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Gupta P, Makowski EK, Kumar S, Zhang Y, Scheer JM, Tessier PM. Antibodies with Weakly Basic Isoelectric Points Minimize Trade-offs between Formulation and Physiological Colloidal Properties. Mol Pharm 2022; 19:775-787. [PMID: 35108018 PMCID: PMC9350878 DOI: 10.1021/acs.molpharmaceut.1c00373] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The widespread interest in antibody therapeutics has led to much focus on identifying antibody candidates with favorable developability properties. In particular, there is broad interest in identifying antibody candidates with highly repulsive self-interactions in standard formulations (e.g., low ionic strength buffers at pH 5-6) for high solubility and low viscosity. Likewise, there is also broad interest in identifying antibody candidates with low levels of non-specific interactions in physiological solution conditions (PBS, pH 7.4) to promote favorable pharmacokinetic properties. To what extent antibodies that possess both highly repulsive self-interactions in standard formulations and weak non-specific interactions in physiological solution conditions can be systematically identified remains unclear and is a potential impediment to successful therapeutic drug development. Here, we evaluate these two properties for 42 IgG1 variants based on the variable fragments (Fvs) from four clinical-stage antibodies and complementarity-determining regions from 10 clinical-stage antibodies. Interestingly, we find that antibodies with the strongest repulsive self-interactions in a standard formulation (pH 6 and 10 mM histidine) display the strongest non-specific interactions in physiological solution conditions. Conversely, antibodies with the weakest non-specific interactions under physiological conditions display the least repulsive self-interactions in standard formulations. This behavior can be largely explained by the antibody isoelectric point, as highly basic antibodies that are highly positively charged under standard formulation conditions (pH 5-6) promote repulsive self-interactions that mediate high colloidal stability but also mediate strong non-specific interactions with negatively charged biomolecules at physiological pH and vice versa for antibodies with negatively charged Fv regions. Therefore, IgG1s with weakly basic isoelectric points between 8 and 8.5 and Fv isoelectric points between 7.5 and 9 typically display the best combinations of strong repulsive self-interactions and weak non-specific interactions. We expect that these findings will improve the identification and engineering of antibody candidates with drug-like biophysical properties.
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Affiliation(s)
- Priyanka Gupta
- Biochemistry and Biophysics Department, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Emily K Makowski
- Department of Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sandeep Kumar
- Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States
| | - Yulei Zhang
- Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Justin M Scheer
- Biotherapeutics Molecule Discovery Department, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, Connecticut 06877, United States.,Janssen R&D, South San Francisco, California 94080, United States
| | - Peter M Tessier
- Biochemistry and Biophysics Department, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department of Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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2
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Math RK, Mudennavar N, Javaregowda PK, Savanur A. In Silico Comparative Analysis of the Functional, Structural, and Evolutionary Properties of SARS-CoV-2 Variant S pike Proteins. JMIR Bioinform Biotech 2022; 3:e37391. [PMID: 35669291 PMCID: PMC9158474 DOI: 10.2196/37391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/25/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND A recent global outbreak of COVID-19 caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) created a pandemic and emerged as a potential threat to humanity. The analysis of virus genetic composition has revealed that the spike protein, one of the major structural proteins, facilitates the entry of the virus to host cells. OBJECTIVE The spike protein has become the main target for prophylactics and therapeutics studies. Here, we compared the spike proteins of SARS-CoV-2 variants using bioinformatics tools. METHODS The spike protein sequences of wild-type SARS-CoV-2 and its 6 variants-D614G, alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2), gamma (P.1), and omicron (B.1.1.529)-were retrieved from the NCBI database. The ClustalX program was used to sequence multiple alignment and perform mutational analysis. Several online bioinformatics tools were used to predict the physiological, immunological, and structural features of the spike proteins of SARS-CoV-2 variants. A phylogenetic tree was constructed using CLC software. Statistical analysis of the data was done using jamovi 2 software. RESULTS Multiple sequence analysis revealed that the P681R mutation in the delta variant, which changed an amino acid from histidine (H) to arginine (R), made the protein more alkaline due to arginine's high pKa value (12.5) compared to histidine's (6.0). Physicochemical properties revealed the relatively higher isoelectric point (7.34) and aliphatic index (84.65) of the delta variant compared to other variants. Statistical analysis of the isoelectric point, antigenicity, and immunogenicity of all the variants revealed significant correlation, with P values ranging from <.007 to .04. The generation of a 2D gel map showed the separation of the delta spike protein from a grouping of the other variants. The phylogenetic tree of the spike proteins showed that the delta variant was close to and a mix of the Rousettus bat coronavirus and MERS-CoV. CONCLUSIONS The comparative analysis of SARS-CoV-2 variants revealed that the delta variant is more aliphatic in nature, which provides more stability to it and subsequently influences virus behavior.
