51
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Gayathri SC, Manoj N. Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases. J Mol Biol 2020; 432:166692. [PMID: 33122004 DOI: 10.1016/j.jmb.2020.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023]
Abstract
PLP-dependent enzymes catalyze a plethora of chemical reactions affecting diverse physiological functions. Here we report the structural determinants of the reaction mechanism in a Group II PLP-dependent decarboxylase by assigning two early intermediates. The in-crystallo complexes of the PLP bound form, and the Dunathan and quinonoid intermediates, allowed direct observation of the active site interactions. The structures reveal that a subtle rearrangement of a conserved Arg residue in concert with a water-mediated interaction with the carboxylate of the Dunathan intermediate, appears to directly stabilize the alignment and facilitate the release of CO2 to yield the quinonoid. Modeling indicates that the conformational change of a dynamic catalytic loop to a closed form controls a conserved network of hydrogen bond interactions between catalytic residues to protonate the quinonoid. Our results provide a structural framework to elucidate mechanistic roles of residues that govern reaction specificity and catalysis in PLP-dependent decarboxylation.
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Affiliation(s)
- Subash Chellam Gayathri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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52
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Matti C, D'Uonnolo G, Artinger M, Melgrati S, Salnikov A, Thelen S, Purvanov V, Strobel TD, Spannagel L, Thelen M, Legler DF. CCL20 is a novel ligand for the scavenging atypical chemokine receptor 4. J Leukoc Biol 2020; 107:1137-1154. [PMID: 32533638 DOI: 10.1002/jlb.2ma0420-295rrr] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
The chemokine CCL20 is broadly produced by endothelial cells in the liver, the lung, in lymph nodes and mucosal lymphoid tissues, and recruits CCR6 expressing leukocytes, particularly dendritic cells, mature B cells, and subpopulations of T cells. How CCL20 is systemically scavenged is currently unknown. Here, we identify that fluorescently labeled human and mouse CCL20 are efficiently taken-up by the atypical chemokine receptor ACKR4. CCL20 shares ACKR4 with the homeostatic chemokines CCL19, CCL21, and CCL25, although with a lower affinity. We demonstrate that all 4 human chemokines recruit β-arrestin1 and β-arrestin2 to human ACKR4. Similarly, mouse CCL19, CCL21, and CCL25 equally activate the human receptor. Interestingly, at the same chemokine concentration, mouse CCL20 did not recruit β-arrestins to human ACKR4. Further cross-species analysis suggests that human ACKR4 preferentially takes-up human CCL20, whereas mouse ACKR4 similarly internalizes mouse and human CCL20. Furthermore, we engineered a fluorescently labeled chimeric chemokine consisting of the N-terminus of mouse CCL25 and the body of mouse CCL19, termed CCL25_19, which interacts with and is taken-up by human and mouse ACKR4.
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Affiliation(s)
- Christoph Matti
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland
| | - Giulia D'Uonnolo
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Marc Artinger
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland
| | - Serena Melgrati
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Angela Salnikov
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland
| | - Sylvia Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Vladimir Purvanov
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland
| | - Tobias D Strobel
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland
| | - Lisa Spannagel
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Daniel F Legler
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland.,Faculty of Biology, University of Konstanz, Konstanz, Germany.,Theodor Kocher Institute, University of Bern, Bern, Switzerland
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53
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Craig PA. Something old, something new: Teaching the BMB lab. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:640-642. [PMID: 32400064 DOI: 10.1002/bmb.21359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Lab courses are a significant component of biochemistry and molecular biology (BMB) education. In teaching the labs, we combine established techniques with novel approaches. Lab formats have also moved from traditional cookbook style labs to guided inquiry to course-based undergraduate research experiences (CUREs), where faculty bring their own research interests into the course setting with a larger number of students in a much more restricted time frame. This presentation is designed to explore some of these ideas and challenge the reader to introduce research opportunities to all students, not just the smaller group of students in their research labs.
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Affiliation(s)
- Paul A Craig
- School of Chemistry & Materials Science, Rochester Institute of Technology, Rochester, New York, USA
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54
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Terai H, Hamamoto J, Emoto K, Masuda T, Manabe T, Kuronuma S, Kobayashi K, Masuzawa K, Ikemura S, Nakayama S, Kawada I, Suzuki Y, Takeuchi O, Suzuki Y, Ohtsuki S, Yasuda H, Soejima K, Fukunaga K. SHOC2 Is a Critical Modulator of Sensitivity to EGFR-TKIs in Non-Small Cell Lung Cancer Cells. Mol Cancer Res 2020; 19:317-328. [PMID: 33106373 DOI: 10.1158/1541-7786.mcr-20-0664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/16/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
EGFR mutation-positive patients with non-small cell lung cancer (NSCLC) respond well to treatment with EGFR-tyrosine kinase inhibitors (EGFR-TKI); however, treatment with EGFR-TKIs is not curative, owing to the presence of residual cancer cells with intrinsic or acquired resistance to this class of drugs. Additional treatment targets that may enhance the efficacy of EGFR-TKIs remain elusive. Using a CRISPR/Cas9-based screen, we identified the leucine-rich repeat scaffold protein SHOC2 as a key modulator of sensitivity to EGFR-TKI treatment. On the basis of in vitro assays, we demonstrated that SHOC2 expression levels strongly correlate with the sensitivity to EGFR-TKIs and that SHOC2 affects the sensitivity to EGFR-TKIs in NSCLC cells via SHOC2/MRAS/PP1c and SHOC2/SCRIB signaling. The potential SHOC2 inhibitor celastrol phenocopied SHOC2 depletion. In addition, we confirmed that SHOC2 expression levels were important for the sensitivity to EGFR-TKIs in vivo. Furthermore, IHC showed the accumulation of cancer cells that express high levels of SHOC2 in lung cancer tissues obtained from patients with NSCLC who experienced acquired resistance to EGFR-TKIs. These data indicate that SHOC2 may be a therapeutic target for patients with NSCLC or a biomarker to predict sensitivity to EGFR-TKI therapy in EGFR mutation-positive patients with NSCLC. Our findings may help improve treatment strategies for patients with NSCLC harboring EGFR mutations. IMPLICATIONS: This study showed that SHOC2 works as a modulator of sensitivity to EGFR-TKIs and the expression levels of SHOC2 can be used as a biomarker for sensitivity to EGFR-TKIs.
