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Pei X, Luo Z, Qiao L, Xiao Q, Zhang P, Wang A, Sheldon RA. Putting precision and elegance in enzyme immobilisation with bio-orthogonal chemistry. Chem Soc Rev 2022; 51:7281-7304. [PMID: 35920313 DOI: 10.1039/d1cs01004b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The covalent immobilisation of enzymes generally involves the use of highly reactive crosslinkers, such as glutaraldehyde, to couple enzyme molecules to each other or to carriers through, for example, the free amino groups of lysine residues, on the enzyme surface. Unfortunately, such methods suffer from a lack of precision. Random formation of covalent linkages with reactive functional groups in the enzyme leads to disruption of the three dimensional structure and accompanying activity losses. This review focuses on recent advances in the use of bio-orthogonal chemistry in conjunction with rec-DNA to affect highly precise immobilisation of enzymes. In this way, cost-effective combination of production, purification and immobilisation of an enzyme is achieved, in a single unit operation with a high degree of precision. Various bio-orthogonal techniques for putting this precision and elegance into enzyme immobilisation are elaborated. These include, for example, fusing (grafting) peptide or protein tags to the target enzyme that enable its immobilisation in cell lysate or incorporating non-standard amino acids that enable the application of bio-orthogonal chemistry.
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Affiliation(s)
- Xiaolin Pei
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Zhiyuan Luo
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Li Qiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Qinjie Xiao
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Pengfei Zhang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Anming Wang
- College of Materials, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, Key Laboratory of Organosilicon Material Technology, Hangzhou Normal University, Zhejiang Province, Hangzhou, 311121, Zhejiang, P. R. China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, 2050, Johannesburg, South Africa. .,Department of Biotechnology, Section BOC, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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2
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Wang M, Zhuang D, Mei M, Ma H, Li Z, He F, Cheng G, Lin G, Zhou W. Frequent mutation of hypoxia-related genes in persistent pulmonary hypertension of the newborn. Respir Res 2020; 21:53. [PMID: 32054482 PMCID: PMC7020588 DOI: 10.1186/s12931-020-1314-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Aims Persistent pulmonary hypertension of the newborn (PPHN) is characterized by sustained high levels of pulmonary vascular resistance after birth with etiology unclear; Arterial blood oxygen saturation of Tibetan newborns at high latitudes is higher than that of Han newborns at low latitudes, suggesting that genetic adaptation may allow sufficient oxygen to confer Tibetan populations with resistance to pulmonary hypertension; We have previously identified genetic factors related to PPHN through candidate gene sequencing; In this study, we first performed whole exome sequencing in PPHN patients to screen for genetic-related factors. Methods and results In this two-phase genetic study, we first sequenced the whole exome of 20 Tibetan PPHN patients and compared it with the published genome sequences of 50 healthy high-altitude Tibetanshypoxia-related genes, a total of 166 PPHN-related variants were found, of which 49% were from 43 hypoxia-related genes; considering many studies have shown that the differences in the genetic background between Tibet and Han are characterized by hypoxia-related genetic polymorphisms, so it is necessary to further verify whether the association between hypoxia-related variants and PPHN is independent of high-altitude life. During the validation phase, 237 hypoxia-related genes were sequenced in another 80 Han PPHN patients living in low altitude areas, including genes at the discovery stage and known hypoxia tolerance, of which 413 variants from 127 of these genes were shown to be significantly associated with PPHN.hypoxia-related genes. Conclusions Our results indicates that the association of hypoxia-related genes with PPHN does not depend on high-altitude life, at the same time, 21 rare mutations associated with PPHN were also found, including three rare variants of the tubulin tyrosine ligase-like family member 3 gene (TTLL3:p.E317K, TTLL3:p.P777S) and the integrin subunit alpha M gene (ITGAM:p.E1071D). These novel findings provide important information on the genetic basis of PPHN.
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Affiliation(s)
- Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, National Health Commision (NHC) Key Laboratory of Neonatal Diseases, Division of Neonatology, National Center for Children's Health, Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Deyi Zhuang
- Xiamen Key Laboratory of Neonatal Diseases, Neonatal Medical Center, Xiamen Children's Hospital, Children's Hospital of Fudan University (Xiamen Branch), Xiamen, 361006, Fujian, China
| | - Mei Mei
- Division of Pulmonology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Haiyan Ma
- Zhuhai Maternal and Children's Hospital, Zhuhai, 519001, Guangdong, China
| | - Zixiu Li
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | | | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, 201102, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, 200436, China
| | - Guang Lin
- Zhuhai Maternal and Children's Hospital, Zhuhai, 519001, Guangdong, China.