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Affiliation(s)
- Renukaradhya K Math
- SDM Research Institute for Biomedical Sciences Shri Dharmasthala Manjunatheshwara University Dharwad India
| | - Nayana Mudennavar
- SDM Research Institute for Biomedical Sciences Shri Dharmasthala Manjunatheshwara University Dharwad India
| | | | - Ambuja Savanur
- SDM Research Institute for Biomedical Sciences Shri Dharmasthala Manjunatheshwara University Dharwad India
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3
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Heffron J, Mayer BK. Improved Virus Isoelectric Point Estimation by Exclusion of Known and Predicted Genome-Binding Regions. Appl Environ Microbiol 2020; 86:e01674-20. [PMID: 32978129 PMCID: PMC7657617 DOI: 10.1128/aem.01674-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/18/2020] [Indexed: 01/16/2023] Open
Abstract
Knowledge of the isoelectric points (pIs) of viruses is beneficial for predicting virus behavior in environmental transport and physical/chemical treatment applications. However, the empirically measured pIs of many viruses have thus far defied simple explanation, let alone prediction, based on the ionizable amino acid composition of the virus capsid. Here, we suggest an approach for predicting the pI of nonenveloped viruses by excluding capsid regions that stabilize the virus polynucleotide via electrostatic interactions. This method was applied first to viruses with known polynucleotide-binding regions (PBRs) and/or three-dimensional (3D) structures. Then, PBRs were predicted in a group of 32 unique viral capsid proteome sequences via conserved structures and sequence motifs. Removing predicted PBRs resulted in a significantly better fit to empirical pI values. After modification, mean differences between theoretical and empirical pI values were reduced from 2.1 ± 2.4 to 0.1 ± 1.7 pH units.IMPORTANCE This model fits predicted pIs to empirical values for a diverse set of viruses. The results suggest that many previously reported discrepancies between theoretical and empirical virus pIs can be explained by coulombic neutralization of PBRs of the inner capsid. Given the diversity of virus capsid structures, this nonarbitrary, heuristic approach to predicting virus pI offers an effective alternative to a simplistic, one-size-fits-all charge model of the virion. The accurate, structure-based prediction of PBRs of the virus capsid employed here may also be of general interest to structural virologists.
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Affiliation(s)
- Joe Heffron
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
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4
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Math RK, Kambiranda D, Yun HD, Ghebreiyessus Y. Binding of cloned Cel enzymes on clay minerals related to the pI of the enzymes and database survey of cellulases of soil bacteria for pI. Biosci Biotechnol Biochem 2019; 84:238-246. [PMID: 31625450 DOI: 10.1080/09168451.2019.1679613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The Cel genes from Bacillus licheniformis MSB03 were cloned and expressed to investigate binding ability on clay minerals and sea sand at pH ranging 3 to 9. FTIR analysis has been done to characterize bound enzymes on clay minerals. Subsequent, surveying of NCBI database for extracellular enzymes of soil bacteria was carried out. Among the five cloned Cel enzymes assayed for binding to clay minerals, only Cel5H enzyme had the binding ability. Enzyme Cel5H exhibited highest binding to montmorillonite followed by kaolinite and sea sand. Interestingly, Cel5H had higher pI value of 9.24 than other proteins (5.2-5.7). Cel5H binding to montmorillonite was shown to be negatively affected below pH 3 and above pH 9. Infrared absorption spectra of the Cel5H-montmorillonite complexes showed distinct peaks for clay minerals and bound proteins. Furthermore, database survey of soil bacterial extracellular enzymes revealed that Bacillus species enzymes had higher pI than other soil bacterial enzymes.
