms on which they show bioactivity is a current major challenge for the growing SL research community. These molecules very likely predate the colonization of land by plants and represent a fascinating example of signalling molecules involved in key innovations during plant evolution.
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Duan H, Li D, Liu H, Liang D, Yang X. Computational insight into novel molecular recognition mechanism of different bioactive GAs and the Arabidopsis receptor GID1A. J Mol Model 2013; 19:4613-24. [PMID: 23982476 DOI: 10.1007/s00894-013-1971-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
Abstract
Gibberellin (GA) is an essential plant hormone and plays a significant role during the growth and development of the higher plants. The molecular recognition mode between GA and receptor Arabidopsis thaliana GIBBERELLIN INSENSITIVE DWARF1 A (AtGID1A) was investigated by molecular docking and dynamics simulations to clarify the selective perceived mechanism of different bioactive GA molecules to AtGID1A. The 6-COOH group of GA, especially its β configuration, was found to be an indispensable pharmacophore group for GA recognition and binding to AtGID1A. Not only does a strong salt bridge interaction between the 6β-COOH group of GA and Arg244 of AtGID1A play a very important role in the GA recognition of the receptor, but also an indirect water bridge interaction between the pharmacophore group 6β-COOH of GA and the residue Tyr322 of AtGID1A is essential for the GA binding to the receptor. The site-directed residues mutant modeling study on the receptor-binding pocket confirmed that the mutations of Arg244 and Tyr322 decreased the GA binding activity due to the disappearances of the salt bridge and the hydrogen bond interaction. The 3β-OH group of GA was well known to be necessary for the GA bioactivity due to its forming a unique hydrogen bond with Tyr127 of AtGID1A. In addition, the hydrophobic interaction between GA and AtGID1A was considered a necessary factor to lock the GA active conformation and stabilize the GA-GID1A complex structure. The novel molecular recognition mode will be beneficial in elucidating the GA regulation function on the growth and development of the higher plants.
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Affiliation(s)
- Hongxia Duan
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, People's Republic of China, 100193,
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Hao GF, Yang SG, Yang GF, Zhan CG. Computational gibberellin-binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor. J Comput Chem 2013; 34:2055-64. [PMID: 23765254 DOI: 10.1002/jcc.23355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/01/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022]
Abstract
Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. In this work, fundamental mechanism of hormone perception by receptor GID1 has been studied by performing computational simulations, revealing a new GA-binding channel of GID1 and a novel hormone perception mechanism involving only one conformational state of GID1. The novel hormone perception mechanism demonstrated here is remarkably different from the previously proposed/speculated mechanism [Murase et al., Nature 2008, 456, 459] involving two conformational states ("OPEN" and "CLOSED") of GID1. According to the new perception mechanism, GA acts as a "conformational stabilizer," rather than the previously speculated "allosteric inducer," to induce the recognition of protein DELLA by GID1. The novel mechanistic insights obtained in this study provide a new starting point for further studies on the detailed molecular mechanisms of GID1 interacting with DELLA and various hormones and for mechanism-based rational design of novel, potent growth regulators that target crops and ornamental plants.
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Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
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