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Bellino C, Herrera FE, Rodrigues D, Garay AS, Huck SV, Reinheimer R. Molecular Evolution of RAMOSA1 (RA1) in Land Plants. Biomolecules 2024; 14:550. [PMID: 38785957 PMCID: PMC11117814 DOI: 10.3390/biom14050550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood. In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here, we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein-protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, the evidence indicates that the RA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalization enabled by gene duplication.
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Affiliation(s)
- Carolina Bellino
- Fellow of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina;
| | - Fernando E. Herrera
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina; (F.E.H.); (D.R.)
| | - Daniel Rodrigues
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina; (F.E.H.); (D.R.)
| | - A. Sergio Garay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina;
| | - Sofía V. Huck
- Fellow of Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina;
| | - Renata Reinheimer
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, FCA, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina
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Khan S, Lang M. A Comprehensive Review on the Roles of Metals Mediating Insect-Microbial Pathogen Interactions. Metabolites 2023; 13:839. [PMID: 37512546 PMCID: PMC10384549 DOI: 10.3390/metabo13070839] [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: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Insects and microbial pathogens are ubiquitous and play significant roles in various biological processes, while microbial pathogens are microscopic organisms that can cause diseases in multiple hosts. Insects and microbial pathogens engage in diverse interactions, leveraging each other's presence. Metals are crucial in shaping these interactions between insects and microbial pathogens. However, metals such as Fe, Cu, Zn, Co, Mo, and Ni are integral to various physiological processes in insects, including immune function and resistance against pathogens. Insects have evolved multiple mechanisms to take up, transport, and regulate metal concentrations to fight against pathogenic microbes and act as a vector to transport microbial pathogens to plants and cause various plant diseases. Hence, it is paramount to inhibit insect-microbe interaction to control pathogen transfer from one plant to another or carry pathogens from other sources. This review aims to succinate the role of metals in the interactions between insects and microbial pathogens. It summarizes the significance of metals in the physiology, immune response, and competition for metals between insects, microbial pathogens, and plants. The scope of this review covers these imperative metals and their acquisition, storage, and regulation mechanisms in insect and microbial pathogens. The paper will discuss various scientific studies and sources, including molecular and biochemical studies and genetic and genomic analysis.
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Affiliation(s)
- Subhanullah Khan
- CAS Center for Excellence in Biotic Interactions, College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minglin Lang
- CAS Center for Excellence in Biotic Interactions, College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China
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3
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Dragone M, Grazioso R, D’Abrosca G, Baglivo I, Iacovino R, Esposito S, Paladino A, Pedone PV, Russo L, Fattorusso R, Malgieri G, Isernia C. Copper (I) or (II) Replacement of the Structural Zinc Ion in the Prokaryotic Zinc Finger Ros Does Not Result in a Functional Domain. Int J Mol Sci 2022; 23:ijms231911010. [PMID: 36232306 PMCID: PMC9569694 DOI: 10.3390/ijms231911010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
A strict interplay is known to involve copper and zinc in many cellular processes. For this reason, the results of copper’s interaction with zinc binding proteins are of great interest. For instance, copper interferences with the DNA-binding activity of zinc finger proteins are associated with the development of a variety of diseases. The biological impact of copper depends on the chemical properties of its two common oxidation states (Cu(I) and Cu(II)). In this framework, following the attention addressed to unveil the effect of metal ion replacement in zinc fingers and in zinc-containing proteins, we explore the effects of the Zn(II) to Cu(I) or Cu(II) replacement in the prokaryotic zinc finger domain. The prokaryotic zinc finger protein Ros, involved in the horizontal transfer of genes from A. tumefaciens to a host plant infected by it, belongs to a family of proteins, namely Ros/MucR, whose members have been recognized in different bacteria symbionts and pathogens of mammals and plants. Interestingly, the amino acids of the coordination sphere are poorly conserved in most of these proteins, although their sequence identity can be very high. In fact, some members of this family of proteins do not bind zinc or any other metal, but assume a 3D structure similar to that of Ros with the residues replacing the zinc ligands, forming a network of hydrogen bonds and hydrophobic interactions that surrogates the Zn-coordinating role. These peculiar features of the Ros ZF domain prompted us to study the metal ion replacement with ions that have different electronic configuration and ionic radius. The protein was intensely studied as a perfectly suited model of a metal-binding protein to study the effects of the metal ion replacement; it appeared to tolerate the Zn to Cd substitution, but not the replacement of the wildtype metal by Ni(II), Pb(II) and Hg(II). The structural characterization reported here gives a high-resolution description of the interaction of copper with Ros, demonstrating that copper, in both oxidation states, binds the protein, but the replacement does not give rise to a functional domain.
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Affiliation(s)
- Martina Dragone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Rinaldo Grazioso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D’Abrosca
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Rosa Iacovino
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sabrina Esposito
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Antonella Paladino
- Institute of Biostructures and Bioimaging, National Research Council (IBB-CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Paolo V. Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
- Correspondence:
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Li J, Zhang L, Yuan Y, Wang Q, Elbaiomy RG, Zhou W, Wu H, Soaud SA, Abbas M, Chen B, Zhao D, El-Sappah AH. In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth. Front Genet 2021; 12:770427. [PMID: 34804129 PMCID: PMC8602080 DOI: 10.3389/fgene.2021.770427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.
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Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Litian Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining, China
| | - Yibing Yuan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | | | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Hui Wu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Deming Zhao
- Yibin Academy of Agricultural Sciences, Yibin, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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Substitution of the Native Zn(II) with Cd(II), Co(II) and Ni(II) Changes the Downhill Unfolding Mechanism of Ros87 to a Completely Different Scenario. Int J Mol Sci 2020; 21:ijms21218285. [PMID: 33167398 PMCID: PMC7663847 DOI: 10.3390/ijms21218285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
The structural effects of zinc replacement by xenobiotic metal ions have been widely studied in several eukaryotic and prokaryotic zinc-finger-containing proteins. The prokaryotic zinc finger, that presents a bigger βββαα domain with a larger hydrophobic core with respect to its eukaryotic counterpart, represents a valuable model protein to study metal ion interaction with metallo-proteins. Several studies have been conducted on Ros87, the DNA binding domain of the prokaryotic zinc finger Ros, and have demonstrated that the domain appears to structurally tolerate Ni(II), albeit with important structural perturbations, but not Pb(II) and Hg(II), and it is in vitro functional when the zinc ion is replaced by Cd(II). We have previously shown that Ros87 unfolding is a two-step process in which a zinc binding intermediate converts to the native structure thorough a delicate downhill folding transition. Here, we explore the folding/unfolding behaviour of Ros87 coordinated to Co(II), Ni(II) or Cd(II), by UV-Vis, CD, DSC and NMR techniques. Interestingly, we show how the substitution of the native metal ion results in complete different folding scenarios. We found a two-state unfolding mechanism for Cd-Ros87 whose metal affinity Kd is comparable to the one obtained for the native Zn-Ros87, and a more complex mechanism for Co-Ros87 and Ni-Ros87, that show higher Kd values. Our data outline the complex cross-correlation between the protein-metal ion equilibrium and the folding mechanism proposing such an interplay as a key factor in the proper metal ion selection by a specific metallo-protein.