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Affiliation(s)
- Hideki Terai
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan. .,Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan.,Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan.,Clinical and Translational Research Center, Keio University School of Medicine, Tokyo, Japan
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan
| | - Katsura Emoto
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tadashi Manabe
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Keigo Kobayashi
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keita Masuzawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinnosuke Ikemura
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Sohei Nakayama
- Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yusuke Suzuki
- Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yukio Suzuki
- Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan.,Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Clinical and Translational Research Center, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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55
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Debets MF, Tastan OY, Wisnovsky SP, Malaker SA, Angelis N, Moeckl LKR, Choi J, Flynn H, Wagner LJS, Bineva-Todd G, Antonopoulos A, Cioce A, Browne WM, Li Z, Briggs DC, Douglas HL, Hess GT, Agbay AJ, Roustan C, Kjaer S, Haslam SM, Snijders AP, Bassik MC, Moerner WE, Li VSW, Bertozzi CR, Schumann B. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proc Natl Acad Sci U S A 2020; 117:25293-25301. [PMID: 32989128 DOI: 10.1101/2020.04.23.057208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Protein glycosylation events that happen early in the secretory pathway are often dysregulated during tumorigenesis. These events can be probed, in principle, by monosaccharides with bioorthogonal tags that would ideally be specific for distinct glycan subtypes. However, metabolic interconversion into other monosaccharides drastically reduces such specificity in the living cell. Here, we use a structure-based design process to develop the monosaccharide probe N-(S)-azidopropionylgalactosamine (GalNAzMe) that is specific for cancer-relevant Ser/Thr(O)-linked N-acetylgalactosamine (GalNAc) glycosylation. By virtue of a branched N-acylamide side chain, GalNAzMe is not interconverted by epimerization to the corresponding N-acetylglucosamine analog by the epimerase N-acetylgalactosamine-4-epimerase (GALE) like conventional GalNAc-based probes. GalNAzMe enters O-GalNAc glycosylation but does not enter other major cell surface glycan types including Asn(N)-linked glycans. We transfect cells with the engineered pyrophosphorylase mut-AGX1 to biosynthesize the nucleotide-sugar donor uridine diphosphate (UDP)-GalNAzMe from a sugar-1-phosphate precursor. Tagged with a bioorthogonal azide group, GalNAzMe serves as an O-glycan-specific reporter in superresolution microscopy, chemical glycoproteomics, a genome-wide CRISPR-knockout (CRISPR-KO) screen, and imaging of intestinal organoids. Additional ectopic expression of an engineered glycosyltransferase, "bump-and-hole" (BH)-GalNAc-T2, boosts labeling in a programmable fashion by increasing incorporation of GalNAzMe into the cell surface glycoproteome. Alleviating the need for GALE-KO cells in metabolic labeling experiments, GalNAzMe is a precision tool that allows a detailed view into the biology of a major type of cancer-relevant protein glycosylation.
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Affiliation(s)
- Marjoke F Debets
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Omur Y Tastan
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lauren J S Wagner
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ganka Bineva-Todd
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Peptide Chemistry Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Anna Cioce
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - William M Browne
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Zhen Li
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Holly L Douglas
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - Anthony J Agbay
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjaer
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Stuart M Haslam
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| | - Benjamin Schumann
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom;
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
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56
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Moparthi L, Koch S. A uniform expression library for the exploration of FOX transcription factor biology. Differentiation 2020; 115:30-36. [PMID: 32858261 DOI: 10.1016/j.diff.2020.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 12/29/2022]
Abstract
Forkhead box (FOX) family transcription factors play essential roles in development, tissue homeostasis, and disease. Although the biology of several FOX proteins has been studied in depth, it is unclear to what extent these findings apply to even closely related family members, which frequently exert overlapping but non-redundant functions. To help address this question, we have generated a uniform, ready-to-use expression library of all 44 human FOX transcription factors with a convenient peptide tag for parallel screening assays. In addition, we have generated multiple universal forkhead box reporter plasmids, which can be used to monitor the transcriptional activity of most FOX proteins with high fidelity. As a proof-of-principle, we use our plasmid library to identify the DNA repair protein XRCC6/Ku70 as a selective FOX interaction partner and regulator of FOX transcriptional activity. We believe that these tools, which we make available via the Addgene plasmid repository, will considerably expedite the investigation of FOX protein biology.
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Affiliation(s)
- Lavanya Moparthi
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Linköping University, Linköping, Sweden.
| | - Stefan Koch
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Linköping University, Linköping, Sweden.
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57
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Tang Y, Saul J, Nagaratnam N, Martin-Garcia JM, Fromme P, Qiu J, LaBaer J. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening. Sci Rep 2020; 10:13323. [PMID: 32770037 PMCID: PMC7414197 DOI: 10.1038/s41598-020-70163-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Baculovirus mediated-insect cell expression systems have been widely used for producing heterogeneous proteins. However, to date, there is still the lack of an easy-to-manipulate system that enables the high-throughput protein characterization in insect cells by taking advantage of large existing Gateway clone libraries. To resolve this limitation, we have constructed a suite of Gateway-compatible pIEx-derived baculovirus expression vectors that allow the rapid and cost-effective construction of expression clones for mass parallel protein expression in insect cells. This vector collection also supports the attachment of a variety of fusion tags to target proteins to meet the needs for different research applications. We first demonstrated the utility of these vectors for protein expression and purification using a set of 40 target proteins of various sizes, cellular localizations and host organisms. We then established a scalable pipeline coupled with the SONICC and TEM techniques to screen for microcrystal formation within living insect cells. Using this pipeline, we successfully identified microcrystals for ~ 16% of the tested protein set, which can be potentially used for structure elucidation by X-ray crystallography. In summary, we have established a versatile pipeline enabling parallel gene cloning, protein expression and purification, and in vivo microcrystal screening for structural studies.
