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Yang Y, Wang X, Yan P, Wang D, Luo T, Zhou Y, Chen S, Liu Q, Hou J, Wang P. Transmembrane protein 117 knockdown protects against angiotensin-II-induced cardiac hypertrophy. Hypertens Res 2023; 46:2326-2339. [PMID: 37488300 PMCID: PMC10550824 DOI: 10.1038/s41440-023-01377-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/26/2023]
Abstract
Mitochondrial dysfunction plays a critical role in the pathogenesis of pathological cardiac hypertrophy. Transmembrane protein 117 modulate mitochondrial membrane potential that may be involved in the regulation of oxidative stress and mitochondrial function. However, its role in the development of angiotensin II (Ang-II)-induced cardiac hypertrophy is unclear. Cardiac-specific TMEM117-knockout and control mice were subjected to cardiac hypertrophy induced by Ang-II infusion. Small-interfering RNAs against TMEM117 or adenovirus-based plasmids encoding TMEM117 were delivered into left ventricles of mice or incubated with neonatal murine ventricular myocytes (NMVMs) before Ang-II stimulation. We found that TMEM117 was upregulated in hypertrophic hearts and cardiomyocytes and TMEM117 deficiency attenuated Ang-II-induced cardiac hypertrophy in vivo. Consistently, the in vitro data demonstrated that Ang-II-induced cardiomyocyte hypertrophy significantly alleviated by TMEM117 knockdown. Conversely, overexpression of TMEM117 exacerbated cardiac hypertrophy and dysfunction. An Ang II-induced increase in cardiac (cardiomyocyte) oxidative stress was alleviated by cardiac-specific knockout (knockdown) of TMEM117 and was worsened by TMEM117 supplementation (overexpression). In addition, TMEM117 knockout decreased endoplasmic reticulum stress induced by Ang-II, which was reversed by TMEM117 supplementation. Furthermore, TMEM117 deficiency mitigated mitochondrial injury in hypertrophic hearts and cardiomyocyte, which was abolished by TMEM117 supplementation (overexpression). Taken together, these findings suggest that upregulation of TMEM117 contributes to the development of cardiac hypertrophy and the downregulation of TMEM117 may be a new therapeutic strategy for the prevention and treatment of cardiac hypertrophy.
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Affiliation(s)
- Yi Yang
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Xinquan Wang
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Peng Yan
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Dan Wang
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Tao Luo
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Yaqiong Zhou
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Shichao Chen
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Qiting Liu
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Jixin Hou
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China
| | - Peijian Wang
- Department of Cardiology, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China.
- Sichuan Clinical Research Center for Geriatrics, The First Affiliated Hospital, Chengdu Medical College, Chengdu, 610500, Sichuan, China.
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, 610500, Sichuan, China.
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Xu AM, He CJ, Tuerxun Z, Anikezi A. FAM172A affects cell proliferation and apoptosis not by targeting β-tubulin in HepG2 cells. Transl Cancer Res 2020; 9:5637-5644. [PMID: 35117927 PMCID: PMC8797783 DOI: 10.21037/tcr-20-2868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/15/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Microtubules pull chromosomes apart during cell mitosis and take part in cell division, Inhibiting the formation of spindle microtubules during mitosis has become one of the current anti-tumor research strategies. Earlier studies have found that the family with sequence similarity 172, member A (FAM172A) can significantly inhibit the proliferation of human colorectal cancer cell line LOVO cells and promote apoptosis. The purpose of this study was to investigate the biological effects of FAM172A on liver cancer cells and the interaction mechanism with tubulin. METHODS Use STRING software predicted the interactions between FAM172A and β-tubulin, and verify by immunoprecipitation. Real-Time qPCR was used to determine the expression levels of β-tubulin in liver cancer cell line HepG2, western blot was performed to detect protein expression levels. Immunofluorescence experiment to detect the distribution, shape and the dynamic behavior of depolymerization-aggregation of β-tubulin in cells. MTT, wound healing and Transwell assay were employed to determine cell proliferation, migration and invasion respectively. Flow cytometry was conducted to determine cell cycle and apoptosis. RESULTS There is no interactions between FAM172A and β-tubulin. We determined that when FAM172A was up-regulated or down-regulated, the mRNA and protein levels of β-tubulin did not change significantly (P>0.05). Furthermore, the distribution, shape of β-tubulin in cells, and the dynamic behavior of depolymerization-aggregation was not affected. After FAM172A overexpression, the migration and invasion of HepG2 cells were significantly inhibited (P<0.05), the cell proliferation was also significantly inhibited (P<0.05) and was time-dependent. The HepG2 cells had apparent S phase arrest and apoptosis (P<0.05). After interfering with FAM172A, the opposite result will appear. CONCLUSIONS The results show that FAM172A may be a new tumor suppressor gene, which has a specific role in cell cycle control and cell proliferation, but the specific mechanism of action has not been explained in this study and needs further exploration.
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Affiliation(s)
- Ai-Min Xu
- Department of Laboratory, The First People's Hospital of Kashgar, Kashi, Kashi 844000, China
| | - Chuan-Jiang He
- Department of Laboratory, The First People's Hospital of Kashgar, Kashi, Kashi 844000, China
| | - Zureguli Tuerxun
- Department of Laboratory, The First People's Hospital of Kashgar, Kashi, Kashi 844000, China
| | - Abuduaini Anikezi
- Department of Laboratory, The First People's Hospital of Kashgar, Kashi, Kashi 844000, China
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Human protein factory for converting the transcriptome into an in vitro-expressed proteome,. Nat Methods 2009; 5:1011-7. [PMID: 19054851 DOI: 10.1038/nmeth.1273] [Citation(s) in RCA: 197] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Appropriate resources and expression technology necessary for human proteomics on a whole-proteome scale are being developed. We prepared a foundation for simple and efficient production of human proteins using the versatile Gateway vector system. We generated 33,275 human Gateway entry clones for protein synthesis, developed mRNA expression protocols for them and improved the wheat germ cell-free protein synthesis system. We applied this protein expression system to the in vitro expression of 13,364 human proteins and assessed their biological activity in two functional categories. Of the 75 tested phosphatases, 58 (77%) showed biological activity. Several cytokines containing disulfide bonds were produced in an active form in a nonreducing wheat germ cell-free expression system. We also manufactured protein microarrays by direct printing of unpurified in vitro-synthesized proteins and demonstrated their utility. Our 'human protein factory' infrastructure includes the resources and expression technology for in vitro proteome research.
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Sauermann M, Sahin O, Sültmann H, Hahne F, Blaszkiewicz S, Majety M, Zatloukal K, Füzesi L, Poustka A, Wiemann S, Arlt D. Reduced expression of vacuole membrane protein 1 affects the invasion capacity of tumor cells. Oncogene 2007; 27:1320-6. [PMID: 17724469 DOI: 10.1038/sj.onc.1210743] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vacuole membrane protein 1 (Vmp1) is described as a cancer-relevant cell cycle modulator, but the function of this protein and its mode of action in tumor progression are still unknown. In this study, we show that the VMP1 mRNA level is significantly reduced in kidney cancer metastases as compared to primary tumors. Further, VMP1 expression is also decreased in the invasive breast cancer cell lines HCC1954 and MDA-MB-231 as compared to the non-invasive cell lines MCF-12A, T-47D and MCF-7. We show for the first time that Vmp1 is a plasma membrane protein and an essential component of initial cell-cell contacts and tight junction formation. It interacts with the tight junction protein Zonula Occludens-1 and colocalizes in spots between neighboring HEK293 cells. Downregulation of VMP1 by RNAi results in loss of cell adherence, and increases the invasion capacity of the non-invasive kidney cancer cell line Caki-2. In conclusion, our findings establish Vmp1 to be a novel cell-cell adhesion protein and that its expression level determines the invasion and metastatic potential of cancer cells.