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Yin J, Wang L, Zhao J, Li Y, Huang R, Jiang X, Zhou X, Zhu X, He Y, He Y, Liu Y, Zhu Y. Genome-wide characterization of the C2H2 zinc-finger genes in Cucumis sativus and functional analyses of four CsZFPs in response to stresses. BMC PLANT BIOLOGY 2020; 20:359. [PMID: 32727369 PMCID: PMC7392682 DOI: 10.1186/s12870-020-02575-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/23/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUNDS C2H2-type zinc finger protein (ZFPs) form a relatively large family of transcriptional regulators in plants, and play many roles in plant growth, development, and stress response. However, the comprehensive analysis of C2H2 ZFPs in cucumber (CsZFPs) and their regulation function in cucumber are still lacking. RESULTS In the current study, the whole genome identification and characterization of CsZFPs, including the gene structure, genome localization, phylogenetic relationship, and gene expression were performed. Functional analysis of 4 selected genes by transient transformation were also conducted. A total of 129 full-length CsZFPs were identified, which could be classified into four groups according to the phylogenetic analysis. The 129 CsZFPs unequally distributed on 7 chromosomes. Promoter cis-element analysis showed that the CsZFPs might involve in the regulation of phytohormone and/or abiotic stress response, and 93 CsZFPs were predicted to be targeted by one to 20 miRNAs. Moreover, the subcellular localization analysis indicated that 10 tested CsZFPs located in the nucleus and the transcriptome profiling analysis of CsZFPs demonstrated that these genes are involved in root and floral development, pollination and fruit spine. Furthermore, the transient overexpression of Csa1G085390 and Csa7G071440 into Nicotiana benthamiana plants revealed that they could decrease and induce leave necrosis in response to pathogen attack, respectively, and they could enhance salt and drought stresses through the initial induction of H2O2. In addition, Csa4G642460 and Csa6G303740 could induce cell death after 5 days transformation. CONCLUSIONS The identification and function analysis of CsZFPs demonstrated that some key individual CsZFPs might play essential roles in response to biotic and abiotic stresses. These results could lay the foundation for understanding the role of CsZFPs in cucumber development for future genetic engineering studies.
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Affiliation(s)
- Junliang Yin
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Jiao Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Yiting Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Rong Huang
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Xinchen Jiang
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Xiaokang Zhou
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Xiongmeng Zhu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yang He
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yiqin He
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yiqing Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yongxing Zhu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
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Salih H, Odongo MR, Gong W, He S, Du X. Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development. BMC PLANT BIOLOGY 2019; 19:400. [PMID: 31510939 PMCID: PMC6739942 DOI: 10.1186/s12870-019-2003-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/30/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND C2H2-zinc finger protein family is commonly found in the plant, and it is known as the key actors in the regulation of transcription and vital component of chromatin structure. A large number of the C2H2-zinc finger gene members have not been well characterized based on their functions and structure in cotton. However, in other plants, only a few C2H2-zinc finger genes have been studied. RESULTS In this work, we performed a comprehensive analysis and identified 386, 196 and 195 C2H2-zinc finger genes in Gossypium hirsutum (upland cotton), Gossypium arboreum and Gossypium raimondii, respectively. Phylogenetic tree analysis of the C2H2-zinc finger proteins encoding the C2H2-zinc finger genes were classified into seven (7) subgroups. Moreover, the C2H2-zinc finger gene members were distributed in all cotton chromosomes though with asymmetrical distribution patterns. All the orthologous genes were detected between tetraploid and the diploid cotton, with 154 orthologous genes pair detected between upland cotton and Gossypium arboreum while 165 orthologous genes were found between upland cotton and Gossypium raimondii. Synonymous (Ks) and non-synonymous (Ka) nucleotide substitution rates (Ka/Ks) analysis indicated that the cotton C2H2-zinc finger genes were highly influenced mainly by negative selection, which maintained their protein levels after the duplication events. RNA-seq data and RT-qPCR validation of the RNA seq result revealed differential expression pattern of some the C2H2-zinc finger genes at different stages of cotton fiber development, an indication that the C2H2-zinc finger genes play an important role in initiating and regulating fiber development in cotton. CONCLUSIONS This study provides a strong foundation for future practical genome research on C2H2-zinc finger genes in upland cotton. The expression levels of C2H2-zinc finger genes family is a pointer of their involvement in various biochemical and physiological functions which are directly related to cotton fiber development during initiation and elongation stages. This work not only provides a basis for determining the nominal role of the C2H2-zinc finger genes in fiber development but also provide valuable information for characterization of potential candidate genes involved in regulation of cotton fiber development.
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Affiliation(s)
- Haron Salih
- College of life sciences, Huazhong Agricultural University, Wuhan, 430070 Hubei China
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
- Zalingei University, Central Darfur, Sudan
| | - Magwanga Richard Odongo
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/ Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Nowacka M, Fernandes H, Kiliszek A, Bernat A, Lach G, Bujnicki JM. Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com. PLoS One 2019; 14:e0214481. [PMID: 31022205 PMCID: PMC6483171 DOI: 10.1371/journal.pone.0214481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/13/2019] [Indexed: 11/18/2022] Open
Abstract
The bacteriophage Mu Com is a small zinc finger protein that binds to its cognate mom mRNA and activates its translation. The Mom protein, in turn, elicits a chemical modification (momification) of the bacteriophage genome, rendering the DNA resistant to cleavage by bacterial restriction endonucleases, and thereby protecting it from defense mechanisms of the host. We examined the basis of specificity in Com-RNA interactions by in vitro selection and probing of RNA structure. We demonstrated that Com recognizes a sequence motif within a hairpin-loop structure of its target RNA. Our data support the model of Com interaction with mom mRNA, in which Com binds to the short hairpin structure proximal to the so-called translation inhibition structure. We also observed that Com binds its target motif weakly if it is within an RNA duplex. These results suggest that the RNA structure, in addition to its sequence, is crucial for Com to recognize its target and that RNA conformational changes may constitute another level of Mom regulation. We determined a crystal structure of a Com binding site variant designed to form an RNA duplex preferentially. Our crystal model forms a 19-mer self-complementary double helix composed of the canonical and non-canonical base pairs. The helical parameters of crystalized RNA indicate why Com may bind it more weakly than a monomeric hairpin form.