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Affiliation(s)
- Yanyang Tang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Justin Saul
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Jose M Martin-Garcia
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
| | - Joshua LaBaer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
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58
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Bostwick AM, Moya GE, Senti ML, Basu U, Shen J, Patel SS, Dittenhafer-Reed KE. Phosphorylation of mitochondrial transcription factor B2 controls mitochondrial DNA binding and transcription. Biochem Biophys Res Commun 2020; 528:580-585. [PMID: 32505352 PMCID: PMC9161741 DOI: 10.1016/j.bbrc.2020.05.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/20/2020] [Indexed: 11/24/2022]
Abstract
Mammalian cells contain genetic information in two compartments, the nucleus and the mitochondria. Mitochondrial gene expression must be coordinated with nuclear gene expression to respond to cellular energetic needs. To gain insight into the coordination between the nucleus and mitochondria, there is a need to understand the regulation of transcription of mitochondrial DNA (mtDNA). Reversible protein post-translational modifications of the mtDNA transcriptional machinery may be one way to control mtDNA transcription. Here we focus on a member of the mtDNA transcription initiation complex, mitochondrial transcription factor B2 (TFB2M). TFB2M melts mtDNA at the promoter to allow the RNA polymerase (POLRMT) to access the DNA template and initiate transcription. Three phosphorylation sites have been previously identified on TFB2M by mass spectrometry: threonine 184, serine 197, and threonine 313. Phosphomimetics were established at these positions. Proteins were purified and analyzed for their ability to bind mtDNA and initiate transcription in vitro. Our results indicate phosphorylation at threonine 184 and threonine 313 impairs promoter binding and prevents transcription. These findings provide a potential regulatory mechanism of mtDNA transcription and help clarify the importance of protein post-translational modifications in mitochondrial function.
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Affiliation(s)
- Alicia M Bostwick
- Hope College, Department of Chemistry, 35 E. 12th Street, Holland, MI, 49423, United States
| | - Gonzalo E Moya
- Hope College, Department of Chemistry, 35 E. 12th Street, Holland, MI, 49423, United States
| | - Mackenna L Senti
- Hope College, Department of Chemistry, 35 E. 12th Street, Holland, MI, 49423, United States
| | - Urmimala Basu
- Rutgers University, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, 683 Hoes Lane, Piscataway, NJ, 08854, United States
| | - Jiayu Shen
- Rutgers University, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, 683 Hoes Lane, Piscataway, NJ, 08854, United States
| | - Smita S Patel
- Rutgers University, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, 683 Hoes Lane, Piscataway, NJ, 08854, United States
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59
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Ding Z, Kloss JM, Tuncali S, Tran NL, Loftus JC. TROY signals through JAK1-STAT3 to promote glioblastoma cell migration and resistance. Neoplasia 2020; 22:352-364. [PMID: 32629176 PMCID: PMC7338993 DOI: 10.1016/j.neo.2020.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 11/26/2022]
Abstract
Glioblastoma (GBM) is the most common primary malignant brain tumor in adults and carries a discouraging prognosis. Its aggressive and highly infiltrative nature renders the current standard treatment of maximal surgical resection, radiation, and chemotherapy relatively ineffective. Identifying the signaling pathways that regulate GBM migration/invasion and resistance is required to develop more effective therapeutic regimens to treat GBM. Expression of TROY, an orphan receptor of the TNF receptor superfamily, increases with glial tumor grade, inversely correlates with patient overall survival, stimulates GBM cell invasion in vitro and in vivo, and increases resistance to temozolomide and radiation therapy. Conversely, silencing TROY expression inhibits GBM cell invasion, increases sensitivity to temozolomide, and prolongs survival in a preclinical intracranial xenograft model. Here, we have identified for the first time that TROY interacts with JAK1. Increased TROY expression increases JAK1 phosphorylation. In addition, increased TROY expression promotes STAT3 phosphorylation and STAT3 transcriptional activity that is dependent upon JAK1. TROY-mediated activation of STAT3 is independent of its ability to stimulate activity of NF-κB. Inhibition of JAK1 activity by ruxolitinib or knockdown of JAK1 expression by siRNA significantly inhibits TROY-induced STAT3 activation, GBM cell migration, and decreases resistance to temozolomide. Taken together, our data indicate that the TROY signaling complex may represent a potential therapeutic target with the distinctive capacity to exert effects on multiple pathways mediating GBM cell invasion and resistance.
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Affiliation(s)
- Zonghui Ding
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85259, United States
| | - Jean M Kloss
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85259, United States
| | - Serdar Tuncali
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85259, United States
| | - Nhan L Tran
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85259, United States; Department of Neurosurgery, Mayo Clinic Arizona, Scottsdale, AZ 85259, United States.
| | - Joseph C Loftus
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, AZ 85259, United States.