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Affiliation(s)
- M Sauermann
- Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
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Starkuviene V, Pepperkok R. The potential of high-content high-throughput microscopy in drug discovery. Br J Pharmacol 2007; 152:62-71. [PMID: 17603554 PMCID: PMC1978277 DOI: 10.1038/sj.bjp.0707346] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fluorescence microscopy is a powerful method to study protein function in its natural habitat, the living cell. With the availability of the green fluorescent protein and its spectral variants, almost any gene of interest can be fluorescently labelled in living cells opening the possibility to study protein localization, dynamics and interactions. The emergence of automated cellular systems allows rapid visualization of large groups of cells and phenotypic analysis in a quantitative manner. Here, we discuss recent advances in high-content high-throughput microscopy and its potential application to several steps of the drug discovery process.
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Affiliation(s)
- V Starkuviene
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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7
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Sauermann M, Hahne F, Schmidt C, Majety M, Rosenfelder H, Bechtel S, Huber W, Poustka A, Arlt D, Wiemann S. High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins. ACTA ACUST UNITED AC 2007; 12:510-20. [PMID: 17478479 DOI: 10.1177/1087057107301271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
After sequencing the human genome, the challenge ahead is to systematically analyze the functions and disease relation of the proteins encoded. Here the authors describe the application of a flow cytometry-based high-throughput assay to screen for apoptosis-activating proteins in transiently transfected cells. The assay is based on the detection of activated caspase-3 with a specific antibody, in cells overexpressing proteins tagged C- or N-terminally with yellow fluorescent protein. Fluorescence intensities are measured using a flow cytometer integrated with a high-throughput autosampler. The applicability of this screen has been tested in a pilot screen with 200 proteins. The candidate proteins were all verified in an independent microscopy-based nuclear fragmentation assay, finally resulting in the identification of 6 apoptosis inducers.
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Affiliation(s)
- Mamatha Sauermann
- Division of Molecular Genome Analysis, German Cancer Research Centre, Heidelberg, Germany
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8
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Oyama M, Kozuka-Hata H, Suzuki Y, Semba K, Yamamoto T, Sugano S. Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics 2007; 6:1000-6. [PMID: 17317662 DOI: 10.1074/mcp.m600297-mcp200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Our previous proteomics analysis of small proteins expressed in human K562 cells provided the first direct evidence of translation of upstream ORFs in human full-length cDNAs (Oyama, M., Itagaki, C., Hata, H., Suzuki, Y., Izumi, T., Natsume, T., Isobe, T., and Sugano, S. (2004) Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res. 14, 2048-2052). In the present study, we performed an in-depth proteomics analysis of human K562 and HEK293 cells using a two-dimensional nano-liquid chromatography-tandem mass spectrometry system. The results led to the identification of eight protein-coding regions besides 197 small proteins with a theoretical mass less than 20 kDa that were already annotated coding sequences in the curated mRNA database. In addition to the upstream ORFs in the presumed 5'-untranslated regions of mRNAs, bioinformatics analysis based on accumulated 5'-end cDNA sequence data provided evidence of novel short coding regions that were likely to be translated from the upstream non-AUG start site or from the new short transcript variants generated by utilization of downstream alternative promoters. Protein expression analysis of the GRINL1A gene revealed that translation from the most upstream start site occurred on the minor alternative splicing transcript, whereas this initiation site was not utilized on the major mRNA, resulting in translation of the downstream ORF from the second initiation codon. These findings reveal a novel post-transcriptional system that can augment the human proteome via the alternative use of diverse translation start sites coupled with transcriptional regulation through alternative promoters or splicing, leading to increased complexity of short protein-coding regions defined by the human transcriptome.
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Affiliation(s)
- Masaaki Oyama
- Medical Proteomics Laboratory, University of Tokyo, Japan.
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Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Söll D. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A 2006; 103:18923-7. [PMID: 17142313 PMCID: PMC1748153 DOI: 10.1073/pnas.0609703104] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The trace element selenium is found in proteins as selenocysteine (Sec), the 21st amino acid to participate in ribosome-mediated translation. The substrate for ribosomal protein synthesis is selenocysteinyl-tRNA(Sec). Its biosynthesis from seryl-tRNA(Sec) has been established for bacteria, but the mechanism of conversion from Ser-tRNA(Sec) remained unresolved for archaea and eukarya. Here, we provide evidence for a different route present in these domains of life that requires the tRNA(Sec)-dependent conversion of O-phosphoserine (Sep) to Sec. In this two-step pathway, O-phosphoseryl-tRNA(Sec) kinase (PSTK) converts Ser-tRNA(Sec) to Sep-tRNA(Sec). This misacylated tRNA is the obligatory precursor for a Sep-tRNA:Sec-tRNA synthase (SepSecS); this protein was previously annotated as SLA/LP. The human and archaeal SepSecS genes complement in vivo an Escherichia coli Sec synthase (SelA) deletion strain. Furthermore, purified recombinant SepSecS converts Sep-tRNA(Sec) into Sec-tRNA(Sec) in vitro in the presence of sodium selenite and purified recombinant E. coli selenophosphate synthetase (SelD). Phylogenetic arguments suggest that Sec decoding was present in the last universal common ancestor. SepSecS and PSTK coevolved with the archaeal and eukaryotic lineages, but the history of PSTK is marked by several horizontal gene transfer events, including transfer to non-Sec-decoding Cyanobacteria and fungi.
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Affiliation(s)
- Jing Yuan
- Departments of *Molecular Biophysics and Biochemistry and
| | | | | | - Dan Su
- Departments of *Molecular Biophysics and Biochemistry and
| | | | | | | | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605
| | - Dieter Söll
- Departments of *Molecular Biophysics and Biochemistry and
- Chemistry, Yale University, New Haven, CT 06520-8114; and
- To whom correspondence should be addressed. E-mail:
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Laketa V, Simpson JC, Bechtel S, Wiemann S, Pepperkok R. High-content microscopy identifies new neurite outgrowth regulators. Mol Biol Cell 2006; 18:242-52. [PMID: 17093056 PMCID: PMC1751310 DOI: 10.1091/mbc.e06-08-0666] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Neurons, with their long axons and elaborate dendritic arbour, establish the complex circuitry that is essential for the proper functioning of the nervous system. Whereas a catalogue of structural, molecular, and functional differences between axons and dendrites is accumulating, the mechanisms involved in early events of neuronal differentiation, such as neurite initiation and elongation, are less well understood, mainly because the key molecules involved remain elusive. Here we describe the establishment and application of a microscopy-based approach designed to identify novel proteins involved in neurite initiation and/or elongation. We identified 21 proteins that affected neurite outgrowth when ectopically expressed in cells. Complementary time-lapse microscopy allowed us to discriminate between early and late effector proteins. Localization experiments with GFP-tagged proteins in fixed and living cells revealed a further 14 proteins that associated with neurite tips either early or late during neurite outgrowth. Coexpression experiments of the new effector proteins provide a first glimpse on a possible functional relationship of these proteins during neurite outgrowth. Altogether, we demonstrate the potential of the systematic microscope-based screening approaches described here to tackle the complex biological process of neurite outgrowth regulation.