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Affiliation(s)
- Martyna Nowacka
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- * E-mail: ; (JMB)
| | - Humberto Fernandes
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agata Bernat
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Grzegorz Lach
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M. Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
- * E-mail: ; (JMB)
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Chen WF, Wei XB, Rety S, Huang LY, Liu NN, Dou SX, Xi XG. Structural analysis reveals a "molecular calipers" mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat. J Biol Chem 2018; 294:142-156. [PMID: 30425099 DOI: 10.1074/jbc.ra118.003956] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/10/2018] [Indexed: 01/13/2023] Open
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies have unraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.
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Affiliation(s)
- Wei-Fei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiao-Bin Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Stephane Rety
- University Lyon, ENS de Lyon, University Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
| | - Ling-Yun Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61 Avenue du Président Wilson, F-94235 Cachan, France.
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10
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Co(II) Coordination in Prokaryotic Zinc Finger Domains as Revealed by UV-Vis Spectroscopy. Bioinorg Chem Appl 2017; 2017:1527247. [PMID: 29386985 PMCID: PMC5745721 DOI: 10.1155/2017/1527247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/03/2017] [Accepted: 10/16/2017] [Indexed: 11/23/2022] Open
Abstract
Co(II) electronic configuration allows its use as a spectroscopic probe in UV-Vis experiments to characterize the metal coordination sphere that is an essential component of the functional structure of zinc-binding proteins and to evaluate the metal ion affinities of these proteins. Here, exploiting the capability of the prokaryotic zinc finger to use different combinations of residues to properly coordinate the structural metal ion, we provide the UV-Vis characterization of Co(II) addition to Ros87 and its mutant Ros87_C27D which bears an unusual CysAspHis2 coordination sphere. Zinc finger sites containing only one cysteine have been infrequently characterized. We show for the CysAspHis2 coordination an intense d-d transition band, blue-shifted with respect to the Cys2His2 sphere. These data complemented by NMR and CD data demonstrate that the tetrahedral geometry of the metal site is retained also in the case of a single-cysteine coordination sphere.
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11
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Chang H, Chen D, Kam J, Richardson T, Drenth J, Guo X, McIntyre CL, Chai S, Rae AL, Xue GP. Abiotic stress upregulated TaZFP34 represses the expression of type-B response regulator and SHY2 genes and enhances root to shoot ratio in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:88-102. [PMID: 27717481 DOI: 10.1016/j.plantsci.2016.07.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
Q-type C2H2 zinc finger proteins (ZFPs) are plant-specific DNA-binding proteins containing a conserved QALGGH motif. This study investigated the function of abiotic stress-inducible and predominantly root-expressed Triticum aestivum ZFPs (TaZFP22, TaZFP34 and TaZFP46) with a focus on TaZFP34. Expression of TaZFP34 in roots was upregulated by high salinity, dehydration, oxidative and cold stresses. Overexpression of TaZFP34 in wheat roots resulted in an increased root-to-shoot ratio, a phenomenon observed during plant adaptation to drying soil. Expression of a number of genes which are potentially involved in modulating root growth was significantly altered in the roots of TaZFP34 overexpressing lines. In particular, the transcript levels of TaRR12B, TaRR12D and TaSHY2 that are homologues of known negative regulators of root growth were significantly reduced. Expression of shoot growth-related genes, such as GA3-ox and expansins, was downregulated in the transgenic shoots. TaZFP34 bound to (C/G)AGT(G/A)-like elements in the promoters of TaZFP34 down-regulated TaRR12D and TaSHY2 and transrepressed the reporter gene expression driven by TaRR12D and TaSHY2 promoters. Expression of the above reporter genes was also repressed by TaZFP46 and TaZFP22. These data suggest that TaZFP34 is a transcriptional repressor and is involved in modulating the root-to-shoot ratio.
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Affiliation(s)
- Hongping Chang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, PR China; CSIRO Agriculture, 306 Carmody Rd., St Lucia, QLD 4067, Australia.
| | - Dandan Chen
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, PR China; CSIRO Agriculture, 306 Carmody Rd., St Lucia, QLD 4067, Australia.
| | - Jason Kam
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Ceredigion, Wales SY23 3EB, UK.
| | - Terese Richardson
- CSIRO Agriculture, Clunies Ross Street, Canberra, ACT 2601, Australia.
| | - Janneke Drenth
- CSIRO Agriculture, 306 Carmody Rd., St Lucia, QLD 4067, Australia.
| | - Xinhong Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, PR China.
| | - C Lynne McIntyre
- CSIRO Agriculture, 306 Carmody Rd., St Lucia, QLD 4067, Australia.
| | - Shoucheng Chai
- College of Agronomy, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, PR China.
| | - Anne L Rae
- CSIRO Agriculture, 306 Carmody Rd., St Lucia, QLD 4067, Australia.
| | - Gang-Ping Xue
- CSIRO Agriculture, 306 Carmody Rd., St Lucia, QLD 4067, Australia.
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12
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D'Abrosca G, Russo L, Palmieri M, Baglivo I, Netti F, de Paola I, Zaccaro L, Farina B, Iacovino R, Pedone PV, Isernia C, Fattorusso R, Malgieri G. The (unusual) aspartic acid in the metal coordination sphere of the prokaryotic zinc finger domain. J Inorg Biochem 2016; 161:91-8. [PMID: 27238756 DOI: 10.1016/j.jinorgbio.2016.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 11/29/2022]
Abstract
The possibility of choices of protein ligands and coordination geometries leads to diverse Zn(II) binding sites in zinc-proteins, allowing a range of important biological roles. The prokaryotic Cys2His2 zinc finger domain (originally found in the Ros protein from Agrobacterium tumefaciens) tetrahedrally coordinates zinc through two cysteine and two histidine residues and it does not adopt a correct fold in the absence of the metal ion. Ros is the first structurally characterized member of a family of bacterial proteins that presents several amino acid changes in the positions occupied in Ros by the zinc coordinating residues. In particular, the second position is very often occupied by an aspartic acid although the coordination of structural zinc by an aspartate in eukaryotic zinc fingers is very unusual. Here, by appropriately mutating the protein Ros, we characterize the aspartate role within the coordination sphere of this family of proteins demonstrating how the presence of this residue only slightly perturbs the functional structure of the prokaryotic zinc finger domain while it greatly influences its thermodynamic properties.
