1
|
Abstract
Tankyrases are ADP-ribosylating enzymes that regulate many physiological processes in the cell and are considered promising drug targets for cancer and fibrotic diseases. The catalytic ADP-ribosyltransferase domain of tankyrases contains a unique zinc-binding motif of unknown function. Recently, this motif was suggested to be involved in the catalytic activity of tankyrases. In this work, we set out to study the effect of the zinc-binding motif on the activity, stability and structure of human tankyrases. We generated mutants of human tankyrase (TNKS) 1 and TNKS2, abolishing the zinc-binding capabilities, and characterized the proteins biochemically and biophysically in vitro. We further generated a crystal structure of TNKS2, in which the zinc ion was oxidatively removed. Our work shows that the zinc-binding motif in tankyrases is a crucial structural element which is particularly important for the structural integrity of the acceptor site. While mutation of the motif rendered TNKS1 inactive, probably due to introduction of major structural defects, the TNKS2 mutant remained active and displayed an altered activity profile compared to the wild-type.
Collapse
Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
2
|
Liang C, Carrel D, Singh NK, Hiester LL, Fanget I, Kim H, Firestein BL. Carboxypeptidase E Independently Changes Microtubule Glutamylation, Dendritic Branching, and Neuronal Migration. ASN Neuro 2022; 14:17590914211062765. [PMID: 35014548 PMCID: PMC8755936 DOI: 10.1177/17590914211062765] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Neuronal migration and dendritogenesis are dependent on dynamic changes to the microtubule (MT) network. Among various factors that regulate MT dynamics and stability, post-translational modifications (PTMs) of MTs play a critical role in conferring specificity of regulatory protein binding to MTs. Thus, it is important to understand the regulation of PTMs during brain development as multiple developmental processes are dependent on MTs. In this study, we identified that carboxypeptidase E (CPE) changes tubulin polyglutamylation, a major PTM in the brain, and we examine the impact of CPE-mediated changes to polyglutamylation on cortical neuron migration and dendrite morphology. We show, for the first time, that overexpression of CPE increases the level of polyglutamylated α-tubulin while knockdown decreases the level of polyglutamylation. We also demonstrate that CPE-mediated changes to polyglutamylation are dependent on the CPE zinc-binding motif and that this motif is necessary for CPE action on p150Glued localization. However, overexpression of a CPE mutant that does not increase MT glutamylation mimics the effects of overexpression of wild type CPE on dendrite branching. Furthermore, although overexpression of wild type CPE does not alter cortical neuron migration, overexpression of the mutant may act in a dominant-negative manner as it decreases the number of neurons that reach the cortical plate (CP), as we previously reported for CPE knockdown. Overall, our data suggest that CPE changes MT glutamylation and redistribution of p150Glued and that this function of CPE is independent of its role in shaping dendrite development but plays a partial role in regulating cortical neuron migration.
Collapse
Affiliation(s)
- Chen Liang
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA.,Molecular Biosciences Graduate Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Damien Carrel
- SPPIN Laboratory, 555089Université de Paris, Centre National de la Recherche Scientifique UMR 8003, Paris, France
| | - Nisha K Singh
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA.,Molecular Biosciences Graduate Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Liam L Hiester
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA
| | - Isabelle Fanget
- SPPIN Laboratory, 555089Université de Paris, Centre National de la Recherche Scientifique UMR 8003, Paris, France
| | - Hyuck Kim
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA
| | - Bonnie L Firestein
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA
| |
Collapse
|
3
|
Camacho E, Sanz L, Escalante T, Pérez A, Villalta F, Lomonte B, Neves-Ferreira AGC, Feoli A, Calvete JJ, Gutiérrez JM, Rucavado A. Novel Catalytically-Inactive PII Metalloproteinases from a Viperid Snake Venom with Substitutions in the Canonical Zinc-Binding Motif. Toxins (Basel) 2016; 8:E292. [PMID: 27754342 PMCID: PMC5086652 DOI: 10.3390/toxins8100292] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 09/28/2016] [Accepted: 09/30/2016] [Indexed: 11/16/2022] Open
Abstract
Snake venom metalloproteinases (SVMPs) play key biological roles in prey immobilization and digestion. The majority of these activities depend on the hydrolysis of relevant protein substrates in the tissues. Hereby, we describe several isoforms and a cDNA clone sequence, corresponding to PII SVMP homologues from the venom of the Central American pit viper Bothriechis lateralis, which have modifications in the residues of the canonical sequence of the zinc-binding motif HEXXHXXGXXH. As a consequence, the proteolytic activity of the isolated proteins was undetectable when tested on azocasein and gelatin. These PII isoforms comprise metalloproteinase and disintegrin domains in the mature protein, thus belonging to the subclass PIIb of SVMPs. PII SVMP homologues were devoid of hemorrhagic and in vitro coagulant activities, effects attributed to the enzymatic activity of SVMPs, but induced a mild edema. One of the isoforms presents the characteristic RGD sequence in the disintegrin domain and inhibits ADP- and collagen-induced platelet aggregation. Catalytically-inactive SVMP homologues may have been hitherto missed in the characterization of snake venoms. The presence of such enzymatically-inactive homologues in snake venoms and their possible toxic and adaptive roles deserve further investigation.