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Affiliation(s)
- Vibor Laketa
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory-Heidelberg, 69117 Heidelberg, Germany.
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Korf U, Kohl T, van der Zandt H, Zahn R, Schleeger S, Ueberle B, Wandschneider S, Bechtel S, Schnölzer M, Ottleben H, Wiemann S, Poustka A. Large-scale protein expression for proteome research. Proteomics 2006; 5:3571-80. [PMID: 16127724 DOI: 10.1002/pmic.200401195] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Access to pure and soluble recombinant proteins is essential for numerous applications in proteome research, such as the production of antibodies, structural characterization of proteins, and protein microarrays. Through the German cDNA Consortium we have access to more than 1500 ORFs encoding uncharacterized proteins. Preparing a large number of recombinant proteins calls for the careful refinement and re-evaluation of protein purification tools. The expression and purification strategy should result in mg quantities of protein that can be employed in microarray-based assays. In addition, the experimental set-up should be robust enough to allow both automated protein expression screening and the production of the proteins on a mg scale. These requirements are best fulfilled by a bacterial expression system such as Escherichia coli. To develop an efficient expression strategy, 75 different ORFs were transferred into suitable expression vectors using the Gateway cloning system. Four different fusion tags (E. coli transcription-termination anti-termination factor (NusA), hexahistidine tag (6xHis), maltose binding protein (MBP) and GST) were analyzed for their effect on yield of induced fusion protein and its solubility, as determined at two different induction temperatures. Affinity-purified fusion proteins were confirmed by MALDI-TOF MS.
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Affiliation(s)
- Ulrike Korf
- Molecular Genome Analysis, DKFZ, Heidelberg, Germany.
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12
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Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda JI, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T. Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene 2005; 364:99-107. [PMID: 16185827 DOI: 10.1016/j.gene.2005.05.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 04/06/2005] [Accepted: 05/30/2005] [Indexed: 10/25/2022]
Abstract
H-Invitational Database (H-InvDB; ) is a human transcriptome database, containing integrative annotation of 41,118 full-length cDNA clones originated from 21,037 loci. H-InvDB is a product of the H-Invitational project, an international collaboration to systematically and functionally validate human genes by analysis of a unique set of high quality full-length cDNA clones using automatic annotation and human curation under unified criteria. Here, 19,574 proteins encoded by these cDNAs were classified into 11,709 function-known and 7865 function-unknown hypothetical proteins by similarity with protein databases and motif prediction (InterProScan). The proportion of "hypothetical proteins" in H-InvDB was as high as 40.4%. In this study, we thus conducted data-mining in H-InvDB with the aim of assigning advanced functional annotations to those hypothetical proteins. First, by data-mining in the H-InvDB version of GTOP, we identified 337 SCOP domains within 7865 H-Inv hypothetical proteins. Second, by data-mining of predicted subcellular localization by SOSUI and TMHMM in H-InvDB, we found 1032 transmembrane proteins within H-Inv hypothetical proteins. These results clearly demonstrate that structural prediction is effective for functional annotation of proteins with unknown functions. All the data in H-InvDB are shown in two main views, the cDNA view and the Locus view, and five auxiliary databases with web-based viewers; DiseaseInfo Viewer, H-ANGEL, Clustering Viewer, G-integra and TOPO Viewer; the data also are provided as flat files and XML files. The data consists of descriptions of their gene structures, novel alternative splicing isoforms, functional RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases, gene expression profiling, and comparisons with mouse full-length cDNAs in the context of molecular evolution. This unique integrative platform for conducting in silico data-mining represents a substantial contribution to resources required for the exploration of human biology and pathology.
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Affiliation(s)
- Chisato Yamasaki
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
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Brosius J. Echoes from the past--are we still in an RNP world? Cytogenet Genome Res 2005; 110:8-24. [PMID: 16093654 DOI: 10.1159/000084934] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 05/04/2004] [Indexed: 11/19/2022] Open
Abstract
Availability of the human genome sequence and those of other species is unmeasured in their value for a comprehensive understanding of the architecture, function and evolution of genomes and cells. Various mechanisms keep genomes in flux and generate intra- and interspecies variation. The conversion of RNA modules into DNA and their more or less random integration into chromosomes (retroposition) is in many lineages including our own the most pervasive and perhaps the most enigmatic. The proclivity of such events in extant multicellular eukaryotes, even in more recent evolutionary times, gives the impression that the transition period from the RNP (ribonucleoprotein) world to the emergence of modern cells, where DNA became the predominant carrier of genetic information, has lasted billions of years and is an endlessly drawn-out process rather than the punctuated event one might expect. Apart from the impact of such RNA-mediated processes as retroposition, the role of RNA in a wide variety of cellular functions has only recently become more widely appreciated.
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Affiliation(s)
- J Brosius
- Institute of Experimental Pathology, ZMBE, University of Munster, Munster, Germany.
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Lin CW, Liu TY, Lin CJ, Hsu SM. Oligoclonal T cells in histiocytic necrotizing lymphadenopathy are associated with TLR9+ plasmacytoid dendritic cells. J Transl Med 2005; 85:267-75. [PMID: 15516971 DOI: 10.1038/labinvest.3700201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Histiocytic necrotizing lymphadenopathy (HNL), a disease of unknown cause, is characterized pathologically by the presence of plasmacytoid dendritic cells (pDCs), which are frequently mixed with oligoclonal T cells (OTCs) and myeloid cells. Toll-like receptors (TLRs 1-10) are a family of pattern recognition receptors of DCs. To investigate the interactions between pDCs and T cells, and to look for an etiology of HNL, we studied 24 HNLs for the profile of TLRs. Transcripts of TLR7, a receptor on pDCs for single-stranded RNA, were found in every case, confirming the universal presence of pDCs. Transcripts of TLR9, another receptor on pDCs for microbial unmethylated CpG-rich DNA, were correlated with OTCs, implying T-cell expansion stimulated by TLR9+ pDCs in response to a microbe. Because PCRs for bacterial 16S rDNAs were negative in the lymph nodes, a bacterial origin seems unlikely, but a virus remains a possible candidate. The pDCs lacked the maturation marker CD83, which suggested ineffective stimulation of T cells and might account for the usually benign course of HNL. Taken together, these data illustrate a novel approach, based upon TLR transcript analysis, for the integration of pathology, immunology, and clinical findings of HNL.