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Affiliation(s)
- Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Fortuna Netti
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ivan de Paola
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Laura Zaccaro
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Rosa Iacovino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy.
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13
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Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
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Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
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14
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Bossak K, Goch W, Piątek K, Frączyk T, Poznański J, Bonna A, Keil C, Hartwig A, Bal W. Unusual Zn(II) Affinities of Zinc Fingers of Poly(ADP-ribose) Polymerase 1 (PARP-1) Nuclear Protein. Chem Res Toxicol 2015; 28:191-201. [DOI: 10.1021/tx500320f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Karolina Bossak
- Institute of Biochemistry
and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Wojciech Goch
- Institute of Biochemistry
and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Piątek
- Institute of Biochemistry
and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz Frączyk
- Institute of Biochemistry
and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry
and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Arkadiusz Bonna
- Institute of Biochemistry
and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Claudia Keil
- Institute of Applied Biosciences, Department of Food
Chemistry and Toxicology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Andrea Hartwig
- Institute of Applied Biosciences, Department of Food
Chemistry and Toxicology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Wojciech Bal
- Institute of Biochemistry
and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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15
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Russo L, Palmieri M, Caso JV, D'Abrosca G, Diana D, Malgieri G, Baglivo I, Isernia C, Pedone PV, Fattorusso R. Towards understanding the molecular recognition process in prokaryotic zinc-finger domain. Eur J Med Chem 2014; 91:100-8. [PMID: 25240418 DOI: 10.1016/j.ejmech.2014.09.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
Eukaryotic Cys2His2 zinc finger domain is one of the most common and important structural motifs involved in protein-DNA interaction. The recognition motif is characterized by the tetrahedral coordination of a zinc ion by conserved cysteine and histidine residues. We have characterized the prokaryotic Cys2His2 zinc finger motif, included in the DNA binding region (Ros87) of Ros protein from Agrobacterium tumefaciens, demonstrating that, although possessing a similar zinc coordination sphere, this domain presents significant differences from its eukaryotic counterpart. Furthermore, basic residues flanking the zinc binding region on either side have been demonstrated, by Electrophoretic Mobility Shift Assay (EMSA) experiments, to be essential for Ros DNA binding. In spite of this wealth of knowledge, the structural details of the mechanism through which the prokaryotic zinc fingers recognize their target genes are still unclear. Here, to gain insights into the molecular DNA recognition process of prokaryotic zinc finger domains we applied a strategy in which we performed molecular docking studies using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations data. The results demonstrate that the MD ensemble provides a reasonable picture of Ros87 backbone dynamics in solution. The Ros87-DNA model indicates that the interaction involves the first two residue of the first α-helix, and several residues located in the basic regions flanking the zinc finger domain. Interestingly, the prokaryotic zinc finger domain, mainly with the C-terminal tail that is wrapped around the DNA, binds a more extended recognition site than the eukaryotic counterpart. Our analysis demonstrates that the introduction of the protein flexibility in docking studies can improve, in terms of accuracy, the quality of the obtained models and could be particularly useful for protein showing high conformational heterogeneity as well as for computational drug design applications.
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Jolanda Valentina Caso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Donatella Diana
- Institute of Biostructures and Bioimaging -CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technology, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.
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16
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Malgieri G, Palmieri M, Esposito S, Maione V, Russo L, Baglivo I, de Paola I, Milardi D, Diana D, Zaccaro L, Pedone PV, Fattorusso R, Isernia C. Zinc to cadmium replacement in the prokaryotic zinc-finger domain. Metallomics 2014; 6:96-104. [PMID: 24287553 DOI: 10.1039/c3mt00208j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Given the similar chemical properties of zinc and cadmium, zinc finger domains have been often proposed as mediators of the toxic and carcinogenic effects exerted by this xenobiotic metal. The effects of zinc replacement by cadmium in different eukaryotic zinc fingers have been reported. In the present work, to evaluate the effects of such substitution in the prokaryotic zinc finger, we report a detailed study of its functional and structural consequences on the Ros DNA binding domain (Ros87). We show that this protein, which bears important structural differences with respect to the eukaryotic domains, appears to structurally tolerate the zinc to cadmium substitution and the presence of cadmium does not affect the DNA binding activity of the protein. Moreover, we show for the first time how zinc to cadmium replacement can also take place in a cellular context. Our findings both complement and extend previous results obtained for different eukaryotic zinc fingers, suggesting that metal substitution in zinc fingers may be of relevance to the toxicity and/or carcinogenicity mechanisms of this metal.
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Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
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17
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Chan KL, Bakman I, Marts AR, Batir Y, Dowd TL, Tierney D, Gibney BR. Characterization of the Zn(II) binding properties of the human Wilms' tumor suppressor protein C-terminal zinc finger peptide. Inorg Chem 2014; 53:6309-20. [PMID: 24893204 PMCID: PMC4066921 DOI: 10.1021/ic500862b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/19/2022]
Abstract
Zinc finger proteins that bind Zn(II) using a Cys2His2 coordination motif within a ββα protein fold are the most abundant DNA binding transcription factor domains in eukaryotic systems. These classic zinc fingers are typically unfolded in the apo state and spontaneously fold into their functional ββα folds upon incorporation of Zn(II). These metal-induced protein folding events obscure the free energy cost of protein folding by coupling the protein folding and metal-ion binding thermodynamics. Herein, we determine the formation constant of a Cys2His2/ββα zinc finger domain, the C-terminal finger of the Wilms' tumor suppressor protein (WT1-4), for the purposes of determining its free energy cost of protein folding. Measurements of individual conditional dissociation constants, Kd values, at pH values from 5 to 9 were determined using fluorescence spectroscopy by direct or competition titration. Potentiometric titrations of apo-WT1-4 followed by NMR spectroscopy provided the intrinsic pKa values of the Cys2His2 residues, and corresponding potentiometric titrations of Zn(II)-WT1-4 followed by fluorescence spectroscopy yielded the effective pKa(eff) values of the Cys2His2 ligands bound to Zn(II). The Kd, pKa, and pKa(eff) values were combined in a minimal, complete equilibrium model to yield the pH-independent formation constant value for Zn(II)-WT1-4, Kf(ML) value of 7.5 × 10(12) M(-1), with a limiting Kd value of 133 fM. This shows that Zn(II) binding to the Cys2His2 site in WT1-4 provides at least -17.6 kcal/mol in driving force to fold the protein scaffold. A comparison of the conditional dissociation constants of Zn(II)-WT1-4 to those from the model peptide Zn(II)-GGG-Cys2His2 over the pH range 5.0 to 9.0 and a comparison of their pH-independent Kf(ML) values demonstrates that the free energy cost of protein folding in WT1-4 is less than +2.1 kcal/mol. These results validate our GGG model system for determining the cost of protein folding in natural zinc finger proteins and support the conclusion that the cost of protein folding in most zinc finger proteins is ≤+4.2 kcal/mol, a value that pales in comparison to the free energy contribution of Zn(II) binding, -17.6 kcal/mol.