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Affiliation(s)
- Renukaradhya K Math
- Research Institute of Agriculture and Life Science, Gyeongsang National University, Chinju, Republic of Korea
| | - Devaiah Kambiranda
- Department of Agricultural Sciences, Southern University Agriculture Research and Extension Center, Baton Rouge, LA, USA
| | - Han Dae Yun
- Research Institute of Agriculture and Life Science, Gyeongsang National University, Chinju, Republic of Korea
| | - Yemane Ghebreiyessus
- Department of Agricultural Sciences, Southern University Agriculture Research and Extension Center, Baton Rouge, LA, USA
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5
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Leuchs B, Frehtman V, Riese M, Müller M, Rommelaere J. A novel scalable, robust downstream process for oncolytic rat parvovirus: isoelectric point-based elimination of empty particles. Appl Microbiol Biotechnol 2017; 101:3143-3152. [PMID: 28091791 PMCID: PMC5380694 DOI: 10.1007/s00253-016-8071-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/15/2016] [Accepted: 12/17/2016] [Indexed: 11/29/2022]
Abstract
The rodent protoparvovirus H-1PV, with its oncolytic and oncosuppressive properties, is a promising anticancer agent currently under testing in clinical trials. This explains the current demand for a scalable, good manufacturing practice-compatible virus purification process yielding high-grade pure infectious particles and overcoming the limitations of the current system based on density gradient centrifugation. We describe here a scalable process offering high purity and recovery. Taking advantage of the isoelectric point difference between full and empty particles, it eliminates most empty particles. Full particles have a significantly higher cationic charge than empty ones, with an isoelectric point of 5.8–6.2 versus 6.3 (as determined by isoelectric focusing and chromatofocusing). Thanks to this difference, infectious full particles can be separated from empty particles and most protein impurities by Convective interaction media® diethylaminoethyl (DEAE) anion exchange chromatography: applying unpurified H-1PV to the column in 0.15 M NaCl leaves, the former on the column and the latter in the flow through. The full particles are then recovered by elution with 0.25 M NaCl. The whole large-scale purification process involves filtration, single-step DEAE anion exchange chromatography, buffer exchange by cross-flow filtration, and final formulation in Visipaque/Ringer solution. It results in 98% contaminating protein removal and 96% empty particle elimination. The final infectious particle concentration reaches 3.5E10 plaque forming units (PFU)/ml, with a specific activity of 6.8E11 PFU/mg protein. Overall recovery is over 40%. The newly established method is suitable for use in commercial production.
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Affiliation(s)
- Barbara Leuchs
- German Cancer Research Center Tumor Virology F010, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Veronika Frehtman
- German Cancer Research Center Tumor Virology F010, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Markus Riese
- German Cancer Research Center Tumor Virology F010, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Marcus Müller
- German Cancer Research Center Tumor Virology F010, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jean Rommelaere
- German Cancer Research Center Tumor Virology F010, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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6
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Ferreira RA, Martins-Dias S. Purification of plant complex protein extracts in non-denaturing conditions by in-solution isoelectric focusing. Anal Biochem 2016; 509:100-3. [PMID: 27396497 DOI: 10.1016/j.ab.2016.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 12/18/2022]
Abstract
An alternative approach for plant complex protein extracts pre-purification by in-solution isoelectric focusing in non-denaturing conditions is presented. The separation of biologically active proteins, in narrow ranges of isoelectric point (pI) was obtained by a modified OFFGEL electrophoresis. Two different water-soluble protein extracts from Phragmites leaves were fractionated into 24 fractions within a 3-10 pI range at 10 °C in the absence of denaturing/reducing agents. One-dimensional electrophoretic analysis revealed different protein distribution patterns and the effective fractionation of both protein extracts. Peroxidase activity of each fraction confirmed that proteins remained active and pre-purification occurred. Biological triplicates assured the needed reproducibility.
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7
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Hifumi E, Matsumoto S, Nakashima H, Itonaga S, Arakawa M, Katayama Y, Kato R, Uda T. A novel method of preparing the monoform structure of catalytic antibody light chain. FASEB J 2015; 30:895-908. [PMID: 26527062 DOI: 10.1096/fj.15-276394] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/19/2015] [Indexed: 11/11/2022]
Abstract
Along with the development of antibody drugs and catalytic antibodies, the structural diversity (heterogeneity) of antibodies has been given attention. For >20 yr, detailed studies on the subject have not been conducted, because the phenomenon presents many difficult and complex problems. Structural diversity provides some (or many) isoforms of an antibody distinguished by different charges, different molecular sizes, and modifications of amino acid residues. For practical use, the antibody and the subunits must have a defined structure. In recent work, we have found that the copper (Cu) ion plays a substantial role in solving the diversity problem. In the current study, we used several catalytic antibody light chains to examine the effect of the Cu ion. In all cases, the different electrical charges of the molecule converged to a single charge, giving 1 peak in cation-exchange chromatography, as well as a single spot in 2-dimensional gel electrophoresis. The Cu-binding site was investigated by using mutagenesis, ultraviolet-visible spectroscopy, atomic force microscope analysis, and molecular modeling, which suggested that histidine and cysteine residues close to the C-terminus are involved with the binding site. The constant region domain of the antibody light chain played an important role in the heterogeneity of the light chain. Our findings may be a significant tool for preparing a single defined, not multiple, isoform structure.