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Affiliation(s)
- Chung-Wu Lin
- Department of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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Lavelin I, Geiger B. Characterization of a novel GTPase-activating protein associated with focal adhesions and the actin cytoskeleton. J Biol Chem 2004; 280:7178-85. [PMID: 15611138 DOI: 10.1074/jbc.m411990200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the present study we characterize a novel RhoGAP protein (RC-GAP72) that interacts with actin stress fibers, focal adhesions, and cell-cell adherens junctions via its 185-amino acid C-terminal region. Overexpression of RC-GAP72 in fibroblasts induces cell rounding with partial or complete disruption of actin stress fibers and formation of membrane ruffles, lamellipodia, and filopodia. RC-GAP72 mutant truncated downstream of the GTPase-activating protein (GAP) domain retains the ability to stimulate membrane protrusions but fails to affect stress fiber integrity or induce cell retraction. A mutant protein consisting of the C terminus of RC-GAP72 and lacking the GAP domain does not exert any visible effect on cellular morphology. Inactivation of the GAP domain by a point mutation does not abolish the effect of RC-GAP72 on actin stress fibers but moderates its capability to induce membrane protrusions. Our data imply that the cytoskeletal localization of RC-GAP72 and its interaction with GTPases are essential for its effect on the integrity of actin stress fibers, whereas the induction of lamellipodia and filopodia depends on the activity of the GAP domain irrespective of binding to the actin cytoskeleton. We propose that RC-GAP72 affects cellular morphology by targeting activated Cdc42 and Rac1 GTPases to specific subcellular sites, triggering local morphological changes. The overall physiological functions of RC-GAP72 are presently unknown, yet our data suggest that RC-GAP72 plays a role in regulating cell morphology and cytoskeletal organization.
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Affiliation(s)
- Irena Lavelin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Hahn Y, Bera TK, Gehlhaus K, Kirsch IR, Pastan IH, Lee B. Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases. Proc Natl Acad Sci U S A 2004; 101:13257-61. [PMID: 15326299 PMCID: PMC516526 DOI: 10.1073/pnas.0405490101] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chromosomal rearrangements resulting in gene fusions are frequently involved in carcinogenesis. Here, we describe a semiautomatic procedure for identifying fusion gene transcripts by using publicly available mRNA and EST databases. With this procedure, we have identified 96 transcript sequences that are derived from 60 known fusion genes. Also, 47 or more additional sequences appear to be derived from 20 or more previously unknown putative fusion genes. We have experimentally verified the presence of a previously unknown IRA1/RGS17 fusion in the breast cancer cell line MCF7. The fusion gene encodes the full-length RGS17 protein, a regulator of G protein-coupled signaling, under the control of the IRA1 gene promoter. This study demonstrates that databases of ESTs can be used to discover fusion genes resulting from structural rearrangement of chromosomes.
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Affiliation(s)
- Yoonsoo Hahn
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
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17
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Wei CL, Ng P, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, Ruan Y. 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A 2004; 101:11701-6. [PMID: 15272081 PMCID: PMC511040 DOI: 10.1073/pnas.0403514101] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Indexed: 11/18/2022] Open
Abstract
Complete genome annotation relies on precise identification of transcription units bounded by a transcription initiation site (TIS) and a polyadenylation site (PAS). To facilitate this process, we developed a set of two complementary methods, 5' Long serial analysis of gene expression (LS) and 3'LS. These analyses are based on the original SAGE and LS methods coupled with full-length cDNA cloning, and enable the high-throughput extraction of the first and the last 20 bp of each transcript. We demonstrate that the mapping of 5'LS and 3'LS tags to the genome allows the localization of TIS and PAS. By using 537 tag pairs mapping to the region of known genes, we confirmed that >90% of the tag pairs appropriately assigned to the first and last exons. Moreover, by using tag sequences as primers for RT-PCRs, we were able to recover putative full-length transcripts in 81% of the attempts. This large-scale generation of transcript terminal tags is at least 20-40 times more efficient than full-length cDNA cloning and sequencing in the identification of complete transcription units. The apparent precision and deep coverage makes 5'LS and 3'LS an advanced approach for genome annotation through whole-transcriptome characterization.
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Affiliation(s)
- Chia-Lin Wei
- Genome Institute of Singapore, 60 Biopolis Street, Genome 02-01, Singapore 138672
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18
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Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto JI, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, Sugano S. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 2003; 36:40-5. [PMID: 14702039 DOI: 10.1038/ng1285] [Citation(s) in RCA: 662] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Accepted: 12/01/2003] [Indexed: 02/06/2023]
Abstract
As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs.
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Affiliation(s)
- Toshio Ota
- Helix Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan
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19
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Prasannan P, Pike S, Peng K, Shane B, Appling DR. Human mitochondrial C1-tetrahydrofolate synthase: gene structure, tissue distribution of the mRNA, and immunolocalization in Chinese hamster ovary calls. J Biol Chem 2003; 278:43178-43187. [PMID: 12937168 PMCID: PMC1457088 DOI: 10.1074/jbc.m304319200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
C1-tetrahydrofolate (THF) synthase is a trifunctional enzyme found in eukaryotes that contains the activities 10-formyl-THF synthetase, 5,10-methenyl-THF cyclohydrolase, and 5,10-methylene-THF dehydrogenase. The cytoplasmic isozyme of C1-THF synthase is well characterized in a number of mammals, including humans; but a mitochondrial isozyme has been previously identified only in the yeast Saccharomyces. Here, we report the identification and characterization of the human gene encoding a functional mitochondrial C1-THF synthase. The gene spans 236 kilobase pairs on chromosome 6 and consists of 28 exons plus one alternative exon. The gene encodes a protein of 978 amino acids, including an N-terminal mitochondrial targeting sequence. The mitochondrial isozyme is 61% identical to the human cytoplasmic isozyme. Expression of the gene was detected in most human tissues, but transcripts were highest in placenta, thymus, and brain. Two mRNAs were detected, a 3.6-kb transcript and a 1.1-kb transcript, and both transcripts were observed in varying ratios in each tissue. The shorter transcript results from an alternative splicing event, where exon 7 is spliced to exon 8a instead of exon 8. Exon 8a is derived from an exonized Alu sequence, sharing no homology with exon 8 of the long transcript, and encodes just 15 amino acids followed by a stop codon and a polyadenylation signal. This short transcript potentially encodes a bifunctional enzyme lacking 10-formyl-THF synthetase activity. Both transcripts initiate at the same 5'-site, 107 nucleotides up-stream of the ATG start codon. The full-length (2934 bp) cDNA fused to a C-terminal V5 epitope tag was expressed in Chinese hamster ovary cells. Immunoblots of subfractionated cells revealed a 107-kDa protein only in the mitochondrial fractions of these cells, confirming the mitochondrial localization of the protein. Yeast cells expressing the full-length human cDNA exhibited elevated 10-formyl-THF synthetase activity, confirming its identification as the human mitochondrial C1-THF synthase.