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60
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Abrams ME, Johnson KA, Perelman SS, Zhang LS, Endapally S, Mar KB, Thompson BM, McDonald JG, Schoggins JW, Radhakrishnan A, Alto NM. Oxysterols provide innate immunity to bacterial infection by mobilizing cell surface accessible cholesterol. Nat Microbiol 2020; 5:929-942. [PMID: 32284563 PMCID: PMC7442315 DOI: 10.1038/s41564-020-0701-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/04/2020] [Indexed: 11/09/2022]
Abstract
Cholesterol 25-hydroxylase (CH25H) is an interferon-stimulated gene that converts cholesterol to the oxysterol 25-hydroxycholesterol (25HC). Circulating 25HC modulates essential immunological processes including antiviral immunity, inflammasome activation and antibody class switching; and dysregulation of CH25H may contribute to chronic inflammatory disease and cancer. Although 25HC is a potent regulator of cholesterol storage, uptake, efflux and biosynthesis, how these metabolic activities reprogram the immunological state of target cells remains poorly understood. Here, we used recently designed toxin-based biosensors that discriminate between distinct pools of plasma membrane cholesterol to elucidate how 25HC prevents Listeria monocytogenes from traversing the plasma membrane of infected host cells. The 25HC-mediated activation of acyl-CoA:cholesterol acyltransferase (ACAT) triggered rapid internalization of a biochemically defined fraction of cholesterol, termed 'accessible' cholesterol, from the plasma membrane while having little effect on cholesterol in complexes with sphingomyelin. We show that evolutionarily distinct bacterial species, L. monocytogenes and Shigella flexneri, exploit the accessible pool of cholesterol for infection and that acute mobilization of this pool by oxysterols confers immunity to these pathogens. The significance of this signal-mediated membrane remodelling pathway probably extends beyond host defence systems, as several other biologically active oxysterols also mobilize accessible cholesterol through an ACAT-dependent mechanism.
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Affiliation(s)
- Michael E Abrams
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kristen A Johnson
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofya S Perelman
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Microbiology, New York University School of Medicine, NY, NY, USA
| | - Li-Shu Zhang
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shreya Endapally
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bonne M Thompson
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Arun Radhakrishnan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Neal M Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Expression, purification, and glycosylation of epidermal growth factor-like repeat 27 from mouse NOTCH1. Protein Expr Purif 2020; 174:105681. [PMID: 32505675 DOI: 10.1016/j.pep.2020.105681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 11/21/2022]
Abstract
Notch receptors have large extracellular domains containing up to 36 tandem epidermal growth factor-like (EGF) repeats, which facilitate cell signaling by binding ligands on neighboring cells. Notch receptors play major roles in a variety of developmental processes by controlling cell fate decisions. Each EGF repeat consists of about 40 amino acids with 3 conserved disulfide bonds. Many of the EGF repeats are modified by O-linked fucose glycans, and more than half have calcium-binding sites, but the sequences of the EGF repeats vary giving distinct roles to each repeat. EGF repeat 27 (EGF27) from mouse NOTCH1 is modified with O-fucose and is 1 of 7 repeats that is differentially modified by specific Fringe enzymes, which are known to regulate NOTCH1 activation and ligand binding. To better understand the role of EGF27 in NOTCH1 function and regulation, the 3-dimensional structures of EGF27 and its glycoforms are being pursued. E. coli cells were used to produce EGF27 in sufficient quantities for nuclear magnetic resonance analysis. Previous attempts to express the repeat alone and refold the repeat under a steady redox environment were unsuccessful due to low yields and extensive mixed-disulfide bond cross-linking. A new strategy using a cleavable maltose binding protein fusion tag increased the solubility and yield of EGF27. With the fusion tag, EGF27 was refolded to produce the correct disulfide bond arrangement, which was verified enzymatically with the glycosyltransferases, Protein O-fucosyltransferase 1 (POFUT1) and Lunatic Fringe (LFNG).
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Gillespie MA, Palii CG, Sanchez-Taltavull D, Shannon P, Longabaugh WJR, Downes DJ, Sivaraman K, Espinoza HM, Hughes JR, Price ND, Perkins TJ, Ranish JA, Brand M. Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Mol Cell 2020; 78:960-974.e11. [PMID: 32330456 PMCID: PMC7344268 DOI: 10.1016/j.molcel.2020.03.031] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/20/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022]
Abstract
Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs' cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.
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Affiliation(s)
| | - Carmen G Palii
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada
| | - Daniel Sanchez-Taltavull
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada; Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Paul Shannon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Karthi Sivaraman
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
| | - Jeffrey A Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
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63
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Carias KV, Zoeteman M, Seewald A, Sanderson MR, Bischof JM, Wevrick R. A MAGEL2-deubiquitinase complex modulates the ubiquitination of circadian rhythm protein CRY1. PLoS One 2020; 15:e0230874. [PMID: 32315313 PMCID: PMC7173924 DOI: 10.1371/journal.pone.0230874] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/10/2020] [Indexed: 01/15/2023] Open
Abstract
MAGEL2 encodes the L2 member of the MAGE (melanoma antigen) protein family. Protein truncating mutations in MAGEL2 cause Schaaf-Yang syndrome, and MAGEL2 is one of a small set of genes deleted in Prader-Willi syndrome. Excessive daytime sleepiness, night-time or early morning waking, and narcoleptic symptoms are seen in people with Prader-Willi syndrome and Schaaf-Yang syndrome, while mice carrying a gene-targeted Magel2 deletion have disrupted circadian rhythms. These phenotypes suggest that MAGEL2 is important for the robustness of the circadian rhythm. However, a cellular role for MAGEL2 has yet to be elucidated. MAGEL2 influences the ubiquitination of substrate proteins to target them for further modification or to alter their stability through proteasomal degradation pathways. Here, we characterized relationships among MAGEL2 and proteins that regulate circadian rhythm. The effect of MAGEL2 on the key circadian rhythm protein cryptochrome 1 (CRY1) was assessed using in vivo proximity labelling (BioID), immunofluorescence microscopy and ubiquitination assays. We demonstrate that MAGEL2 modulates the ubiquitination of CRY1. Further studies will clarify the cellular role MAGEL2 normally plays in circadian rhythm, in part through ubiquitination and regulation of stability of the CRY1 protein.