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Affiliation(s)
- Emi Hifumi
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Shingo Matsumoto
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Hiroki Nakashima
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Shogo Itonaga
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Mitsue Arakawa
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Yoshiki Katayama
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Ryuichi Kato
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
| | - Taizo Uda
- *Research Promotion Institute and Department of Applied Chemistry, Faculty of Engineering, Oita University, Oita, Japan; Nanotechnology Laboratory, Institute of Systems, Information Technologies, and Nanotechnologies (ISIT), Fukuoka, Japan; Graduate School of System Life Science, Kyushu University, Fukuoka, Japan; Tottori College of Nursing, Tottori, Japan; and High Energy Accelerator Research Organization, Tsukuba, Japan
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Abstract
Amphoteric azo dyes were used for internal control of pI values in Comparative two-dimensional Fluorescence Gel Electrophoresis (CoFGE) [1]. The 2D-gel images of separated Escherichia coli proteins as well as those of colored amphoteric dyes separated by isoelectric focussing are presented. The latter were used to correct for variation in the first electrophoretic dimension and further improve protein coordinate assignment in 2D-gel electrophoresis. Data tables are supplied to demonstrate pI-value calibration and the effect on the assignment of protein spot coordinates.
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Affiliation(s)
- Marina Hanneken
- Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Germany
| | - Karel Šlais
- Institute of Analytical Chemistry of the ASCR, v. v. i., Brno, Czech Republic
| | - Simone König
- Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Germany
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9
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Muñoz-Fambuena N, Mesejo C, Reig C, Agustí M, Tárraga S, Lisón P, Iglesias DJ, Primo-Millo E, González-Mas MC. Proteomic study of 'Moncada' mandarin buds from on- versus off-crop trees. Plant Physiol Biochem 2013; 73:41-55. [PMID: 24056126 DOI: 10.1016/j.plaphy.2013.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
A proteomic analysis of buds from mandarin trees with contrasting fruit load (on- and off-crop trees) was carried out during the onset of low-temperature induction. The aim of the study was to find out more about the molecular mechanism relating to alternate bearing in Citrus and its relationship with flowering. The 'Moncada' variety (Clementine 'Oroval'x'Kara' mandarin), displaying remarkable behaviour in alternate production, was used in this study. From 2D DIGE gel, 192 spots were isolated: 97 showed increased expression in the off-crop buds as compared to the on-crop buds, while 95 exhibited enhanced expression in the on-crop buds versus the off-crop buds. These spots were identified by MALDI-MS or LC-MS-MS. The largest groups of proteins up-expressed in the off-crop buds were the proteins involved in carbohydrate and amino acid metabolism, and the proteins expressed in response to stimuli such as reactive oxygen species. The largest groups of proteins up-expressed in the on-crop buds were related to primary metabolism, oxidative stress and defence responses. Depending on their function, some of these proteins can stimulate the flowering, such as fructose-bisphosphate aldolase or leucine-rich repeat transmembrane protein kinase, while others can inhibit it, such as cytochrome c oxidase subunit II. Twenty-two other proteins with unknown functions were up-expressed in the on- or off-crop buds.