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MESH Headings
- Alternative Splicing
- Amino Acid Sequence
- Aminohydrolases/biosynthesis
- Aminohydrolases/chemistry
- Aminohydrolases/genetics
- Animals
- Blotting, Northern
- CHO Cells
- Chromosomes, Human, Pair 6
- Cloning, Molecular
- Codon, Initiator
- Codon, Terminator
- Cricetinae
- Cytoplasm/enzymology
- Cytoplasm/metabolism
- DNA, Complementary/metabolism
- Epitopes
- Exons
- Formate-Tetrahydrofolate Ligase/biosynthesis
- Formate-Tetrahydrofolate Ligase/chemistry
- Formate-Tetrahydrofolate Ligase/genetics
- Humans
- Immunoblotting
- Introns
- Methylenetetrahydrofolate Dehydrogenase (NADP)/biosynthesis
- Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry
- Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics
- Mitochondria/enzymology
- Mitochondria/metabolism
- Models, Biological
- Models, Genetic
- Molecular Sequence Data
- Multienzyme Complexes/biosynthesis
- Multienzyme Complexes/chemistry
- Multienzyme Complexes/genetics
- Protein Isoforms
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- Sequence Homology, Amino Acid
- Subcellular Fractions/metabolism
- Tissue Distribution
- Transfection
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Affiliation(s)
- Priya Prasannan
- Department of Chemistry & Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin TX 78712
| | - Schuyler Pike
- Department of Chemistry & Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin TX 78712
| | - Kun Peng
- Department of Nutritional Sciences, University of California, Berkeley CA 94720
| | - Barry Shane
- Department of Nutritional Sciences, University of California, Berkeley CA 94720
| | - Dean R Appling
- Department of Chemistry & Biochemistry, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin TX 78712
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20
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Bijnens APJJ, Gils A, Jutten B, Faber BCG, Heeneman S, Kitslaar PJEHM, Tordoir JHM, de Vries CJM, Kroon AA, Daemen MJAP, Cleutjens KBJM. Vasculin, a novel vascular protein differentially expressed in human atherogenesis. Blood 2003; 102:2803-10. [PMID: 12842993 DOI: 10.1182/blood-2003-01-0306] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Recent suppressive subtractive hybridization analysis on human atherosclerotic plaque-derived RNA revealed genes upregulated in plaques with a thrombus versus stable plaques. Clone SSH6, containing part of a putative open reading frame of an unknown protein, was further investigated. Full-length cDNA, coding for a 473-amino acid (aa) protein, was identified in a vascular smooth muscle cell (SMC) cDNA library. Bioinformatics suggested the presence of multiple SSH6 variants due to alternative splicing of exon 3. Multiple-tissue Northern blot analysis demonstrated a differential expression pattern of these variants, as a ubiquitously expressed SSH6 mRNA missing exon 3, was detected apart from a putative vascular SMC-specific form containing exon 3. Western blot analysis indicated a ubiquitous 35-kDa protein (SSH6-beta), in addition to a 45-kDa protein (vasculin), detected in the vascular wall and in plasma. Analysis of arteries displaying various stages of atherosclerosis indicated that the vasculin/SSH6-beta ratio increases throughout atherogenesis. Immunohistochemical analysis demonstrated cytoplasmic expression of SSH6 gene products in macrophages, endothelial cells, and SMCs. In summary, we identified a novel mRNA/protein, vasculin, in the arterial wall and plasma. The regulated expression of vasculin in plaques suggests a role in atherogenesis. Moreover, its presence in plasma opens perspectives for vasculin as a marker for atherosclerosis.
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Affiliation(s)
- Ann P J J Bijnens
- Department of Pathology, Cardiovascular Research Institute Maastricht, University of Maastricht, The Netherlands
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21
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Sato T, Mishina M. Representational difference analysis, high-resolution physical mapping, and transcript identification of the zebrafish genomic region for a motor behavior. Genomics 2003; 82:218-29. [PMID: 12837271 DOI: 10.1016/s0888-7543(03)00071-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Zebrafish is one of the best model organisms for investigating gene functions in vertebrates. By 4,5',8-trimethylpsoralen mutagenesis, we isolated a zebrafish mutant, vibrato, with defects in the spontaneous contraction and touch response. Whole genome subtraction between the wild-type and the mutant genomes by representational difference analysis yielded polymorphic markers tightly linked to the vibrato locus. Using these markers, we constructed a high-resolution physical map and localized the vibrato locus within a genomic region of 720 kb. Direct cDNA selection with the contig led to the identification of a novel gene, solo, encoding a protein with SEC14 and spectrin repeat domains. These domains of Solo shared significant amino acid sequence identities with those of mammalian Trio and Karilin. In addition, we found the zebrafish orthologs for mammalian TTN, COL5A2, and CED-6 in the vibrato region. Mapping of these genes localized human chromosomal regions possibly involved in motor disorders. Our results suggest that representational difference analysis provides an efficient way to isolate mutated genomic regions in zebrafish.
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Affiliation(s)
- Tomomi Sato
- Department of Molecular Neurobiology and Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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22
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Abaza A, Soleilhac JM, Westendorf J, Piel M, Crevel I, Roux A, Pirollet F. M phase phosphoprotein 1 is a human plus-end-directed kinesin-related protein required for cytokinesis. J Biol Chem 2003; 278:27844-52. [PMID: 12740395 PMCID: PMC2652640 DOI: 10.1074/jbc.m304522200] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human M phase phosphoprotein 1 (MPP1), previously identified through a screening of a subset of proteins specifically phosphorylated at the G2/M transition (Matsumoto-Taniura, N., Pirollet, F., Monroe, R., Gerace, L., and Westendorf, J. M. (1996) Mol. Biol. Cell 7, 1455-1469), is characterized as a plus-end-directed kinesin-related protein. Recombinant MPP1 exhibits in vitro microtubule-binding and microtubule-bundling properties as well as microtubule-stimulated ATPase activity. In gliding experiments using polarity-marked microtubules, MPP1 is a slow molecular motor that moves toward the microtubule plus-end at a 0.07 microm/s speed. In cycling cells, MPP1 localizes mainly to the nuclei in interphase. During mitosis, MPP1 is diffuse throughout the cytoplasm in metaphase and subsequently localizes to the midzone to further concentrate on the midbody. MPP1 suppression by RNA interference induces failure of cell division late in cytokinesis. We conclude that MPP1 is a new mitotic molecular motor required for completion of cytokinesis.