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Affiliation(s)
- Ka Lam Chan
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Inna Bakman
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - Amy R. Marts
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yuksel Batir
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Terry L. Dowd
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - David
L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Brian R. Gibney
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
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18
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Grandperret V, Nicolas-Francès V, Wendehenne D, Bourque S. Type-II histone deacetylases: elusive plant nuclear signal transducers. PLANT, CELL & ENVIRONMENT 2014; 37:1259-69. [PMID: 24236403 DOI: 10.1111/pce.12236] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/04/2013] [Accepted: 11/10/2013] [Indexed: 05/20/2023]
Abstract
Since the beginning of the 21st century, numerous studies have concluded that the plant cell nucleus is one of the cellular compartments that define the specificity of the cellular response to an external stimulus or to a specific developmental stage. To that purpose, the nucleus contains all the enzymatic machinery required to carry out a wide variety of nuclear protein post-translational modifications (PTMs), which play an important role in signal transduction pathways leading to the modulation of specific sets of genes. PTMs include protein (de)acetylation which is controlled by the antagonistic activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Regarding protein deacetylation, plants are of particular interest: in addition to the RPD3-HDA1 and Sir2 HDAC families that they share with other eukaryotic organisms, plants have developed a specific family called type-II HDACs (HD2s). Interestingly, these HD2s are well conserved in plants and control fundamental biological processes such as seed germination, flowering or the response to pathogens. The aim of this review was to summarize current knowledge regarding this fascinating, but still poorly understood nuclear protein family.
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Affiliation(s)
- Vincent Grandperret
- Pôle Mécanisme et Gestion des Interactions Plantes-microorganismes - ERL CNRS 6300, Université de Bourgogne, UMR 1347 Agroécologie, 17 rue Sully, BP 86510, Dijon cedex, 21065, France
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19
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Palmieri M, Russo L, Malgieri G, Esposito S, Baglivo I, Rivellino A, Farina B, de Paola I, Zaccaro L, Milardi D, Isernia C, Pedone PV, Fattorusso R. Deciphering the zinc coordination properties of the prokaryotic zinc finger domain: The solution structure characterization of Ros87 H42A functional mutant. J Inorg Biochem 2014; 131:30-6. [DOI: 10.1016/j.jinorgbio.2013.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 11/26/2022]
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20
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Baglivo I, Palmieri M, Rivellino A, Netti F, Russo L, Esposito S, Iacovino R, Farina B, Isernia C, Fattorusso R, Pedone PV, Malgieri G. Molecular strategies to replace the structural metal site in the prokaryotic zinc finger domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:497-504. [PMID: 24389235 DOI: 10.1016/j.bbapap.2013.12.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/20/2013] [Accepted: 12/24/2013] [Indexed: 11/18/2022]
Abstract
The specific arrangement of secondary elements in a local motif often totally relies on the formation of coordination bonds between metal ions and protein ligands. This is typified by the ~30 amino acid eukaryotic zinc finger motif in which a β-sheet and an α-helix are clustered around a zinc ion by various combinations of four ligands. The prokaryotic zinc finger domain (found in the Ros protein from Agrobacterium tumefaciens) is different from the eukaryotic counterpart as it consists of 58 amino acids arranged in a βββαα topology stabilized by a 15-residue hydrophobic core. Also, this domain tetrahedrally coordinates zinc and unfolds in the absence of the metal ion. The characterization of proteins belonging to the Ros homologs family has however shown that the prokaryotic zinc finger domain can overcome the metal requirement to achieve the same fold and DNA-binding activity. In the present work, two zinc-lacking Ros homologs (Ml4 and Ml5 proteins) have been thoroughly characterized using bioinformatics, biochemical and NMR techniques. We show how in these proteins a network of hydrogen bonds and hydrophobic interactions surrogate the zinc coordination role in the achievement of the same functional fold.
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Affiliation(s)
- Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alessia Rivellino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy
| | - Fortuna Netti
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sabrina Esposito
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy
| | - Rosa Iacovino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy; Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy; Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100 Caserta, Italy.