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, National Health Commision (NHC) Key Laboratory of Neonatal Diseases, Division of Neonatology, National Center for Children's Health, Children's Hospital of Fudan University, Shanghai, 201102, China.
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3
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Identifying tumor promoting genomic alterations in tumor-associated fibroblasts via retrovirus-insertional mutagenesis. Oncotarget 2017; 8:97231-97245. [PMID: 29228606 PMCID: PMC5722558 DOI: 10.18632/oncotarget.21881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/21/2017] [Indexed: 01/01/2023] Open
Abstract
Tumor-associated fibroblasts (TAFs) are often essential for solid tumor growth. However, few genetic or epigenetic alterations have been found in TAFs during the progression of solid tumors. Employing a tumor-stromal cell co-injection model, we adapted here retroviral-insertional mutagenesis to stromal cells to identify novel tumor-associated genes in TAFs. We successfully identified 20 gene candidates that might modulate tumor growth if altered in TAFs at genomic level. To validate our finding, the function of one of the candidate genes, tubulin tyrosine ligase (Ttl), was further studied in TAFs from fibrosarcoma, colon, breast and hepatocarcinoma. We demonstrated that down-regulated TTL expression in TAFs indeed promoted tumor growth in mice. Interestingly, decreased expression of TTL in tumor stromal cells also correlated with poor outcome in human colon carcinoma. Thus, the co-injection model of tumor cells with retrovirus-modified fibroblasts proved a valid method to identify tumor-modulating genes in TAFs, allowing for a deeper insight into the role of the stroma for tumor development.
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4
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Schumacher D, Lemke O, Helma J, Gerszonowicz L, Waller V, Stoschek T, Durkin PM, Budisa N, Leonhardt H, Keller BG, Hackenberger CPR. Broad substrate tolerance of tubulin tyrosine ligase enables one-step site-specific enzymatic protein labeling. Chem Sci 2017; 8:3471-3478. [PMID: 28507719 PMCID: PMC5418632 DOI: 10.1039/c7sc00574a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/18/2017] [Indexed: 12/31/2022] Open
Abstract
The broad substrate tolerance of tubulin tyrosine ligase enables its wide applicability for protein functionalization.
The broad substrate tolerance of tubulin tyrosine ligase is the basic rationale behind its wide applicability for chemoenzymatic protein functionalization. In this context, we report that the wild-type enzyme enables ligation of various unnatural amino acids that are substantially bigger than and structurally unrelated to the natural substrate, tyrosine, without the need for extensive protein engineering. This unusual substrate flexibility is due to the fact that the enzyme's catalytic pocket forms an extended cavity during ligation, as confirmed by docking experiments and all-atom molecular dynamics simulations. This feature enabled one-step C-terminal biotinylation and fluorescent coumarin labeling of various functional proteins as demonstrated with ubiquitin, an antigen binding nanobody, and the apoptosis marker Annexin V. Its broad substrate tolerance establishes tubulin tyrosine ligase as a powerful tool for in vitro enzyme-mediated protein modification with single functional amino acids in a specific structural context.
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Affiliation(s)
- Dominik Schumacher
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Jonas Helma
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Lena Gerszonowicz
- Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Verena Waller
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Tina Stoschek
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Patrick M Durkin
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Nediljko Budisa
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Heinrich Leonhardt
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Christian P R Hackenberger
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
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5
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Site-specific fluorescent labeling of tubulin. Methods Cell Biol 2013. [PMID: 23973062 DOI: 10.1016/b978-0-12-407757-7.00001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescent tubulin can be prepared in which a fluorophore is covalently bound to the protein at only the carboxy terminus of the α-subunit of the αβ-tubulin dimer. This two-step procedure consists of an enzymatic reaction followed by a bioorthogonal chemical reaction. In the first step of the process, the enzyme tubulin tyrosine ligase is used to attach a reactive tyrosine derivative, 3-formyltyrosine, to the protein. In the second step of the procedure, a fluorophore possessing a complementary reactive functional group, such as a hydrazine, hydrazide, or hydroxylamine, is allowed to react with the protein under conditions that are compatible with native tubulin. Polymerization-competent, fluorescently labeled tubulin can be prepared in just a few hours using this protocol. The method described here should be useful for attaching virtually any probe or material to tubulin at this site.