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MESH Headings
- Adenosine Triphosphatases/metabolism
- Amino Acid Sequence
- Animals
- Cell Cycle Proteins
- Cell Division/physiology
- Cell Line
- Cell Movement
- Cells, Cultured
- Cloning, Molecular
- Cytoplasm/metabolism
- DNA, Complementary/metabolism
- Electrophoresis, Polyacrylamide Gel
- Epitopes
- Flow Cytometry
- G2 Phase
- Gene Library
- Genome
- Green Fluorescent Proteins
- HeLa Cells
- Humans
- Immunoblotting
- Insecta
- Kinesins/metabolism
- Kinetics
- Luminescent Proteins/metabolism
- Metaphase
- Microscopy, Fluorescence
- Microtubules/metabolism
- Mitosis
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Phosphoproteins/metabolism
- Phosphoproteins/physiology
- Phosphorylation
- Protein Structure, Tertiary
- RNA Interference
- RNA, Small Interfering/metabolism
- Recombinant Fusion Proteins/metabolism
- Recombinant Proteins/metabolism
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Time Factors
- Tissue Distribution
- Transfection
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Affiliation(s)
- Aouatef Abaza
- Organisation Fonctionnelle du Cytosquelette
INSERM : U366Université Joseph Fourier - Grenoble ICea LYON
17, Rue Des Martyrs
38054 Grenoble Cedex 9,FR
| | - Jean-Marc Soleilhac
- Organisation Fonctionnelle du Cytosquelette
INSERM : U366Université Joseph Fourier - Grenoble ICea LYON
17, Rue Des Martyrs
38054 Grenoble Cedex 9,FR
| | - Joanne Westendorf
- Organisation Fonctionnelle du Cytosquelette
INSERM : U366Université Joseph Fourier - Grenoble ICea LYON
17, Rue Des Martyrs
38054 Grenoble Cedex 9,FR
| | - Matthieu Piel
- CDC, Compartimentation et dynamique cellulaires
CNRS : UMR144Institut Curie26 Rue d'Ulm
75248 Paris Cedex 05,FR
| | | | - Aurelien Roux
- UPCC, Unite physico-chimie Curie
CNRS : UMR168Institut CurieBâtiment Curie
26 rue d'Ulm
75248 Paris Cedex 05,FR
| | - Fabienne Pirollet
- Organisation Fonctionnelle du Cytosquelette
INSERM : U366Université Joseph Fourier - Grenoble ICea LYON
17, Rue Des Martyrs
38054 Grenoble Cedex 9,FR
- * Correspondence should be adressed to: Fabienne Pirollet
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23
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Davies BA, Topp JD, Sfeir AJ, Katzmann DJ, Carney DS, Tall GG, Friedberg AS, Deng L, Chen Z, Horazdovsky BF. Vps9p CUE domain ubiquitin binding is required for efficient endocytic protein traffic. J Biol Chem 2003; 278:19826-33. [PMID: 12654912 DOI: 10.1074/jbc.m301059200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rab5 GTPases are key regulators of protein trafficking through the early stages of the endocytic pathway. The yeast Rab5 ortholog Vps21p is activated by its guanine nucleotide exchange factor Vps9p. Here we show that Vps9p binds ubiquitin and that the CUE domain is necessary and sufficient for this interaction. Vps9p ubiquitin binding is required for efficient endocytosis of Ste3p but not for the delivery of the biosynthetic cargo carboxypeptidase Y to the vacuole. In addition, Vps9p is itself monoubiquitylated. Ubiquitylation is dependent on a functional CUE domain and Rsp5p, an E3 ligase that participates in cell surface receptor endocytosis. These findings define a new ubiquitin binding domain and implicate ubiquitin as a modulator of Vps9p function in the endocytic pathway.
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Affiliation(s)
- Brian A Davies
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
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24
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Anderson LM, Choe SE, Yukhananov RY, Hopfner RL, Church GM, Pratt RE, Dzau VJ. Identification of a novel set of genes regulated by a unique liver X receptor-alpha -mediated transcription mechanism. J Biol Chem 2003; 278:15252-60. [PMID: 12551904 DOI: 10.1074/jbc.m208644200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have reported previously that liver X receptor-alpha (LXRalpha) can mediate a novel cAMP-dependent increase in renin and c-myc gene transcription by binding as a monomer to a unique regulatory element termed the cAMP-negative response element (CNRE). To determine whether this novel action of LXRalpha has global implications on gene regulation, we employed expression profiling to identify other genes regulated by this unique mechanism. Here we report the existence of a set of known and unknown transcripts regulated in parallel with renin. Querying the Celera Mouse Genome Assembly revealed that a majority of these genes contained the consensus CNRE. We have confirmed the functionality of these CNREs by competition for LXRalpha binding via electrophoretic mobility shift assays (EMSA) and by the use of CNRE decoy molecules documenting the abolishment of the cAMP-mediated gene induction. Taken together, these results demonstrate that the interaction between cAMP-activated LXRalpha and the CNRE enhancer element is responsible for widespread changes in gene expression and identify a set of LXRalpha/cAMP-regulated genes that may have important biological implications.
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Affiliation(s)
- Leonard M Anderson
- Department of Medicine, Division of Cardiovascular Research, Laboratory of Genetic Physiology, Pain Research Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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25
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Paulding CA, Ruvolo M, Haber DA. The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc Natl Acad Sci U S A 2003; 100:2507-11. [PMID: 12604796 PMCID: PMC151371 DOI: 10.1073/pnas.0437015100] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene duplication and domain accretion are thought to be the major mechanisms for the emergence of novel genes during evolution. Such events are thought to have occurred at early stages in the vertebrate lineage, but genomic sequencing has recently revealed extensive amplification events during the evolution of higher primates. We report here that the Tre2 (USP6) oncogene is derived from the chimeric fusion of two genes, USP32 (NY-REN-60), and TBC1D3. USP32 is an ancient, highly conserved gene, whereas TBC1D3 is derived from a recent segmental duplication, which is absent in most other mammals and shows rapid amplification and dispersal through the primate lineage. Remarkably, the chimeric gene Tre2 exists only in the hominoid lineage of primates. This hominoid-specific oncogene arose as recently as 21-33 million years ago, after proliferation of the TBC1D3 segmental duplication in the primate lineage. In contrast to the broad expression pattern of USP32 and TBC1D3, expression of Tre2 is testis-specific, a pattern proposed for novel genes implicated in the emergence of reproductive barriers. The sudden emergence of chimeric proteins, such as that encoded by Tre2, may have contributed to hominoid speciation.
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Affiliation(s)
- Charles A Paulding
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
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26
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Kyogoku Y, Fujiyoshi Y, Shimada I, Nakamura H, Tsukihara T, Akutsu H, Odahara T, Okada T, Nomura N. Structural genomics of membrane proteins. Acc Chem Res 2003; 36:199-206. [PMID: 12641477 DOI: 10.1021/ar0101279] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A program on the structural genomics of membrane proteins has started at the BIRC, AIST, involving other academic institutions and industrial companies. Emphasis is being put on the development of techniques for the structural determination of membrane proteins of biological importance and ligand-receptor interactions by means of electron microscopy, X-ray diffraction, NMR, and computer simulation. Most efforts at the present stage, however, are being directed to finding suitable expression and purification systems and crystallization conditions for such proteins. The program is expected to be linked with the human full-length cDNA project and should lead to medical and industrial uses.
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Affiliation(s)
- Yoshimasa Kyogoku
- Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan
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27
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Heinemann U, Büssow K, Mueller U, Umbach P. Facilities and methods for the high-throughput crystal structural analysis of human proteins. Acc Chem Res 2003; 36:157-63. [PMID: 12641472 DOI: 10.1021/ar010129t] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Facilities and methods for the high-throughput crystal structure analysis of human proteins are described as recently established in the Protein Structure Factory, a Berlin-area structural genomics project. Genes encoding human proteins are expressed in either recombinant Escherichia coli or yeast (Saccharomyces cerevisiae or Pichia pastoris). To facilitate and standardize protein purification, the target proteins are produced with various tags for affinity chromatography. For high-throughput crystallization, a robotic station is being set up that has the capacity to handle 960 000 experiments simultaneously. The resulting protein crystals will be subjected to X-ray diffraction experiments at the third-generation synchrotron storage ring BESSY where protein crystallography beamlines are currently under construction. The Protein Structure Factory's strategy for high-throughput production and structure analysis of human proteins is evaluated based on first results.
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Affiliation(s)
- Udo Heinemann
- Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany.