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Affiliation(s)
- K. Vanessa Carias
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Mercedes Zoeteman
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Abigail Seewald
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | | | - Jocelyn M. Bischof
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- * E-mail:
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64
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Lear TB, Lockwood KC, Larsen M, Tuncer F, Kennerdell JR, Morse C, Valenzi E, Tabib T, Jurczak MJ, Kass DJ, Evankovich JW, Finkel T, Lafyatis R, Liu Y, Chen BB. Kelch-like protein 42 is a profibrotic ubiquitin E3 ligase involved in systemic sclerosis. J Biol Chem 2020; 295:4171-4180. [PMID: 32071084 PMCID: PMC7105301 DOI: 10.1074/jbc.ac119.012066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Systemic scleroderma (SSc) is an autoimmune disease that affects over 2.5 million people globally. SSc results in dysfunctional connective tissues with excessive profibrotic signaling, affecting skin, cardiovascular, and particularly lung tissue. Over three-quarters of individuals with SSc develop pulmonary fibrosis within 5 years, the main cause of SSc mortality. No approved medicines to manage lung SSc currently exist. Recent research suggests that profibrotic signaling by transforming growth factor β (TGF-β) is directly tied to SSc. Previous studies have also shown that ubiquitin E3 ligases potently control TGF-β signaling through targeted degradation of key regulatory proteins; however, the roles of these ligases in SSc-TGF-β signaling remain unclear. Here we utilized primary SSc patient lung cells for high-throughput screening of TGF-β signaling via high-content imaging of nuclear translocation of the profibrotic transcription factor SMAD family member 2/3 (SMAD2/3). We screened an RNAi library targeting ubiquitin E3 ligases and observed that knockdown of the E3 ligase Kelch-like protein 42 (KLHL42) impairs TGF-β-dependent profibrotic signaling. KLHL42 knockdown reduced fibrotic tissue production and decreased TGF-β-mediated SMAD activation. Using unbiased ubiquitin proteomics, we identified phosphatase 2 regulatory subunit B'ϵ (PPP2R5ϵ) as a KLHL42 substrate. Mechanistic experiments validated ubiquitin-mediated control of PPP2R5ϵ stability through KLHL42. PPP2R5ϵ knockdown exacerbated TGF-β-mediated profibrotic signaling, indicating a role of PPP2R5ϵ in SSc. Our findings indicate that the KLHL42-PPP2R5ϵ axis controls profibrotic signaling in SSc lung fibroblasts. We propose that future studies could investigate whether chemical inhibition of KLHL42 may ameliorate profibrotic signaling in SSc.
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Affiliation(s)
- Travis B Lear
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261; Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Karina C Lockwood
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Mads Larsen
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Ferhan Tuncer
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Jason R Kennerdell
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Christina Morse
- Division of Rheumatology and Clinical Immunology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Eleanor Valenzi
- Division of Rheumatology and Clinical Immunology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Michael J Jurczak
- Division of Endocrinology and Metabolism, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Daniel J Kass
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - John W Evankovich
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213; Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Toren Finkel
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213; Division of Cardiology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Yuan Liu
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213; Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213.
| | - Bill B Chen
- Aging Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213; Acute Lung Injury Center of Excellence, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213; Vascular Medicine Institute, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213.
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Garranzo-Asensio M, Guzmán-Aránguez A, Povedano E, Ruiz-Valdepeñas Montiel V, Poves C, Fernandez-Aceñero MJ, Montero-Calle A, Solís-Fernández G, Fernandez-Diez S, Camps J, Arenas M, Rodríguez-Tomàs E, Joven J, Sanchez-Martinez M, Rodriguez N, Dominguez G, Yáñez-Sedeño P, Pingarrón JM, Campuzano S, Barderas R. Multiplexed monitoring of a novel autoantibody diagnostic signature of colorectal cancer using HaloTag technology-based electrochemical immunosensing platform. Theranostics 2020; 10:3022-3034. [PMID: 32194852 PMCID: PMC7053203 DOI: 10.7150/thno.42507] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/02/2020] [Indexed: 12/15/2022] Open
Abstract
Background and Purpose: The humoral immune response in cancer patients can be used for early detection of the disease. Autoantibodies raised against tumor-associated antigens (TAAs) are promising clinical biomarkers for reliable cancer diagnosis, prognosis, and therapy monitoring. In this study, an electrochemical disposable multiplexed immunosensing platform able to integrate difficult- and easy-to-express colorectal cancer (CRC) TAAs is reported for the sensitive determination of eight CRC-specific autoantibodies. Methods: The electrochemical immunosensing approach involves the use of magnetic microcarriers (MBs) as solid supports modified with covalently immobilized HaloTag fusion proteins for the selective capture of specific autoantibodies. After magnetic capture of the modified MBs onto screen-printed carbon working electrodes, the amperometric responses measured using the hydroquinone (HQ)/H2O2 system were related to the levels of autoantibodies in plasma. Results: The biosensing platform was applied to the analysis of autoantibodies against 8 TAAs described for the first time in this work in plasma samples from healthy asymptomatic individuals (n=3), and patients with high-risk of developing CRC (n=3), and from patients already diagnosed with colorectal (n=3), lung (n=2) or breast (n=2) cancer. The developed bioplatform demonstrated an improved discrimination between CRC patients and controls (asymptomatic healthy individuals and breast and lung cancer patients) compared to an ELISA-like luminescence test. Conclusions: The proposed methodology uses a just-in-time produced protein in a simpler protocol, with low sample volume, and involves cost-effective instrumentation, which could be used in a high-throughput manner for reliable population screening to facilitate the detection of early CRC patients at affordable cost.