Collapse
Affiliation(s)
- Erika Camacho
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica.
| | - Libia Sanz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia 46010, Spain.
| | - Teresa Escalante
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica.
| | - Alicia Pérez
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia 46010, Spain.
| | - Fabián Villalta
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica.
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica.
| | | | - Andrés Feoli
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica.
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia 46010, Spain.
- Departamento de Biotecnología, Universidad Politécnica de Valencia, Valencia 46022, Spain.
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica.
| | - Alexandra Rucavado
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica.
| |
Collapse
|
4
|
Wang W, Su X, Wang X, Yang J, Zhang T, Wang M, Wan R, Tan G, Lu J. Iron inhibits Escherichia coli topoisomerase I activity by targeting the first two zinc-binding sites in the C-terminal domain. Protein Sci 2014; 23:1619-28. [PMID: 25176012 DOI: 10.1002/pro.2542] [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: 07/22/2014] [Revised: 08/26/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022]
Abstract
Escherichia coli DNA topoisomerase I (TopA) contains a 67 kDa N-terminal catalytic domain and a 30 kDa C-terminal zinc-binding region (ZD domain) which has three adjacent tetra-cysteine zinc-binding motifs. Previous studies have shown that E. coli TopA can bind both iron and zinc, and that iron binding in TopA results in failure to unwind the negatively supercoiled DNA. Here, we report that each E. coli TopA monomer binds one atom of iron via the first two zinc-binding motifs in ZD domain and both the first and second zinc-binding motifs are required for iron binding in TopA. The site-directed mutagenesis studies further reveal that while the mutation of the third zinc-binding motif has very little effect on TopA's activity, mutation of the first two zinc-binding motifs in TopA greatly diminishes the topoisomerase activity in vitro and in vivo, indicating that the first two zinc-binding motifs in TopA are crucial for its function. The DNA-binding activity assay and intrinsic tryptophan fluorescence measurements show that iron binding in TopA may decrease the single-stranded (ss) DNA-binding activity of ZD domain and also change the protein structure of TopA, which subsequently modulate topoisomerase activity.
Collapse
Affiliation(s)
- Wu Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Boussardon C, Avon A, Kindgren P, Bond CS, Challenor M, Lurin C, Small I. The cytidine deaminase signature HxE(x)n CxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1. New Phytol 2014; 203:1090-1095. [PMID: 25041347 DOI: 10.1111/nph.12928] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [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: 04/06/2014] [Accepted: 06/12/2014] [Indexed: 05/02/2023]
Abstract
In flowering plants, RNA editing involves deamination of specific cytidines to uridines in both mitochondrial and chloroplast transcripts. Pentatricopeptide repeat (PPR) proteins and multiple organellar RNA editing factor (MORF) proteins have been shown to be involved in RNA editing but none have been shown to possess cytidine deaminase activity. The DYW domain of some PPR proteins contains a highly conserved signature resembling the zinc-binding active site motif of known nucleotide deaminases. We modified these highly conserved amino acids in the DYW motif of DYW1, an editing factor required for editing of the ndhD-1 site in Arabidopsis chloroplasts. We demonstrate that several amino acids of this signature motif are required for RNA editing in vivo and for zinc binding in vitro. We conclude that the DYW domain of DYW1 has features in common with cytidine deaminases, reinforcing the hypothesis that this domain forms part of the active enzyme that carries out RNA editing in plants.