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Zhan K, Vattem KM, Bauer BN, Dever TE, Chen JJ, Wek RC. Phosphorylation of eukaryotic initiation factor 2 by heme-regulated inhibitor kinase-related protein kinases in Schizosaccharomyces pombe is important for fesistance to environmental stresses. Mol Cell Biol 2002; 22:7134-46. [PMID: 12242291 PMCID: PMC139816 DOI: 10.1128/mcb.22.20.7134-7146.2002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protein synthesis is regulated by the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2alpha) in response to different environmental stresses. One member of the eIF2alpha kinase family, heme-regulated inhibitor kinase (HRI), is activated under heme-deficient conditions and blocks protein synthesis, principally globin, in mammalian erythroid cells. We identified two HRI-related kinases from Schizosaccharomyces pombe which have full-length homology with mammalian HRI. The two HRI-related kinases, named Hri1p and Hri2p, exhibit autokinase and kinase activity specific for Ser-51 of eIF2alpha, and both activities were inhibited in vitro by hemin, as previously described for mammalian HRI. Overexpression of Hri1p, Hri2p, or the human eIF2alpha kinase, double-stranded-RNA-dependent protein kinase (PKR), impeded growth of S. pombe due to elevated phosphorylation of eIF2alpha. Cells from strains with deletions of the hri1(+) and hri2(+) genes, individually or in combination, exhibited a reduced growth rate when exposed to heat shock or to arsenic compounds. Measurements of in vivo phosphorylation of eIF2alpha suggest that Hri1p and Hri2p differentially phosphorylate eIF2alpha in response to these stress conditions. These results demonstrate that HRI-related enzymes are not unique to vertebrates and suggest that these eIF2alpha kinases are important participants in diverse stress response pathways in some lower eukaryotes.
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Affiliation(s)
- Ke Zhan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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29
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Claudio JO, Masih-Khan E, Tang H, Gonçalves J, Voralia M, Li ZH, Nadeem V, Cukerman E, Francisco-Pabalan O, Liew CC, Woodgett JR, Stewart AK. A molecular compendium of genes expressed in multiple myeloma. Blood 2002; 100:2175-86. [PMID: 12200383 DOI: 10.1182/blood-2002-01-0008] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We have created a molecular resource of genes expressed in primary malignant plasma cells using a combination of cDNA library construction, 5' end single-pass sequencing, bioinformatics, and microarray analysis. In total, we identified 9732 nonredundant expressed genes. This dataset is available as the Myeloma Gene Index (www.uhnres.utoronto.ca/akstewart_lab).Predictably, the sequenced profile of myeloma cDNAs mirrored the known function of immunoglobulin-producing, high-respiratory rate, low-cycling, terminally differentiated plasma cells. Nevertheless, approximately 10% of myeloma-expressed sequences matched only entries in the database of Expressed Sequence Tags (dbEST) or the high-throughput genomic sequence (htgs) database. Numerous novel genes of potential biologic significance were identified. We therefore spotted 4300 sequenced cDNAs on glass slides creating a myeloma-enriched microarray. Several of the most highly expressed genes identified by sequencing, such as a novel putative disulfide isomerase (MGC3178), tumor rejection antigen TRA1, heat shock 70-kDa protein 5, and annexin A2, were also differentially expressed between myeloma and B lymphoma cell lines using this myeloma-enriched microarray. Furthermore, a defined subset of 34 up-regulated and 18 down-regulated genes on the array were able to differentiate myeloma from nonmyeloma cell lines. These not only include genes involved in B-cell biology such as syndecan, BCMA, PIM2, MUM1/IRF4, and XBP1, but also novel uncharacterized genes matching sequences only in the public databases. In summary, our expressed gene catalog and myeloma-enriched microarray contains numerous genes of unknown function and may complement other commercially available arrays in defining the molecular portrait of this hematopoietic malignancy. GenBank Accession numbers include BF169967-BF176369, BF185966-BF185969, and BF177280-BF177455.
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Affiliation(s)
- Jaime O Claudio
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, 610 University Avenue, Toronto, Ontario, M5G 2M9 Canada
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Scott MP, Zappacosta F, Kim EY, Annan RS, Miller WT. Identification of novel SH3 domain ligands for the Src family kinase Hck. Wiskott-Aldrich syndrome protein (WASP), WASP-interacting protein (WIP), and ELMO1. J Biol Chem 2002; 277:28238-46. [PMID: 12029088 DOI: 10.1074/jbc.m202783200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The importance of the SH3 domain of Hck in kinase regulation, substrate phosphorylation, and ligand binding has been established. However, few in vivo ligands are known for the SH3 domain of Hck. In this study, we used mass spectrometry to identify approximately 25 potential binding partners for the SH3 domain of Hck from the monocyte cell line U937. Two major interacting proteins were the actin binding proteins Wiskott-Aldrich syndrome protein (WASP) and WASP-interacting protein (WIP). We also focused on a novel interaction between Hck and ELMO1, an 84-kDa protein that was recently identified as the mammalian ortholog of the Caenorhabditis elegans gene, ced-12. In mammalian cells, ELMO1 interacts with Dock180 as a component of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. Using purified proteins, we confirmed that WASP-interacting protein and ELMO1 interact directly with the SH3 domain of Hck. We also show that Hck and ELMO1 interact in intact cells and that ELMO1 is heavily tyrosine-phosphorylated in cells that co-express Hck, suggesting that it is a substrate of Hck. The binding of ELMO1 to Hck is specifically dependent on the interaction of a polyproline motif with the SH3 domain of Hck. Our results suggest that these proteins may be novel activators/effectors of Hck.
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Affiliation(s)
- Margaret Porter Scott
- Department of Physiology and Biophysics, School of Medicine, State University of New York, Stony Brook, New York 11794-8661, USA
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31
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Derrien V, Couillault C, Franco M, Martineau S, Montcourrier P, Houlgatte R, Chavrier P. A conserved C-terminal domain of EFA6-family ARF6-guanine nucleotide exchange factors induces lengthening of microvilli-like membrane protrusions. J Cell Sci 2002; 115:2867-79. [PMID: 12082148 DOI: 10.1242/jcs.115.14.2867] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We recently reported the identification of EFA6 (exchange factor for ARF6), a brain-specific Sec7-domain-containing guanine nucleotide exchange factor that works specifically on ARF6. Here, we have characterized the product of a broadly expressed gene encoding a novel 1056 amino-acid protein that we have named EFA6B. We show that EFA6B, which contains a Sec7 domain that is highly homologous to EFA6, works as an ARF6-specific guanine exchange factor in vitro. Like EFA6, which will be referred to as EFA6A from now on, EFA6B is involved in membrane recycling and colocalizes with ARF6 in actin-rich membrane ruffles and microvilli-like protrusions on the dorsal cell surface in transfected baby hamster kidney cells. Strikingly, homology between EFA6A and EFA6B is not limited to the Sec7 domain but extends to an adjacent pleckstrin homology (PH) domain and a ∼150 amino-acid C-terminal region containing a predicted coiled coil motif. Association of EFA6A with membrane ruffles and microvilli-like structures depends on the PH domain, which probably interacts with phosphatidylinositol 4,5-biphosphate. Moreover, we show that overexpression of the PH domain/C-terminal region of EFA6A or EFA6B in the absence of the Sec7 domain promotes lengthening of dorsal microvillar protrusions. This morphological change requires the integrity of the coiled-coil motif. Lastly, database analysis reveals that the EFA6-family comprises at least four members in humans and is conserved in multicellular organisms throughout evolution. Our results suggest that EFA6 family guanine exchange factors are modular proteins that work through the coordinated action of the catalytic Sec7 domain to promote ARF6 activation, through the PH domain to regulate association with specific subdomains of the plasma membrane and through the C-terminal region to control actin cytoskeletal reorganization.