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Netti F, Malgieri G, Esposito S, Palmieri M, Baglivo I, Isernia C, Omichinski JG, Pedone PV, Lartillot N, Fattorusso R. An Experimentally Tested Scenario for the Structural Evolution of Eukaryotic Cys2His2 Zinc Fingers from Eubacterial Ros Homologs. Mol Biol Evol 2013; 30:1504-13. [DOI: 10.1093/molbev/mst068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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23
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Palmieri M, Malgieri G, Russo L, Baglivo I, Esposito S, Netti F, Del Gatto A, de Paola I, Zaccaro L, Pedone PV, Isernia C, Milardi D, Fattorusso R. Structural Zn(II) Implies a Switch from Fully Cooperative to Partly Downhill Folding in Highly Homologous Proteins. J Am Chem Soc 2013; 135:5220-8. [DOI: 10.1021/ja4009562] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maddalena Palmieri
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Luigi Russo
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Sabrina Esposito
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Fortuna Netti
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Ivan de Paola
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging-CNR (Naples), Via Mezzocannone 16, 80134
Naples, Italy
| | - Paolo V. Pedone
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Carla Isernia
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
| | - Danilo Milardi
- Institute of Biostructures and Bioimaging-CNR (Catania), Viale A. Doria 6, 95125
Catania, Italy
| | - Roberto Fattorusso
- Department of Environmental,
Biological and Pharmaceutical Science and Technology, Second University of Naples, Via Vivaldi 43, 81100
Caserta, Italy
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24
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Barraud P, Schubert M, Allain FHT. A strong 13C chemical shift signature provides the coordination mode of histidines in zinc-binding proteins. JOURNAL OF BIOMOLECULAR NMR 2012; 53:93-101. [PMID: 22528293 DOI: 10.1007/s10858-012-9625-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/30/2012] [Indexed: 05/31/2023]
Abstract
Zinc is the second most abundant metal ion incorporated in proteins, and is in many cases a crucial component of protein three-dimensional structures. Zinc ions are frequently coordinated by cysteine and histidine residues. Whereas cysteines bind to zinc via their unique S(γ) atom, histidines can coordinate zinc with two different coordination modes, either N(δ1) or N(ε2) is coordinating the zinc ion. The determination of this coordination mode is crucial for the accurate structure determination of a histidine-containing zinc-binding site by NMR. NMR chemical shifts contain a vast amount of information on local electronic and structural environments and surprisingly their utilization for the determination of the coordination mode of zinc-ligated histidines has been limited so far to (15)N nuclei. In the present report, we observed that the (13)C chemical shifts of aromatic carbons in zinc-ligated histidines represent a reliable signature of their coordination mode. Using a statistical analysis of (13)C chemical shifts, we show that (13)C(δ2) chemical shift is sensitive to the histidine coordination mode and that the chemical shift difference δ{(13)C(ε1)} - δ{(13)C(δ2)} provides a reference-independent marker of this coordination mode. The present approach allows the direct determination of the coordination mode of zinc-ligated histidines even with non-isotopically enriched protein samples and without any prior structural information.
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Affiliation(s)
- Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, 8093 Zurich, Switzerland.
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25
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Musumeci D, Bucci EM, Roviello GN, Sapio R, Valente M, Moccia M, Bianchi ME, Pedone C. DNA-based strategies for blocking HMGB1 cytokine activity: design, synthesis and preliminary in vitro/in vivo assays of DNA and DNA-like duplexes. MOLECULAR BIOSYSTEMS 2011; 7:1742-52. [PMID: 21431162 DOI: 10.1039/c1mb05009e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this work we report the design and synthesis of kinked oligonucleotide duplexes as potential inhibitors of HMGB1, a cytokine which triggers a broad range of immunological effects. We found that the designed ligands can interact with HMGB1, as evidenced by circular dichroism spectroscopy, and are able to block some extracellular effects induced by the protein, such as cellular proliferation and migration, as we demonstrated by in vitro biological assays. After selecting the most stable and active kinked duplex, we synthesized the corresponding PNA/DNA chimeric duplex which resulted to be more resistant to enzymatic degradation, and showed a biological activity comparable to that of the natural duplex. Preliminary in vivo assays in a mouse inflammatory model, showed a significant decrease of the mortality after administration of the PNA/DNA kinked duplex to LPS-treated mice.
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Affiliation(s)
- Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy.
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26
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Horigome A, Nagasawa N, Ikeda K, Ito M, Itoh JI, Nagato Y. Rice open beak is a negative regulator of class 1 knox genes and a positive regulator of class B floral homeotic gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:724-736. [PMID: 19207212 DOI: 10.1111/j.1365-313x.2009.03823.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Numerous genes are involved in the regulation of plant development, including those that regulate floral homeotic genes, We identified two recessive allelic rice mutants, open beak-1 (opb-1) and opb-2, which exhibited pleiotropic defects in leaf morphogenesis, inflorescence architecture, and floral organ identity. Abnormal cell proliferation was observed in the leaves and spikelets, and ectopic or overexpression of several class 1 knox genes was detected; thus, the abnormal cell proliferation in opb mutants is probably caused by ectopic class 1 knox gene expression. The opb mutants also had defects in floral organ identity, resulting in the development of mosaic organs, including gluminous lodicules, staminoid lodicules, and pistiloid stamens. These results, together with the reduced expression of a class B gene, indicate that OPB positively regulates the expression of class B genes. Map-based cloning revealed that OPB encodes a transcription factor that is orthologous to the Arabidopsis JAGGED gene and is expressed in leaf primordia, inflorescence meristem, rachis branch meristems, floral meristem, and floral organ primordia. Taken together, our data suggest that the OPB gene affects cellular proliferation and floral organ identity through the regulation of class 1 knox genes and floral homeotic genes.
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Affiliation(s)
- Ayako Horigome
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
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27
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Baglivo I, Russo L, Esposito S, Malgieri G, Renda M, Salluzzo A, Di Blasio B, Isernia C, Fattorusso R, Pedone PV. The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains. Proc Natl Acad Sci U S A 2009; 106:6933-8. [PMID: 19369210 PMCID: PMC2678482 DOI: 10.1073/pnas.0810003106] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Indexed: 11/18/2022] Open
Abstract
The recent characterization of the prokaryotic Cys(2)His(2) zinc-finger domain, identified in Ros protein from Agrobacterium tumefaciens, has demonstrated that, although possessing a similar zinc coordination sphere, this domain is structurally very different from its eukaryotic counterpart. A search in the databases has identified approximately 300 homologues with a high sequence identity to the Ros protein, including the amino acids that form the extensive hydrophobic core in Ros. Surprisingly, the Cys(2)His(2) zinc coordination sphere is generally poorly conserved in the Ros homologues, raising the question of whether the zinc ion is always preserved in these proteins. Here, we present a functional and structural study of a point mutant of Ros protein, Ros(56-142)C82D, in which the second coordinating cysteine is replaced by an aspartate, 5 previously-uncharacterized representative Ros homologues from Mesorhizobium loti, and 2 mutants of the homologues. Our results indicate that the prokaryotic zinc-finger domain, which in Ros protein tetrahedrally coordinates Zn(II) through the typical Cys(2)His(2) coordination, in Ros homologues can either exploit a CysAspHis(2) coordination sphere, previously never described in DNA binding zinc finger domains to our knowledge, or lose the metal, while still preserving the DNA-binding activity. We demonstrate that this class of prokaryotic zinc-finger domains is structurally very adaptable, and surprisingly single mutations can transform a zinc-binding domain into a nonzinc-binding domain and vice versa, without affecting the DNA-binding ability. In light of our findings an evolutionary link between the prokaryotic and eukaryotic zinc-finger domains, based on bacteria-to-eukaryota horizontal gene transfer, is discussed.