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Affiliation(s)
- María Garranzo-Asensio
- Departamento de Bioquímica y Biología Molecular, Facultad de Óptica y Optometría, Universidad Complutense de Madrid, 28037 Madrid, Spain
- UFIEC, Chronic Disease Programme, Instituto de Salud Carlos III, Majadahonda 28220, Madrid, Spain
| | - Ana Guzmán-Aránguez
- Departamento de Bioquímica y Biología Molecular, Facultad de Óptica y Optometría, Universidad Complutense de Madrid, 28037 Madrid, Spain
| | - Eloy Povedano
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Víctor Ruiz-Valdepeñas Montiel
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Carmen Poves
- Gastroenterology Unit, Hospital Universitario Clínico San Carlos, E-28040, Madrid, Spain
| | | | - Ana Montero-Calle
- UFIEC, Chronic Disease Programme, Instituto de Salud Carlos III, Majadahonda 28220, Madrid, Spain
| | | | | | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d´Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus (Spain)
| | - Meritxell Arenas
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d´Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus (Spain)
| | - Elisabeth Rodríguez-Tomàs
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d´Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus (Spain)
- Department of Radiation Oncology, Hospital Universitari Sant Joan, Institut d´Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus (Spain)
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d´Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus (Spain)
| | | | - Nuria Rodriguez
- Medical Oncology Department, Hospital Universitario La Paz, E-28046, Madrid, Spain
| | - Gemma Dominguez
- Departamento de Medicina, Facultad de Medicina, Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, E-28029, Madrid, Spain
| | - Paloma Yáñez-Sedeño
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - José Manuel Pingarrón
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Susana Campuzano
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Rodrigo Barderas
- UFIEC, Chronic Disease Programme, Instituto de Salud Carlos III, Majadahonda 28220, Madrid, Spain
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Phenotypic and genotypic characterization of families with complex intellectual disability identified pathogenic genetic variations in known and novel disease genes. Sci Rep 2020; 10:968. [PMID: 31969655 PMCID: PMC6976666 DOI: 10.1038/s41598-020-57929-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/03/2020] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability (ID), which presents itself during childhood, belongs to a group of neurodevelopmental disorders (NDDs) that are clinically widely heterogeneous and highly heritable, often being caused by single gene defects. Indeed, NDDs can be attributed to mutations at over 1000 loci, and all type of mutations, ranging from single nucleotide variations (SNVs) to large, complex copy number variations (CNVs), have been reported in patients with ID and other related NDDs. In this study, we recruited seven different recessive NDD families with comorbidities to perform a detailed clinical characterization and a complete genomic analysis that consisted of a combination of high throughput SNP-based genotyping and whole-genome sequencing (WGS). Different disease-associated loci and pathogenic gene mutations were identified in each family, including known (n = 4) and novel (n = 2) mutations in known genes (NAGLU, SLC5A2, POLR3B, VPS13A, SYN1, SPG11), and the identification of a novel disease gene (n = 1; NSL1). Functional analyses were additionally performed in a gene associated with autism-like symptoms and epileptic seizures for further proof of pathogenicity. Lastly, detailed genotype-phenotype correlations were carried out to assist with the diagnosis of prospective families and to determine genomic variation with clinical relevance. We concluded that the combination of linkage analyses and WGS to search for disease genes still remains a fruitful strategy for complex diseases with a variety of mutated genes and heterogeneous phenotypic manifestations, allowing for the identification of novel mutations, genes, and phenotypes, and leading to improvements in both diagnostic strategies and functional characterization of disease mechanisms.
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Abstract
There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly®. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.
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Affiliation(s)
- Joshua J. Timmons
- Lattice Automation Inc., Boston, Massachusetts, United States of America
| | - Doug Densmore
- Lattice Automation Inc., Boston, Massachusetts, United States of America
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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68
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Identification of tumor-associated antigens with diagnostic ability of colorectal cancer by in-depth immunomic and seroproteomic analysis. J Proteomics 2020; 214:103635. [PMID: 31918032 DOI: 10.1016/j.jprot.2020.103635] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/02/2020] [Accepted: 01/05/2020] [Indexed: 12/18/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death worldwide. Its diagnosis at early stages would significantly improve the survival of CRC patients. The humoral immune response has been demonstrated useful for cancer diagnosis, predating clinical symptoms up to 3 years. Here, we employed an in-depth seroproteomic approach to identify proteins that elicit a humoral immune response in CRC patients. The seroproteomic approach relied on the immunoprecipitation with patient-derived autoantibodies of proteins from CRC cell lines with different metastatic properties followed by LC-MS/MS. After bioinformatics, we focused on 31 targets of CRC autoantibodies. After WB and IHC validation, ERP44 and TALDO1 showed potential to discriminate disease-free and metastatic CRC patients, and time to recurrence of CRC patients in stage II. Using plasma samples of 30 healthy individuals, 28 premalignant individuals, and 32 CRC patients, nine out of 13 selected targets for seroreactive analysis showed significant diagnostic ability to discriminate either CRC patients or premalignant subjects from controls. Our results suggest that the here defined panel of CRC autoantibodies and their target proteins should be included in CRC blood-based biomarker panels to get a clinically useful blood-based diagnostic signature for CRC detection. SIGNIFICANCE: Colorectal cancer is one of the deadliest cancer types mainly due to its late diagnosis. Its early diagnosis, therefore, is of great importance since it would significantly improve the survival of CRC patients. In our work, the in-depth seroproteomic analysis of colorectal cancer using isolated IgGs from colorectal cancer patients and controls and protein extract of colorectal cancer cells provide the identification of valuable biomarkers with diagnostic and prognostic ability of the disease.