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Affiliation(s)
- Natalia Muñoz-Fambuena
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, C/Ingeniero Fausto Elio, E-46022 Valencia, Spain
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10
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Turell L, Botti H, Bonilla L, Torres MJ, Schopfer F, Freeman BA, Armas L, Ricciardi A, Alvarez B, Radi R. HPLC separation of human serum albumin isoforms based on their isoelectric points. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 944:144-151. [PMID: 24316526 DOI: 10.1016/j.jchromb.2013.11.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 11/05/2013] [Accepted: 11/09/2013] [Indexed: 12/31/2022]
Abstract
Human serum albumin (HSA) is the most abundant protein in plasma. Cys34, the only free Cys residue, is the predominant plasma thiol and a relevant sacrificial antioxidant. Both in vivo circulating HSA and pharmaceutical preparations are heterogeneous with respect to the oxidation state of Cys34. In this work, we developed an external pH gradient chromatofocusing procedure that allows the analysis of the oxidation status of HSA in human plasma and biopharmaceutical products based on the different apparent isoelectric points and chemical properties of the redox isoforms. Specifically, reduced-mercury blocked HSA (HSA-SHg(+)), HSA with Cys34 oxidized to sulfenic acid (HSA-SOH) and HSA oxidized to sulfinate anion (HSA-SO2(-)) can be separated with resolutions of 1.4 and 3.1 (first and last pair) and hence quantified and purified. In addition, an N-terminally degraded isoform (HSA3-585) in different redox states can be resolved as well. Confirmation of the identity of the chromatofocusing isolated isoforms was achieved by high resolution whole protein MS. It is proposed that the chromatofocusing procedure can be used to produce more exact and complete descriptions of the redox status of HSA in vivo and in vitro. Finally, the scalability capabilities of the chromatofocusing procedure allow for the preparation of highly pure standards of several redox isoforms of HSA.
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Affiliation(s)
- Lucía Turell
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay.,Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay.,Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, 11800, Uruguay
| | - Horacio Botti
- Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, 11800, Uruguay.,Unidad de Cristalografía de Proteínas, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay
| | - Lucía Bonilla
- Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, 11800, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, 11800, Uruguay
| | - María José Torres
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay.,Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, 11800, Uruguay
| | - Francisco Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Bruce A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Larissa Armas
- Laboratorio de Biofármacos: Control de Calidad y Desarrollo, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay
| | - Alejandro Ricciardi
- Laboratorio de Biofármacos: Control de Calidad y Desarrollo, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, 11400, Uruguay.,Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, 11800, Uruguay
| | - Rafael Radi
- Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, 11800, Uruguay.,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, 11800, Uruguay
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11
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Li M, Gao Z, Wang Y, Wang H, Zhang S. Identification, expression and bioactivity of hexokinase in amphioxus: insights into evolution of vertebrate hexokinase genes. Gene 2014; 535:318-26. [PMID: 24262936 DOI: 10.1016/j.gene.2013.10.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/11/2013] [Accepted: 10/27/2013] [Indexed: 11/23/2022]
Abstract
Hexokinase family includes hexokinases I, II, III and IV, that catalyze the phosphorylation of glucose to produce glucose 6-phosphate. Hexokinase IV, also known as glucokinase, is only half size of the other types of hexokinases that contain two hexokinase domains. Despite the enormous progress in the study of hexokinases, the evolutionary relationship between glucokinase and other hexokinases is still uncertain, and the molecular processes leading to the emergence of hexokinases in vertebrates remain controversial. Here we clearly demonstrated the presence of a single hexokinase-like gene in the amphioxus Branchiostoma japonicum, Bjhk, which shows a tissue-specific expression pattern, with the most abundant expression in the hepatic caecum, testis and ovary. The phylogenetic and synteny analyses both reveal that BjHK is the archetype of vertebrate hexokinases IV, i.e. glucokinases. We also found for the first time that recombinant BjHK showed functional enzyme activity resembling vertebrate hexokinases I, II, III and IV. In addition, a native glucokinase activity was detected in the hepatic caecum. Finally, glucokinase activity in the hepatic caecum was markedly reduced by fasting, whereas it was considerably increased by feeding. Altogether, these suggest that Bjhk represents the archetype of glucokinases, from which vertebrate hexokinase gene family was evolved by gene duplication, and that the hepatic caecum plays a role in the control of glucose homeostasis in amphioxus, in favor of the notion that the hepatic caecum is a tissue homologous to liver.