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Affiliation(s)
- Ilaria Baglivo
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Luigi Russo
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Sabrina Esposito
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Gaetano Malgieri
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Mario Renda
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Antonio Salluzzo
- Department of Environment, Global Change, and Sustainable Development, Portici Research Center, Italian National Agency for New Technologies, Energy, and the Environment, Via Vecchio Macello, 80055 Portici, Italy
| | - Benedetto Di Blasio
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Carla Isernia
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Roberto Fattorusso
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
| | - Paolo V. Pedone
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via Vivaldi 43, 81100 Caserta, Italy; and
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Kam J, Gresshoff PM, Shorter R, Xue GP. The Q-type C2H2 zinc finger subfamily of transcription factors in Triticum aestivum is predominantly expressed in roots and enriched with members containing an EAR repressor motif and responsive to drought stress. PLANT MOLECULAR BIOLOGY 2008; 67:305-322. [PMID: 18347915 DOI: 10.1007/s11103-008-9319-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 03/04/2008] [Indexed: 05/26/2023]
Abstract
Q-type C2H2 zinc finger proteins (ZFPs) form a subfamily of transcription factors that contain a plant-specific QALGGH amino acid motif. A total of 47 expressed Q-type C2H2 zinc finger genes in bread wheat (Triticum aestivum) (designated TaZFP) were identified from the current databases. Protein sequence analysis for the presence of ERF-associated amphiphilic repressor (EAR) motif sequences from known transcriptional repressors revealed that 26% of the TaZFP subfamily members contain an EAR motif. Quantitative RT-PCR analysis of the mRNA distribution of 44 TaZFP genes in various organs revealed that 30 genes were predominantly expressed in the roots. The majority of the TaZFP genes showed significant changes in their mRNA levels during leaf development and aging. Expression of 37 TaZFP genes in the leaves and roots responded to drought stress at least in one organ with 74% of the drought-responsive TaZFP genes being down-regulated in the drought-stressed roots. In contrast, only 6 out of the 44 TaZFP genes showed expression changes in the leaves with sucrose treatment. Expression of 50% of the drought-responsive TaZFP genes in the leaves (16 genes analysed) did not respond to ABA treatment, indicating that some TaZFP genes are involved in ABA-independent signalling pathways. These results indicate that the Q-type TaZFP subfamily is likely to have an important role in wheat roots and is enriched with members that are potentially involved in regulating cellular activities during changes of the physiological status of plant cells, as it occurs during drought stress or leaf development/aging.
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Affiliation(s)
- Jason Kam
- CSIRO Plant Industry, St. Lucia, QLD 4067, Australia
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29
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The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain. Proc Natl Acad Sci U S A 2007; 104:17341-6. [PMID: 17956987 DOI: 10.1073/pnas.0706659104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first putative prokaryotic Cys(2)His(2) zinc-finger domain has been identified in the transcriptional regulator Ros from Agrobacterium tumefaciens, indicating that the Cys(2)His(2) zinc-finger domain, originally thought to be confined to the eukaryotic kingdom, could be widespread throughout the living kingdom from eukaryotic, both animal and plant, to prokaryotic. In this article we report the NMR solution structure of Ros DNA-binding domain (Ros87), providing 79 structural characterization of a prokaryotic Cys(2)His(2) zinc-finger domain. The NMR structure of Ros87 shows that the putative prokaryotic Cys(2)His(2) zinc-finger sequence is indeed part of a significantly larger zinc-binding globular domain that possesses a novel protein fold very different from the classical fold reported for the eukaryotic classical zinc-finger. The Ros87 globular domain consists of 58 aa (residues 9-66), is arranged in a betabetabetaalphaalpha topology, and is stabilized by an extensive 15-residue hydrophobic core. A backbone dynamics study of Ros87, based on (15)N R(1), (15)N R(2), and heteronuclear (15)N-{(1)H}-NOE measurements, has further confirmed that the globular domain is uniformly rigid and flanked by two flexible tails. Mapping of the amino acids necessary for the DNA binding onto Ros87 structure reveals the protein surface involved in the DNA recognition mechanism of this new zinc-binding protein domain.
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30
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Uehara Y, Takahashi Y, Berberich T, Miyazaki A, Takahashi H, Matsui K, Ohme-Takagi M, Saitoh H, Terauchi R, Kusano T. Tobacco ZFT1, a transcriptional repressor with a Cys2/His2 type zinc finger motif that functions in spermine-signaling pathway. PLANT MOLECULAR BIOLOGY 2005; 59:435-48. [PMID: 16235109 DOI: 10.1007/s11103-005-0272-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Accepted: 06/27/2005] [Indexed: 05/04/2023]
Abstract
We previously proposed that a spermine (Spm)-mediated signal transduction pathway is involved in the hypersensitive response induced by Tobacco mosaic virus (TMV) in tobacco plants. To identify regulatory component(s) of this pathway, we surveyed a tobacco cDNA library and found that the ZFT1 gene, which encodes a Cys2/His2 type zinc-finger protein, is Spm-responsive. ZFT1 was not induced by two other polyamines, putrescine and spermidine, or by salicylic acid (SA), jasmonic acid or ethylene. Furthermore, ZFT1 was upregulated in TMV- inoculated tobacco plants in an N gene-dependent manner. Notably, induction of ZFT1 by Spm and by TMV infection was unimpaired in NahG-transgenic tobacco plants, indicating that cross-talk with an SA signaling pathway is not involved in this response. Within the Spm-signaling pathway, we found that ZFT1 functioned downstream of both mitochondrial dysfunction and mitogen-activated protein kinase activation. The ZFT1 protein has two zinc finger motifs and shows a high degree of similarity to ZPT2-3 in petunia and SCOF1 in soybean. However, unlike the latter two proteins, ZFT1 binds to the EP1S sequence and functions as a transcription repressor. Moreover, interestingly, ZFT1 overexpression rendered tobacco plants more tolerant to TMV. Based on the results presented here, we propose that ZFT1 functions as a transcription repressor in a Spm signaling pathway, thereby accelerating necrotic local region formation in tobacco leaves.