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69
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Palanirajan SK, Gummadi SN. Heavy-Metals-Mediated Phospholipids Scrambling by Human Phospholipid Scramblase 3: A Probable Role in Mitochondrial Apoptosis. Chem Res Toxicol 2019; 33:553-564. [PMID: 31769662 DOI: 10.1021/acs.chemrestox.9b00406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human phospholipid scramblases are a family of four homologous transmembrane proteins (hPLSCR1-4) mediating phospholipids (PLs) translocation in plasma membrane upon Ca2+ activation. hPLSCR3, the only homologue localized to mitochondria, plays a vital role in mitochondrial structure, function, maintenance, and apoptosis. Upon Ca2+ activation, hPLSCR3 mediates PL translocation at the mitochondrial membrane enhancing t-bid-induced cytochrome c release and apoptosis. Mitochondria are important target organelles for heavy-metals-induced apoptotic signaling cascade and are the central executioner of apoptosis to trigger. Pb2+ and Hg2+ toxicity mediates apoptosis by increased reactive oxygen species (ROS) and cytochrome c release from mitochondria. To discover the role of hPLSCR3 in heavy metal toxicity, hPLSCR3 was overexpressed as a recombinant protein in Escherichia coli Rosetta (DE3) and purified by affinity chromatography. The biochemical assay using synthetic proteoliposomes demonstrated that hPLSCR3 translocated aminophospholipids in the presence of micromolar concentrations of Pb2+ and Hg2+. A point mutation in the Ca2+-binding motif (F258V) led to a ∼60% loss in the functional activity and decreased binding affinities for Pb2+ and Hg2+ implying that the divalent heavy metal ions bind to the Ca2+-binding motif. This was further affirmed by the characteristic spectra observed with stains-all dye. The conformational changes upon heavy metal binding were monitored by circular dichroism, intrinsic tryptophan fluorescence, and light-scattering studies. Our results revealed that Pb2+ and Hg2+ bind to hPLSCR3 with higher affinity than Ca2+ thus mediating scramblase activity. To summarize, this is the first biochemical evidence for heavy metals binding to the mitochondrial membrane protein leading to bidirectional translocation of PLs specifically toward phosphatidylethanolamine.
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Affiliation(s)
- Santosh Kumar Palanirajan
- Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600 036 , India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600 036 , India
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Helassa N, Nugues C, Rajamanoharan D, Burgoyne RD, Haynes LP. A centrosome-localized calcium signal is essential for mammalian cell mitosis. FASEB J 2019; 33:14602-14610. [PMID: 31682764 PMCID: PMC6910830 DOI: 10.1096/fj.201901662r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/23/2019] [Indexed: 02/02/2023]
Abstract
Mitosis defects can lead to premature ageing and cancer. Understanding mitosis regulation therefore has important implications for human disease. Early data suggested that calcium (Ca2+) signals could influence mitosis, but these have hitherto not been observed in mammalian cells. Here, we reveal a prolonged yet spatially restricted Ca2+ signal at the centrosomes of actively dividing cells. Local buffering of the centrosomal Ca2+ signals, by flash photolysis of the caged Ca2+ chelator diazo-2-acetoxymethyl ester, arrests mitosis. We also provide evidence that this Ca2+ signal emanates from the endoplasmic reticulum. In summary, we characterize a unique centrosomal Ca2+ signal as a functionally essential input into mitosis.-Helassa, N., Nugues, C., Rajamanoharan, D., Burgoyne, R. D., Haynes, L. P. A centrosome-localized calcium signal is essential for mammalian cell mitosis.
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Affiliation(s)
- Nordine Helassa
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Charlotte Nugues
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Dayani Rajamanoharan
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Robert D. Burgoyne
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Lee P. Haynes
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
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Salas-Lloret D, Agabitini G, González-Prieto R. TULIP2: An Improved Method for the Identification of Ubiquitin E3-Specific Targets. Front Chem 2019; 7:802. [PMID: 31850303 PMCID: PMC6901917 DOI: 10.3389/fchem.2019.00802] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/07/2019] [Indexed: 01/27/2023] Open
Abstract
Protein modification by Ubiquitin or Ubiquitin-like modifiers is mediated by an enzyme cascade composed of E1, E2, and E3 enzymes. E1s, or ubiquitin-activating enzymes, perform ubiquitin activation. Next, ubiquitin is transferred to ubiquitin-conjugating enzymes or E2s. Finally, ubiquitin ligases or E3s catalyze the transfer of ubiquitin to the acceptor proteins. E3 enzymes are responsible for determining the substrate specificity. Determining which E3 enzyme maps to which substrate is a major challenge that is greatly facilitated by the TULIP2 methodology. TULIP2 methodology is fast, precise, and cost-effective. Compared to the previous TULIP methodology protocol, TULIP2 methodology achieves a more than 50-fold improvement in the purification yield and two orders of magnitude improvement in the signal-to-background ratio after label free quantification by mass spectrometry analysis. The method includes the generation of TULIP2 cell lines, subsequent purification of TULIP2 conjugates, preparation, and analysis of samples by mass spectrometry.
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Affiliation(s)
- Daniel Salas-Lloret
- González-Prieto Laboratory, Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Giulia Agabitini
- González-Prieto Laboratory, Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Román González-Prieto
- González-Prieto Laboratory, Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, Netherlands
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72
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Schlachter CR, Klapper V, Radford T, Chruszcz M. Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase. Biol Chem 2019; 400:1567-1581. [PMID: 31141475 DOI: 10.1515/hsz-2019-0106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/15/2019] [Indexed: 11/15/2022]
Abstract
Aspergillus fumigatus is a ubiquitous fungus that is not only a problem in agriculture, but also in healthcare. Aspergillus fumigatus drug resistance is becoming more prominent which is mainly attributed to the widespread use of fungicides in agriculture. The fungi-specific 2-methylcitrate cycle is responsible for detoxifying propionyl-CoA, a toxic metabolite produced as the fungus breaks down proteins and amino acids. The enzyme responsible for this detoxification is 2-methylcitrate synthase (mcsA) and is a potential candidate for the design of new anti-fungals. However, mcsA is very similar in structure to human citrate synthase (hCS) and catalyzes the same reaction. Therefore, both enzymes were studied in parallel to provide foundations for design of mcsA-specific inhibitors. The first crystal structures of citrate synthase from humans and 2-methylcitrate synthase from A. fumigatus are reported. The determined structures capture various conformational states of the enzymes and several inhibitors were identified and characterized. Despite a significant homology, mcsA and hCS display pronounced differences in substrate specificity and cooperativity. Considering that the active sites of the enzymes are almost identical, the differences in reactions catalyzed by enzymes are caused by residues that are in the vicinity of the active site and influence conformational changes of the enzymes.