Collapse
Affiliation(s)
- Clément Boussardon
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/UEVE - ERL CNRS, SPS Labex, CP 5708, 91057, Evry Cedex, France
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Alexandra Avon
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/UEVE - ERL CNRS, SPS Labex, CP 5708, 91057, Evry Cedex, France
| | - Peter Kindgren
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Michael Challenor
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Claire Lurin
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA/UEVE - ERL CNRS, SPS Labex, CP 5708, 91057, Evry Cedex, France
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| |
Collapse
|
6
|
Gwyn LM, Peak MM, De P, Rahman NS, Rodgers KK. A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity. J Mol Biol 2009; 390:863-78. [PMID: 19500590 PMCID: PMC2782368 DOI: 10.1016/j.jmb.2009.05.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/28/2009] [Indexed: 11/24/2022]
Abstract
The recombination-activating protein, RAG1, a key component of the V(D)J recombinase, binds multiple Zn(2+) ions in its catalytically required core region. However, the role of zinc in the DNA cleavage activity of RAG1 is not well resolved. To address this issue, we determined the stoichiometry of Zn(2+) ions bound to the catalytically active core region of RAG1 under various conditions. Using metal quantitation methods, we determined that core RAG1 can bind up to four Zn(2+) ions. Stripping the full complement of bound Zn(2+) ions to produce apoprotein abrogated DNA cleavage activity. Moreover, even partial removal of zinc-binding equivalents resulted in a significant diminishment of DNA cleavage activity, as compared to holo-Zn(2+) core RAG1. Mutants of the intact core RAG1 and the isolated core RAG1 domains were studied to identify the location of zinc-binding sites. Significantly, the C-terminal domain in core RAG1 binds at least two Zn(2+) ions, with one zinc-binding site containing C902 and C907 as ligands (termed the CC zinc site) and H937 and H942 coordinating a Zn(2+) ion in a separate site (HH zinc site). The latter zinc-binding site is essential for DNA cleavage activity, given that the H937A and H942A mutants were defective in both in vitro DNA cleavage assays and cellular recombination assays. Furthermore, as mutation of the active-site residue E962 reduces Zn(2+) coordination, we propose that the HH zinc site is located in close proximity to the DDE active site. Overall, these results demonstrate that Zn(2+) serves an important auxiliary role for RAG1 DNA cleavage activity. Furthermore, we propose that one of the zinc-binding sites is linked to the active site of core RAG1 directly or indirectly by E962.
Collapse
Affiliation(s)
| | | | - Pallabi De
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center Oklahoma City, Oklahoma 73190
| | - Negar S. Rahman
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center Oklahoma City, Oklahoma 73190
| | - Karla K. Rodgers
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center Oklahoma City, Oklahoma 73190
| |
Collapse
|
7
|
Watnick RS, Herring SC, Palmer AG, Gottesman ME. The carboxyl terminus of phage HK022 Nun includes a novel zinc-binding motif and a tryptophan required for transcription termination. Genes Dev 2000; 14:731-9. [PMID: 10733532 PMCID: PMC316458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The amino-terminal arginine-rich motif of the phage HK022 Nun protein binds phage lambda nascent mRNA transcripts while the carboxy-terminal domain binds RNA polymerase and arrests transcription. The role of specific residues in the carboxy-terminal domain in transcription termination were investigated by mutagenesis, in vitro and in vivo functional assays, and NMR spectroscopy. Coordination of zinc to three histidine residues in the carboxy-terminus inhibited RNA binding by the amino-terminal domain; however, only two of these histidines were required for transcription arrest. These results suggest that additional zinc-coordinating residues are supplied by RNA polymerase in the context of the Nun-RNA polymerase complex. Substitution of the penultimate carboxy-terminal tryptophan residue with alanine or leucine blocks transcription arrest, whereas a tyrosine substitution is innocuous. Wild-type Nun fails to arrest transcription on single-stranded templates. These results suggest that Nun inhibition of transcription elongation is due in part to interactions between the carboxy-terminal tryptophan of Nun and double-stranded DNA, possibly by intercalation. A model for the termination activity of Nun is developed on the basis of these data.
Collapse
Affiliation(s)
- R S Watnick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032 USA
| | | | | | | |
Collapse
|