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Affiliation(s)
- Valérie Derrien
- Laboratoire de la Dynamique de la Membrane et du Cytosquelette, UMR 144, Centre National de la Recherche Scientifique, Institut Curie, Section Recherche. 26 rue d'Ulm, 75241 Paris Cedex 5, France
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Nam DK, Lee S, Zhou G, Cao X, Wang C, Clark T, Chen J, Rowley JD, Wang SM. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci U S A 2002; 99:6152-6. [PMID: 11972056 PMCID: PMC122918 DOI: 10.1073/pnas.092140899] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2002] [Indexed: 11/18/2022] Open
Abstract
We have analyzed a systematic flaw in the current system of gene identification: the oligo(dT) primer widely used for cDNA synthesis generates a high frequency of truncated cDNAs through internal poly(A) priming. Such truncated cDNAs may contribute to 12% of the expressed sequence tags in the current dbEST database. By using a synthetic transcript and real mRNA templates as models, we characterized the patterns of internal poly(A) priming by oligo(dT) primer. We further demonstrated that the internal poly(A) priming can be effectively diminished by replacing the oligo(dT) primer with a set of anchored oligo(dT) primers for reverse transcription. Our study indicates that cDNAs designed for genomewide gene identification should be synthesized by use of the anchored oligo(dT) primers, rather than the oligo(dT) primers, to diminish the generation of truncated cDNAs caused by internal poly(A) priming.
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Affiliation(s)
- Douglas Kyung Nam
- Department of Medicine, Center for Functional Genomics, University of Chicago, 5841 South Maryland Avenue, MC2115, Chicago, IL 60637, USA
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Kuruvilla FG, Shamji AF, Sternson SM, Hergenrother PJ, Schreiber SL. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 2002; 416:653-7. [PMID: 11948353 DOI: 10.1038/416653a] [Citation(s) in RCA: 306] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Small molecules that alter protein function provide a means to modulate biological networks with temporal resolution. Here we demonstrate a potentially general and scalable method of identifying such molecules by application to a particular protein, Ure2p, which represses the transcription factors Gln3p and Nil1p. By probing a high-density microarray of small molecules generated by diversity-oriented synthesis with fluorescently labelled Ure2p, we performed 3,780 protein-binding assays in parallel and identified several compounds that bind Ure2p. One compound, which we call uretupamine, specifically activates a glucose-sensitive transcriptional pathway downstream of Ure2p. Whole-genome transcription profiling and chemical epistasis demonstrate the remarkable Ure2p specificity of uretupamine and its ability to modulate the glucose-sensitive subset of genes downstream of Ure2p. These results demonstrate that diversity-oriented synthesis and small-molecule microarrays can be used to identify small molecules that bind to a protein of interest, and that these small molecules can regulate specific functions of the protein.
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Affiliation(s)
- Finny G Kuruvilla
- Howard Hughes Medical Institute, Institute for Chemistry and Cell Biology, Bauer Center for Genomics Research, Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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Doi N, Takashima H, Kinjo M, Sakata K, Kawahashi Y, Oishi Y, Oyama R, Miyamoto-Sato E, Sawasaki T, Endo Y, Yanagawa H. Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. Genome Res 2002; 12:487-92. [PMID: 11875038 PMCID: PMC155293 DOI: 10.1101/gr.218802] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We developed and tested a simple method for fluorescence labeling and interaction analysis of proteins based on a highly efficient in vitro translation system combined with high-throughput technologies such as microarrays and fluorescence cross-correlation spectroscopy (FCCS). By use of puromycin analogs linked to various fluorophores through a deoxycytidylic acid linker, a single fluorophore can be efficiently incorporated into a protein at the carboxyl terminus during in vitro translation. We confirmed that the resulting fluorescently labeled proteins are useful for probing protein-protein and protein-DNA interactions by means of pulldown assay, DNA microarrays, and FCCS in model experiments. These fluorescence assay systems can be easily extended to highly parallel analysis of protein interactions in studies of functional genomics.
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Affiliation(s)
- Nobuhide Doi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan
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Zheng X, Chung D, Takayama TK, Majerus EM, Sadler JE, Fujikawa K. Structure of von Willebrand factor-cleaving protease (ADAMTS13), a metalloprotease involved in thrombotic thrombocytopenic purpura. J Biol Chem 2001; 276:41059-63. [PMID: 11557746 DOI: 10.1074/jbc.c100515200] [Citation(s) in RCA: 565] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Thrombotic thrombocytopenic purpura is associated with acquired or congenital deficiency of a plasma von Willebrand factor-cleaving protease (VWFCP). Based on partial amino acid sequence, VWFCP was identified recently as a new member of the ADAMTS family of metalloproteases and designated ADAMTS13. The 4.6-kilobase pair cDNA sequence for VWFCP has now been determined. By Northern blotting, full-length VWFCP mRNA was detected only in liver. VWFCP consists of 1427 amino acid residues and has a signal peptide, a short propeptide terminating in the sequence RQRR, a reprolysin-like metalloprotease domain, a disintegrin-like domain, a thrombospondin-1 repeat, a Cys-rich domain, an ADAMTS spacer, seven additional thrombospondin-1 repeats, and two CUB domains. VWFCP apparently is made as a zymogen that requires proteolytic activation, possibly by furin intracellularly. Sites for Zn(2+) and Ca(2+) ions are conserved in the protease domain. The Cys-rich domain contains an RGDS sequence that could mediate integrin-dependent binding to platelets or other cells. Alternative splicing gives rise to at least seven potential variants that truncate the protein at different positions after the protease domain. Alternative splicing may have functional significance, producing proteins with distinct abilities to interact with cofactors, connective tissue, platelets, and von Willebrand factor.
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Affiliation(s)
- X Zheng
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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36
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Affiliation(s)
- R L Strausberg
- Cancer Genomics Office, National Cancer Institute, Bethesda, MD 20892, USA.
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37
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Abstract
Genome and expressed sequence tag projects are rapidly cataloguing and cloning the genes of higher organisms, including humans. An emerging challenge is to rapidly uncover the functions of genes and to identify gene products with desired properties. We have developed a microarray-driven gene expression system for the functional analysis of many gene products in parallel. Mammalian cells are cultured on a glass slide printed in defined locations with different DNAs. Cells growing on the printed areas take up the DNA, creating spots of localized transfection within a lawn of non-transfected cells. By printing sets of complementary DNAs cloned in expression vectors, we make microarrays whose features are clusters of live cells that express a defined cDNA at each location. Here we demonstrate two uses for our approach: as an alternative to protein microarrays for the identification of drug targets, and as an expression cloning system for the discovery of gene products that alter cellular physiology. By screening transfected cell microarrays expressing 192 different cDNAs, we identified proteins involved in tyrosine kinase signalling, apoptosis and cell adhesion, and with distinct subcellular distributions.
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Affiliation(s)
- J Ziauddin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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