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6
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Banerjee A, Panosian TD, Mukherjee K, Ravindra R, Gal S, Sackett DL, Bane S. Site-specific orthogonal labeling of the carboxy terminus of alpha-tubulin. ACS Chem Biol 2010; 5:777-85. [PMID: 20545322 PMCID: PMC2924941 DOI: 10.1021/cb100060v] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A fluorescent probe has been attached to the carboxy terminus of the alpha-subunit of alpha,beta-tubulin by an enzymatic reaction followed by a chemical reaction. The unnatural amino acid 3-formyltyrosine is attached to the carboxy terminus of alpha-tubulin through the use of the enzyme tubulin tyrosine ligase. The aromatic aldehyde of the unnatural amino acid serves as an orthogonal electrophile that specifically reacts with a fluorophore containing an aromatic hydrazine functional group, which in this case is 7-hydrazino-4-methyl coumarin. Conditions for covalent bond formation between the unnatural amino acid and the fluorophore are mild, allowing fluorescently labeled tubulin to retain its ability to assemble into microtubules. A key feature of the labeling reaction is that it produces a red shift in the fluorophore's absorption and emission maxima, accompanied by an increase in its quantum yield; thus, fluorescently labeled protein can be observed in the presence of unreacted fluorophore. Both the enzymatic and coupling reaction can occur in living cells. The approach presented here should be applicable to a wide variety of in vitro systems.
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Affiliation(s)
- Abhijit Banerjee
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902
| | - Timothy D. Panosian
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902
| | - Kamalika Mukherjee
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902
| | - Rudravajhala Ravindra
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902
| | - Susannah Gal
- Department of Biological Sciences, Binghamton University, Bethesda MD 20892
| | - Dan L. Sackett
- Laboratory of Integrative and Medical Biophysics, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892
| | - Susan Bane
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902
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7
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Utreras E, Jiménez-Mateos EM, Contreras-Vallejos E, Tortosa E, Pérez M, Rojas S, Saragoni L, Maccioni RB, Avila J, González-Billault C. Microtubule-Associated Protein 1B Interaction with Tubulin Tyrosine Ligase Contributes to the Control of Microtubule Tyrosination. Dev Neurosci 2007; 30:200-10. [DOI: 10.1159/000109863] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 05/15/2007] [Indexed: 01/24/2023] Open
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8
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Fonrose X, Ausseil F, Soleilhac E, Masson V, David B, Pouny I, Cintrat JC, Rousseau B, Barette C, Massiot G, Lafanechère L. Parthenolide inhibits tubulin carboxypeptidase activity. Cancer Res 2007; 67:3371-8. [PMID: 17409447 DOI: 10.1158/0008-5472.can-06-3732] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microtubules are centrally involved in cell division, being the principal components of mitotic spindle. Tubulin, the constituent of microtubules, can be cyclically modified on its alpha-subunit by enzymatic removal of the COOH-terminal tyrosine residue by an ill-defined tubulin carboxypeptidase (TCP) and its readdition by tubulin tyrosine ligase (TTL). We and others have previously shown that suppression of TTL and resulting accumulation of detyrosinated tubulin are frequent in human cancers of poor prognosis. Explanations for the involvement of TTL and detyrosinated tubulin in tumor progression arise from the recent discovery that tubulin detyrosination leads to CAP-Gly protein mislocalization, which correlates with defects in spindle positioning during mitosis. Impaired control of spindle positioning is one factor favoring tumor invasiveness. Thus, TCP could be a target for developing novel therapeutic strategies against advanced stages of cancers. Inhibitors of TCP, by reversing abnormal detyrosinated tubulin accumulation in tumor cells, could impair tumor progression. TCP has never been isolated and this has hampered search of specific inhibitors. In this article, we describe a cell-based assay of TCP activity and its use to screen a library of natural extracts for their inhibitory potency. This led to the isolation of two sesquiterpene lactones. We subsequently found that parthenolide, a structurally related compound, can efficiently inhibit TCP. This inhibitory activity is a new specific property of parthenolide independent of its action on the nuclear factor-kappaB pathway. Parthenolide is also known for its anticancer properties. Thus, TCP inhibition could be one of the underlying mechanisms of these anticancer properties.