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Ratanajanchai M, Soodvilai S, Pimpha N, Sunintaboon P. Polyethylenimine-immobilized core-shell nanoparticles: synthesis, characterization, and biocompatibility test. Mater Sci Eng C Mater Biol Appl 2013; 34:377-83. [PMID: 24268272 DOI: 10.1016/j.msec.2013.09.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 09/04/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
Abstract
Herein, we prepared PEI-immobilized core-shell particles possessing various types of polymer cores via a visible light-induced surfactant-free emulsion polymerization (SFEP) of three vinyl monomers: styrene (St), methyl methacrylate (MMA), and 2-hydroxyethyl methacrylate (HEMA). An effect of monomers on the polymerization and characteristics of resulting products was investigated. Monomers with high polarity can provide high monomer conversion, high percentage of grafted PEI, stable particles with uniform size distribution but less amino groups per particles. All prepared nanoparticles exhibited a core-shell nanostructure, containing PEI on the shell with hydrodynamic size around 140-230nm. For in-vitro study in Caco-2 cells, we found that the incorporation of PEI into these core-shell nanoparticles can significantly reduce its cytotoxic effect and also be able to internalized within the cells. Accordingly, these biocompatible particles would be useful for various biomedical applications, including gene transfection and intracellular drug delivery.
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Affiliation(s)
- Montri Ratanajanchai
- Department of Chemistry, Faculty of Science, Mahidol University, Phuttamonthon 4 Road, Nakhon Pathom 73170, Thailand
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Chen HL, Mao HY, Cao MJ, Cai QF, Su WJ, Zhang YX, Liu GM. Purification, physicochemical and immunological characterization of arginine kinase, an allergen of crayfish (Procambarus clarkii). Food Chem Toxicol 2013; 62:475-84. [PMID: 24055770 DOI: 10.1016/j.fct.2013.09.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 11/17/2022]
Abstract
Arginine kinase (AK) has attracted considerable attention because it has been identified as a shellfish allergen. However, little information is available about AK in crayfish (Procambarus clarkii). In this study, crayfish AK was purified and cloned. Its physicochemical properties, processing stability, and immunological characteristics were analyzed. Crayfish AK was purified by column chromatography, which revealed a single band with molecular mass of 40 kDa; this result was further confirmed by mass spectrometry. The full-length gene sequence of crayfish AK was 1462 bp and encoded a protein of 357 amino acid residues. The results of this study revealed that crayfish AK is a glycoprotein with an isoelectric point of approximately 6.5. Thermal stability assays revealed that crayfish AK easily forms aggregates at temperatures >44°C and was stable at pH 4.0-8.0. SDS-PAGE and dot blotting were used to assess processing stability of purified AK. The results revealed that the IgE-binding activity of crayfish AK is reduced after boiling.
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Affiliation(s)
- Heng-Li Chen
- College of Biological Engineering, The Key Laboratory of Science and Technology for Aquaculture and Food Safety, Jimei University, 43 Yindou Road, Xiamen 361021, Fujian, China
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Mohindra V, Tripathi RK, Singh RK, Lal KK. Molecular characterization and expression analysis of PPP1R3C in hypoxia-tolerant Indian catfish, Clarias batrachus (Linnaeus, 1758) under hypoxia. Gene 2013; 530:127-33. [PMID: 23948083 DOI: 10.1016/j.gene.2013.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 07/03/2013] [Accepted: 07/08/2013] [Indexed: 01/09/2023]
Abstract
Hypoxia is an important environmental stressor that leads to rapid adaptive changes in metabolic organization. However, the molecular mechanisms of hypoxia tolerance in fish remain largely unknown. The present work was focused on understanding the molecular mechanisms and signaling pathways that may lead to tolerance of Clarias batrachus to hypoxic stress. Protein phosphatase 1 regulatory subunit 3C (PPP1R3C) is a new hypoxia-inducible factor (HIF) targeted gene and is regulated by HIF-1 under hypoxic conditions. Overexpression of PPP1R3C increases glycogen accumulation through activation of several enzymes and processes. In this study, for the first time, full length cDNA of PPP1R3C from C. batrachus was characterized and its expression pattern in the brain, liver, muscle and spleen under short (progressive hypoxia; PH, 1h, 6h and 12h) and long-term (natural) hypoxic conditions was investigated. The complete cDNA of PPP1R3C was of 1499 bp, encoding 285 amino acid residues. The identified protein had a protein phosphatase 1 binding motif and a carbohydrate binding domain, thought to be involved in the regulation of glycogen metabolism. Short-term hypoxia exposure caused significant increase in PPP1R3C transcripts in the liver (6h; 6.96 fold and 12h; 3.91 fold) and muscle (progressive hypoxia; 3.46 fold), while, after long-term hypoxia exposure, significant up-regulation in the liver (7.77 fold) and spleen (6.59 fold) tissues was observed. No significant differences were observed in the brain for any time periods. Thus PPP1R3C may play an important role in the tolerance of C. batrachus to hypoxia.