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Affiliation(s)
- Yukiko Uehara
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, 980-8577, Aoba, Sendai, Miyagi, Japan
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31
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Holmes-Davis R, Li G, Jamieson AC, Rebar EJ, Liu Q, Kong Y, Case CC, Gregory PD. Gene regulation in planta by plant-derived engineered zinc finger protein transcription factors. PLANT MOLECULAR BIOLOGY 2005; 57:411-423. [PMID: 15830130 DOI: 10.1007/s11103-004-7820-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Accepted: 12/20/2004] [Indexed: 05/24/2023]
Abstract
The ability to modify plant traits is of great commercial potential in agricultural biotechnology. To this end we have engineered plant-based zinc finger protein transcription factors (ZFP TFs) that minimize the use of non-plant DNA sequences. This novel architecture supports the use of tandem arrays of zinc-finger DNA recognition domains such that the ZFP TF binds a contiguous DNA target site - thus emulating the design of ZFP TFs described previously for mammalian gene regulation. We show that this plant-based ZFP TF architecture supports high affinity DNA binding while allowing the specificity of the DNA-protein interaction to be determined by the amino acid sequences of the recognition helices. This plant-based backbone thus supports the use of previously characterized DNA recognition helices originally identified in a mammalian ZFP context without using mammalian DNA sequences. Moreover, we show that plant-based ZFP TFs employing this new architecture can up-regulate endogenous ADH activity by > 20-fold in transgenic Arabidopsis. Thus plant-based ZFP TFs are shown to be potent regulators of gene expression in vivo.
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32
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Matousek WM, Alexandrescu AT. NMR structure of the C-terminal domain of SecA in the free state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1702:163-71. [PMID: 15488768 DOI: 10.1016/j.bbapap.2004.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2004] [Revised: 08/14/2004] [Accepted: 08/17/2004] [Indexed: 11/18/2022]
Abstract
SecA is an integral component of the prokaryotic Sec preprotein secretory translocase system. We report here the solution NMR structure of a fragment corresponding to the C-terminal domain of Escherichia coli SecA. In the presence of Zn2+, the fragment adopts a shortened version of the classic betabetaalpha zinc finger fold. The isolated C-terminal domain shows substantial differences from the X-ray structure of a homologous SecA domain bound to the chaperone-like cofactor SecB. The differences between the structures of the free and bound forms suggest that binding to SecB causes a perturbation of the C-terminal domain's intrinsically favored betabetaalpha fold.
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Affiliation(s)
- William M Matousek
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, U-3125, Storrs, CT 06269-3125, USA
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33
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Englbrecht CC, Schoof H, Böhm S. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 2004; 5:39. [PMID: 15236668 PMCID: PMC481060 DOI: 10.1186/1471-2164-5-39] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 07/05/2004] [Indexed: 11/17/2022] Open
Abstract
Background The classical C2H2 zinc finger domain is involved in a wide range of functions and can bind to DNA, RNA and proteins. The comparison of zinc finger proteins in several eukaryotes has shown that there is a lot of lineage specific diversification and expansion. Although the number of characterized plant proteins that carry the classical C2H2 zinc finger motifs is growing, a systematic classification and analysis of a plant genome zinc finger gene set is lacking. Results We found through in silico analysis 176 zinc finger proteins in Arabidopsis thaliana that hence constitute the most abundant family of putative transcriptional regulators in this plant. Only a minority of 33 A. thaliana zinc finger proteins are conserved in other eukaryotes. In contrast, the majority of these proteins (81%) are plant specific. They are derived from extensive duplication events and form expanded families. We assigned the proteins to different subgroups and families and focused specifically on the two largest and evolutionarily youngest families (A1 and C1) that are suggested to be primarily involved in transcriptional regulation. The newly defined family A1 (24 members) comprises proteins with tandemly arranged zinc finger domains. Family C1 (64 members), earlier described as the EPF-family in Petunia, comprises proteins with one isolated or two to five dispersed fingers and a mostly invariant QALGGH motif in the zinc finger helices. Based on the amino acid pattern in these helices we could describe five different signature sequences prevalent in C1 zinc finger domains. We also found a number of non-finger domains that are conserved in these families. Conclusions Our analysis of the few evolutionarily conserved zinc finger proteins of A. thaliana suggests that most of them could be involved in ancient biological processes like RNA metabolism and chromatin-remodeling. In contrast, the majority of the unique A. thaliana zinc finger proteins are known or suggested to be involved in transcriptional regulation. They exhibit remarkable differences in the features of their zinc finger sequences and zinc finger arrangements compared to animal zinc finger proteins. The different zinc finger helix signatures we found in family C1 may have important implications for the sequence specific DNA recognition and allow inferences about the evolution of the members in this family.
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Affiliation(s)
- Claudia C Englbrecht
- GSF-Forschungszentrum für Umwelt und Gesundheit, Institut für Bioinformatik, Ingolstädter Landstrasse1, D-85764 Neuherberg, Germany
| | - Heiko Schoof
- Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D-85354 Freising-Weihenstephan, Germany
| | - Siegfried Böhm
- Max-Delbrück-Centrum für Molekulare Medizin, Department of Genetics, Bioinformatics and Structural Biology, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany
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Ohno CK, Reddy GV, Heisler MGB, Meyerowitz EM. The Arabidopsis JAGGED gene encodes a zinc finger protein that promotes leaf tissue development. Development 2004; 131:1111-22. [PMID: 14973281 DOI: 10.1242/dev.00991] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Important goals in understanding leaf development are to identify genes involved in pattern specification, and also genes that translate this information into cell types and tissue structure. Loss-of-function mutations at the JAGGED (JAG) locus result in Arabidopsisplants with abnormally shaped lateral organs including serrated leaves, narrow floral organs, and petals that contain fewer but more elongate cells. jag mutations also suppress bract formation in leafy,apetala1 and apetala2 mutant backgrounds. The JAG gene was identified by map-based cloning to be a member of the zinc finger family of plant transcription factors and encodes a protein similar in structure to SUPERMAN with a single C2H2-type zinc finger, a proline-rich motif and a short leucine-rich repressor motif. JAG mRNA is localized to lateral organ primordia throughout the plant but is not found in the shoot apical meristem. Misexpression of JAG results in leaf fusion and the development of ectopic leaf-like outgrowth from both vegetative and floral tissues. Thus, JAG is necessary for proper lateral organ shape and is sufficient to induce the proliferation of lateral organ tissue.
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Affiliation(s)
- Carolyn K Ohno
- Division of Biology 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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