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Affiliation(s)
- Xavier Fonrose
- Centre de Criblage pour Molécules Bio-Actives, institut de Recherches en Technologies et Sciences pour le Vivant, Commissariat à l'Energie Atomique-Grenoble, Grenoble, France
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9
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Hilpert K, Winkler DFH, Hancock REW. Cellulose-bound Peptide Arrays: Preparation and Applications. Biotechnol Genet Eng Rev 2007; 24:31-106. [DOI: 10.1080/02648725.2007.10648093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Pan JZ, Wei H, Hecker JG, Tobias JW, Eckenhoff RG, Eckenhoff MF. Rat brain DNA transcript profile of halothane and isoflurane exposure. Pharmacogenet Genomics 2006; 16:171-82. [PMID: 16495776 DOI: 10.1097/01.fpc.0000189795.21770.08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Inhaled anesthetics produce many effects and bind to a large number of brain proteins, but it is not yet clear if this is accompanied by widespread changes in gene expression of the biological targets. Such changes in expression might implicate functionally important targets from the large pool of binding targets. Both rats and isolated primary cortical neurons were exposed to anesthetics and DNA oligonucleotide microarrays were used to detect and quantify transcriptional changes in neural tissue. Using analysis of variance with multiple testing correction, multiple exposures of rats to 0.8 MAC (minimum alveolar concentration) halothane only produced significant changes in a few metabolic genes. No significant in-vivo gene transcriptional response to 0.8 MAC isoflurane was detected. The use of primary cortical neurons allowed exposure to 3 MAC anesthetics without evidence of toxicity. Isoflurane altered several genes involved with neurotransmitter transport, signaling and cellular structure, whereas halothane produced few detectable changes in these cultured cells. Selected genes were confirmed by quantitative reverse transcription-polymerase chain reaction. Although indicating only a small degree of transcriptional regulation, these data implicate several plausible targets, including synaptic vesicle handling, that might contribute to drug action. In addition, the data show different gene expression profiles for the two inhaled anesthetics, suggesting unique pharmacological targets and mechanisms in each case.
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Affiliation(s)
- Jonathan Z Pan
- Department of Anesthesiology and Critical Care, University of Pennsylvania Health System, Philadelphia, Pennsylvania 19104, USA
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11
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Soucek K, Kamaid A, Phung AD, Kubala L, Bulinski JC, Harper RW, Eiserich JP. Normal and prostate cancer cells display distinct molecular profiles of alpha-tubulin posttranslational modifications. Prostate 2006; 66:954-65. [PMID: 16541425 DOI: 10.1002/pros.20416] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Multiple diverse posttranslational modifications of alpha-tubulin such as detyrosination, further cleavage of the penultimate glutamate residue (Delta2-tubulin), acetylation, and polyglutamylation increase the structural and functional diversity of microtubules. METHODS Herein, we characterized the molecular profile of alpha-tubulin posttranslational modifications in normal human prostate epithelial cells (PrEC), immortalized normal prostate epithelial cells (PZ-HPV-7), androgen-dependent prostate cancer cells (LNCaP), transitional androgen-independent prostate cancer cells (LNCaP-cds and CWR22Rv1), and androgen-independent prostate cancer cells (PC3). RESULTS Compared to PrEC and PZ-HPV-7 cells, all cancer cells exhibited elevated levels of detyrosinated and polyglutamylated alpha-tubulin, that was paralleled by decreased protein levels of tubulin tyrosine ligase (TTL). In contrast, PrEC and PZ-HPV-7 cells expressed markedly higher levels of Delta2-tubulin. Whereas alpha-tubulin acetylation levels were generally equivalent in all the cell lines, PC3 cells did not display detectable levels of Ac-tubulin. CONCLUSION These data may reveal novel biomarkers of prostate cancer and new therapeutic targets.
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Affiliation(s)
- Karel Soucek
- Department of Internal Medicine, University of California, Davis, California 95616, USA
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12
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Stradal TEB, Pusch R, Kliche S. Molecular regulation of cytoskeletal rearrangements during T cell signalling. Results Probl Cell Differ 2006; 43:219-44. [PMID: 17068974 DOI: 10.1007/400_022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Regulation of the cytoskeleton in cells of the haematopoietic system is essential for fulfilling diverse tasks such as migration towards a chemoattractant, phagocytosis or cell-cell communication. This is particularly true for the many types of T cells, which are at the foundation of the adaptive immune system in vertebrates. Deregulation of actin filament turnover is known to be involved in the development of severe immunodeficiencies or immunoproliferative diseases. Therefore, molecular dissection of signalling complexes and effector molecules, which leads to controlled cytoskeletal assembly, has been the focus of immunological research in the last decade. In the past, cytoskeletal remodelling was frequently understood as the finish line of signalling, while today it becomes increasingly evident that actin and microtubule dynamics are required for proper signal transmission in many processes such as T cell activation. Significant effort is made in many laboratories to further elucidate the contribution of cytoskeletal remodelling to immune function. The objective of this article is to summarise the current knowledge on how actin and microtubules are reorganised to support the formation of structures as diverse as the immunological synapse and peripheral protrusions during cell migration.