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Affiliation(s)
- Vindhya Mohindra
- National Bureau of Fish Genetic Resources (ICAR), Canal Ring Road, P.O. Dilkusha, Lucknow 226002, UP, India.
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Shi Z, Wang ZJ, Xu HL, Tian Y, Li X, Bao JK, Sun SR, Yue BS. Modeling, docking and dynamics simulations of a non-specific li pid transfer protein from Peganum harmala L. Comput Biol Chem 2013; 47:56-65. [PMID: 23891721 DOI: 10.1016/j.compbiolchem.2013.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/03/2013] [Accepted: 07/04/2013] [Indexed: 12/18/2022]
Abstract
Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid-protein interactions, indicating some future applications of ns-LTP-mediated transport.
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Affiliation(s)
- Zheng Shi
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, School of Life Sciences, Sichuan University, Chengdu 610064, China; School of Life Sciences, Guizhou Normal University, Guiyang 550001, China
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Li C, Chen S, Song J, Liu H, Gu W, Ai H, Zhao B, Zhang S. Molecular cloning and characterization of TNFSF14 (LIGHT) and its receptor TNFRSF14 (HVEM) in guinea pig (Cavia porcellus). Gene 2013; 526:374-84. [PMID: 23732292 DOI: 10.1016/j.gene.2013.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/15/2013] [Indexed: 01/05/2023]
Abstract
LIGHT (lymphotoxin-related inducible ligand that competes with herpes simplex virus (HSV) glycoprotein D for herpesvirus entry mediator on T cells) is a member of the tumor necrosis factor (TNF) ligand superfamily, which plays important roles in inflammatory and immune responses. In the present study, the cDNAs of guinea pig (Cavia porcellus) LIGHT (designated as gpLIGHT) and its receptor herpes virus entry mediator (designated as gpHVEM) were amplified from spleen by reverse transcription polymerase chain reaction (RT-PCR). The ORFs of gpLIGHT and gpHVEM cover 726 and 861 bp, encoding predicted proteins with 241 and 286 aas, respectively. The three-dimensional (3D) structure, phylogenetic relationships, and characterization of both genes were also analyzed. We also generated a 3D model to verify interaction between the two proteins. Real-time quantitative PCR (qPCR) analysis revealed that both LIGHT and HVEM are constitutively expressed in guinea pig various tissues. A fusion protein SUMO (Small Ubiquitin-like Modifier)-gpsLIGHT (the soluble mature part of gpLIGHT) was efficiently expressed in Escherichia coli BL21 (DE3) and purified using metal chelate affinity chromatography (Ni-NTA). Laser scanning confocal microscopy (LSCM) showed that gpsLIGHT can bind its receptors on T cells. The LIGHT-HVEM signaling pathway plays an important role in the immune system, and our results might provide a platform for further research into the effects of LIGHT and HVEM.
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Affiliation(s)
- Chunlan Li
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, Life Sciences College, Nanjing Normal University, Nanjing 210046, China
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Yamazaki A, Nishizawa Y, Matsuura I, Hayashi F, Usukura J, Bondarenko VA. Microtubule-associated protein tau in bovine retinal photoreceptor rod outer segments: comparison with brain tau. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1549-59. [PMID: 23712071 DOI: 10.1016/j.bbadis.2013.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/09/2013] [Accepted: 05/17/2013] [Indexed: 01/09/2023]
Abstract
Recent studies have suggested a possible involvement of abnormal tau in some retinal degenerative diseases. The common view in these studies is that these retinal diseases share the mechanism of tau-mediated degenerative diseases in brain and that information about these brain diseases may be directly applied to explain these retinal diseases. Here we collectively examine this view by revealing three basic characteristics of tau in the rod outer segment (ROS) of bovine retinal photoreceptors, i.e., its isoforms, its phosphorylation mode and its interaction with microtubules, and by comparing them with those of brain tau. We find that ROS contains at least four isoforms: three are identical to those in brain and one is unique in ROS. All ROS isoforms, like brain isoforms, are modified with multiple phosphate molecules; however, ROS isoforms show their own specific phosphorylation pattern, and these phosphorylation patterns appear not to be identical to those of brain tau. Interestingly, some ROS isoforms, under the normal conditions, are phosphorylated at the sites identical to those in Alzheimer's patient isoforms. Surprisingly, a large portion of ROS isoforms tightly associates with a membranous component(s) other than microtubules, and this association is independent of their phosphorylation states. These observations strongly suggest that tau plays various roles in ROS and that some of these functions may not be comparable to those of brain tau. We believe that knowledge about tau in the entire retinal network and/or its individual cells are also essential for elucidation of tau-mediated retinal diseases, if any.