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Affiliation(s)
- Theresia E B Stradal
- Signalling and Motility Group, German Research Centre for Biotechnology (GBF), Braunschweig, Germany
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13
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Cappelletti G, Maggioni MG, Ronchi C, Maci R, Tedeschi G. Protein tyrosine nitration is associated with cold- and drug-resistant microtubules in neuronal-like PC12 cells. Neurosci Lett 2006; 401:159-64. [PMID: 16567039 DOI: 10.1016/j.neulet.2006.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 03/06/2006] [Accepted: 03/06/2006] [Indexed: 10/24/2022]
Abstract
Among the myriad of cellular functions played by nitric oxide in the brain, there is increasing evidence that nitric oxide might be a primary player in the program of neurogenesis and neuronal differentiation. We have recently reported that tyrosine nitration of proteins is implicated in the signaling pathway triggered by nitric oxide during NGF-induced neuronal differentiation in PC12 cells. The cytoskeleton becomes the main cellular fraction containing nitrotyrosinated proteins, and the cytoskeletal proteins alpha-tubulin and tau are two of the targets. Here, we have studied the association of nitrated proteins with the cytoskeletal fraction in differentiating PC12 cells following exposure to microtubule depolymerising treatments and found that nitration of the cytoskeleton correlates with the increased microtubule stability underlying the progression of neuronal differentiation. These results suggest a novel functional role for nitrated cytoskeletal proteins in the stabilisation of neurites occurring in differentiated neuronal cells.
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14
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Hepner F, Myung JK, Ulfig N, Pollak A, Lubec G. Detection of hypothetical proteins in human fetal perireticular nucleus. J Proteome Res 2006; 4:2379-85. [PMID: 16335990 DOI: 10.1021/pr050133p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a legion of hypothetical proteins (HP) in prokaryotic and eukaryotic proteomes and the aim of this study was to describe HP in the perireticular nucleus (PN), a key structure in human brain development. Tissue from four PNs was homogenized and extracted proteins were run on two-dimensional gel electrophoresis followed by in-gel digestion and mass spectrometrical identification of proteins. Several databases were used for obtaining bioinformatic information and searching for functional and structural domains. Five spots represented HP: KIAA0423 protein (Q9Y4F4), hypothetical protein KIAA0153 (Q14166), hypothetical protein DKFZp564A2416 (Q9NTW4), hypothetical protein DKFZp564H1122 (Q9H0W9), and hypothetical protein DKFZp564D1378 (Q9H0R4). These structures were predicted to serve in cell cycle, DNA-condensation, neurogenesis, or apoptosis. The existence of formerly HP proteins in the PN of human fetal brain is shown, thus extending knowledge of the brain proteome and proposing the method used as a suitable analytical tool for searching HP.
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Affiliation(s)
- Felix Hepner
- Department of Pediatrics, Medical University of Vienna, Austria
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15
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Erck C, MacLeod RAF, Wehland J. Cloning and genomic organization of the TTL gene on mouse chromosome 2 and human chromosome 2q13. Cytogenet Genome Res 2004; 101:47-53. [PMID: 14571137 DOI: 10.1159/000073418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2002] [Accepted: 04/09/2003] [Indexed: 11/19/2022] Open
Abstract
Tubulin tyrosine ligase (TTL) is a cytosolic enzyme involved in the posttranslational modification of tubulin. In the assembled form microtubules are detyrosinated over time at the C-terminus of alpha-tubulin. After microtubular disassembly TTL restores tyrosine residues back to the detyrosinated tubulin leading to a cycle of detyrosination/tyrosination. Here we report the isolation of the human and mouse TTL cDNA. In comparison with other known TTL sequences, namely bovine, rat and porcine, we found that only porcine TTL deviates in length by having an insertion of two glutamate residues. In mouse and human TTL the genomic coding sequence is composed of seven exons with normal intron/exon boundaries. Using fluorescence in situ hybridization (FISH), we mapped the murine TTL gene to mouse chromosome 2 (MMU2). Human TTL has been located to chromosome 2q13 (HSA2q13). In addition, we found frequently truncated PCR products of hTTL transcripts with aberrant splicing in tumors.
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MESH Headings
- 5' Flanking Region/genetics
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Base Sequence
- Cell Line, Tumor
- Chromosome Mapping
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Mammalian/genetics
- Cloning, Molecular
- DNA/chemistry
- DNA/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Exons
- Genes/genetics
- HeLa Cells
- Humans
- In Situ Hybridization, Fluorescence
- Introns
- Mice
- Mice, Inbred Strains
- Molecular Sequence Data
- NIH 3T3 Cells
- Peptide Synthases/genetics
- Phylogeny
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- C Erck
- Department of Cell Biology, German Research Center of Biotechnology, Braunschweig, Germany.
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Olbrich H, Fliegauf M, Hoefele J, Kispert A, Otto E, Volz A, Wolf MT, Sasmaz G, Trauer U, Reinhardt R, Sudbrak R, Antignac C, Gretz N, Walz G, Schermer B, Benzing T, Hildebrandt F, Omran H. Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. Nat Genet 2003; 34:455-9. [PMID: 12872122 DOI: 10.1038/ng1216] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2003] [Accepted: 06/19/2003] [Indexed: 11/09/2022]
Abstract
Nephronophthisis (NPHP), a group of autosomal recessive cystic kidney disorders, is the most common genetic cause of progressive renal failure in children and young adults. NPHP may be associated with Leber congenital amaurosis, tapeto-retinal degeneration, cerebellar ataxia, cone-shaped epiphyses, congenital oculomotor apraxia and hepatic fibrosis. Loci associated with an infantile type of NPHP on 9q22-q31 (NPHP2), juvenile types of NPHP on chromosomes 2q12-q13 (NPHP1) and 1p36 (NPHP4) and an adolescent type of NPHP on 3q21-q22 (NPHP3) have been mapped. NPHP1 and NPHP4 have been identified, and interaction of the respective encoded proteins nephrocystin and nephrocystin-4 has been shown. Here we report the identification of NPHP3, encoding a novel 1,330-amino acid protein that interacts with nephrocystin. We describe mutations in NPHP3 in families with isolated NPHP and in families with NPHP with associated hepatic fibrosis or tapeto-retinal degeneration. We show that the mouse ortholog Nphp3 is expressed in the node, kidney tubules, retina, respiratory epithelium, liver, biliary tract and neural tissues. In addition, we show that a homozygous missense mutation in Nphp3 is probably responsible for the polycystic kidney disease (pcy) mouse phenotype. Interventional studies in the pcy mouse have shown beneficial effects by modification of protein intake and administration of methylprednisolone, suggesting therapeutic strategies for treating individuals with NPHP3.
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Affiliation(s)
- Heike Olbrich
- Department of Pediatrics and Adolescent Medicine, University Hospital Freiburg, 79106 Freiburg, Germany
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Kalisz HM, Erck C, Plessmann U, Wehland J. Incorporation of nitrotyrosine into alpha-tubulin by recombinant mammalian tubulin-tyrosine ligase. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1481:131-8. [PMID: 11004583 DOI: 10.1016/s0167-4838(00)00110-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Tubulin-tyrosine ligase (TTL, EC 6.3.2.25) from porcine brain, which catalyses the readdition of tyrosine to the C-terminus of detyrosinated alpha-tubulin, was cloned and expressed in Escherichia coli as a glutathione S-transferase-fusion protein. Upon cleavage of the immobilised fusion protein, an electrophoretically homogeneous enzyme was obtained. Recombinant TTL, which exhibited similar catalytic properties as the mammalian enzyme purified from brain tissue, was capable of using nitrotyrosine as an alternative substrate in vitro. Incorporation of tyrosine into tubulin was competitively inhibited by nitrotyrosine with an apparent K(i) of 0.24 mM. The TTL-catalysed incorporation of nitrotyrosine as sole substrate into alpha-tubulin was clearly detectable at concentrations of 10 microM by immunological methods using nitrotyrosine specific antibodies. However, in competition with tyrosine 20-fold higher concentrations of nitrotyrosine were necessary before its incorporation became evident. Analysis of the C-terminal peptides of in vitro modified alpha-tubulin by MALDI-MS confirmed the covalent incorporation of nitrotyrosine into tubulin by TTL. In contrast to the C-terminal tyrosine, pancreatic carboxypeptidase A was incapable of cleaving nitrotyrosine from the modified alpha-tubulin.
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Affiliation(s)
- H M Kalisz
- Gesellschaft für Biotechnologische Forschung, Abteilung Zellbiologie, Braunschweig, Germany
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