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Bruschi M, Santucci L, Candiano G, Ghiggeri GM. Albumin heterogeneity in low-abundance fluids. The case of urine and cerebro-s pinal fluid. Biochim Biophys Acta Gen Subj 2013; 1830:5503-8. [PMID: 23628703 DOI: 10.1016/j.bbagen.2013.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 11/18/2022]
Abstract
BACKGROUND Serum albumin is a micro-heterogeneous protein composed of at least 40 isoforms. Its heterogeneity is even more pronounced in biological fluids other than serum, the major being urine and cerebrospinal fluid. Modification 'in situ' and/or selectivity of biological barriers, such as in the kidney, determines the final composition of albumin and may help in definition of inflammatory states. SCOPE OF REVIEW This review focuses on various aspects of albumin heterogeneity in low 'abundance fluids' and highlights the potential source of information in diseases. MAJOR CONCLUSIONS The electrical charge of the protein in urine and CSF is modified but with an opposite change and depending on clinical conditions. In normal urine, the bulk of albumin is more anionic than in serum for the presence of ten times more fatty acids that introduce equivalent anionic charges and modify hydrophobicity of the protein. At the same time, urinary albumin is more glycosylated compared to the serum homolog. Finally, albumin fragments can be detected in urine in patients with proteinuria. For albumin in CSF, we lack information relative to normal conditions since ethical problems do not allow normal CSF to be studied. In multiple sclerosis, the albumin charge in CSF is more cationic than in serum, this change possibly involving structural anomalies or small molecules bindings. GENERAL SIGNIFICANCE Massively fatty albumin could be toxic for tubular cells and be eliminated on this basis. Renal handling of glycosylated albumin can alter the normal equilibrium of filtration/reabsorption and trigger mechanisms leading to glomerulosclerosis and tubulo-interstitial fibrosis. This article is part of a Special Issue entitled Serum Albumin.
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Affiliation(s)
- Maurizio Bruschi
- Division of Nephrology, Dialysis, and Transplantation, Istituto Giannina Gaslini, Genoa, Italy; Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa, Italy
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Hopff D, Wienkoop S, Lüthje S. The plasma membrane proteome of maize roots grown under low and high iron conditions. J Proteomics 2013; 91:605-18. [PMID: 23353019 DOI: 10.1016/j.jprot.2013.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 12/11/2012] [Accepted: 01/09/2013] [Indexed: 10/27/2022]
Abstract
Iron (Fe) homeostasis is essential for life and has been intensively investigated for dicots, while our knowledge for species in the Poaceae is fragmentary. This study presents the first proteome analysis (LC-MS/MS) of plasma membranes isolated from roots of 18-day old maize (Zea mays L.). Plants were grown under low and high Fe conditions in hydroponic culture. In total, 227 proteins were identified in control plants, whereas 204 proteins were identified in Fe deficient plants and 251 proteins in plants grown under high Fe conditions. Proteins were sorted by functional classes, and most of the identified proteins were classified as signaling proteins. A significant number of PM-bound redox proteins could be identified including quinone reductases, heme and copper-containing proteins. Most of these components were constitutive, and others could hint at an involvement of redox signaling and redox homeostasis by change in abundance. Energy metabolism and translation seem to be crucial in Fe homeostasis. The response to Fe deficiency includes proteins involved in development, whereas membrane remodeling and assembly and/or repair of Fe-S clusters is discussed for Fe toxicity. The general stress response appears to involve proteins related to oxidative stress, growth regulation, an increased rigidity and synthesis of cell walls and adaption of nutrient uptake and/or translocation. This article is part of a Special Issue entitled: Plant Proteomics in Europe.
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Affiliation(s)
- David Hopff
- University of Hamburg, Biocenter Klein Flottbek and Botanical Garden, Plant Physiology, Ohnhorststraße 18, D-22609 Hamburg, Germany
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