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Affiliation(s)
- Caleb R Schlachter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Vincent Klapper
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Taylor Radford
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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73
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Larson GP, Tran V, Yú S, Caì Y, Higgins CA, Smith DM, Baker SF, Radoshitzky SR, Kuhn JH, Mehle A. EPS8 Facilitates Uncoating of Influenza A Virus. Cell Rep 2019; 29:2175-2183.e4. [PMID: 31747592 PMCID: PMC6929677 DOI: 10.1016/j.celrep.2019.10.064] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/20/2019] [Accepted: 10/15/2019] [Indexed: 12/02/2022] Open
Abstract
All viruses balance interactions between cellular machinery co-opted to support replication and host factors deployed to halt the infection. We use gene correlation analysis to perform an unbiased screen for host factors involved in influenza A virus (FLUAV) infection. Our screen identifies the cellular factor epidermal growth factor receptor pathway substrate 8 (EPS8) as the highest confidence pro-viral candidate. Knockout and overexpression of EPS8 confirm its importance in enhancing FLUAV infection and titers. Loss of EPS8 does not affect virion attachment, uptake, or fusion. Rather, our data show that EPS8 specifically functions during virion uncoating. EPS8 physically associates with incoming virion components, and subsequent nuclear import of released ribonucleoprotein complexes is significantly delayed in the absence of EPS8. Our study identifies EPS8 as a host factor important for uncoating, a crucial step of FLUAV infection during which the interface between the virus and host is still being discovered.
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Affiliation(s)
- Gloria P Larson
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Vy Tran
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shuǐqìng Yú
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, NIH, Frederick, MD 21702, USA
| | - Yíngyún Caì
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, NIH, Frederick, MD 21702, USA
| | - Christina A Higgins
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Danielle M Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Steven F Baker
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sheli R Radoshitzky
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, NIH, Frederick, MD 21702, USA
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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74
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Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. J Struct Biol 2019; 208:137-151. [PMID: 31445086 DOI: 10.1016/j.jsb.2019.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023]
Abstract
Formation of the internal aldimine (LLP) is the first regulatory step that activates pyridoxal 5'-phosphate (PLP) dependent enzymes. The process involves a nucleophilic attack on PLP by an active site Lys residue, followed by proton transfers resulting in a carbinolamine (CBA) intermediate that undergoes dehydration to form the aldimine. Despite a general understanding of the pathway, the structural basis of the mechanistic roles of specific residues in each of these steps is unclear. Here we determined the crystal structure of the LLP form (holo-form) of a Group II PLP-dependent decarboxylase from Methanocaldococcus jannaschii (MjDC) at 1.7 Å resolution. By comparing the crystal structure of MjDC in the LLP form with that of the pyridoxal-P (non-covalently bound aldehyde) form, we demonstrate structural evidence for a water-mediated mechanism of LLP formation. A conserved extended hydrogen-bonding network around PLP coupled to the pyridinyl nitrogen influences activation and catalysis by affecting the electronic configuration of PLP. Furthermore, the two cofactor bound forms revealed open and closed conformations of the catalytic loop (CL) in the absence of a ligand, supporting a hypothesis for a regulatory link between LLP formation and CL dynamics. The evidence suggests that activation of Group II decarboxylases involves a complex interplay of interactions between the electronic states of PLP, the active site micro-environment and CL dynamics.
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75
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The specific seroreactivity to ∆Np73 isoforms shows higher diagnostic ability in colorectal cancer patients than the canonical p73 protein. Sci Rep 2019; 9:13547. [PMID: 31537884 PMCID: PMC6753153 DOI: 10.1038/s41598-019-49960-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/31/2019] [Indexed: 02/05/2023] Open
Abstract
The p53-family is tightly regulated at transcriptional level. Due to alternative splicing, up to 40 different theoretical proteoforms have been described for p73 and at least 20 and 10 for p53 and p63, respectively. However, only the canonical proteins have been evaluated as autoantibody targets in cancer patients for diagnosis. In this study, we have cloned and expressed in vitro the most upregulated proteoforms of p73, ΔNp73α and ΔNp73β, for the analysis of their seroreactivity by a developed luminescence based immunoassay test using 145 individual plasma from colorectal cancer, premalignant individuals and healthy controls. ∆Np73α seroreactivity showed the highest diagnostic ability to discriminate between groups. The combination of ∆Np73α, ∆Np73β and p73 proteoforms seroreactivity were able to improve their individual diagnostic ability. Competitive inhibition experiments further demonstrated the presence of unique specific epitopes in ΔNp73 isoforms not present in p73, with several colorectal patients showing unique and specific seroreactivity to the ΔNp73 proteoforms. Overall, we have increased the complexity of the humoral immune response to the p53-family in cancer patients, showing that the proteoforms derived from the alternative splicing of p73 possess a higher diagnostic ability than the canonical protein, which might be extensive for p53 and p63 proteins.
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76
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Roberts R, Hall B, Daubner C, Goodman A, Pikaart M, Sikora A, Craig P. Flexible Implementation of the BASIL CURE. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:498-505. [PMID: 31381264 DOI: 10.1002/bmb.21287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/28/2019] [Accepted: 07/18/2019] [Indexed: 05/25/2023]
Abstract
Course-based Undergraduate Research Experiences (CUREs) can be a very effective means to introduce a large number of students to research. CUREs are often an extension of the instructor's research, which may make them difficult to replicate in other settings because of differences in expertise or facilities. The BASIL (Biochemistry Authentic Scientific Inquiry Lab) CURE has evolved over the past 4 years as faculty members with different backgrounds, facilities, and campus cultures have all contributed to a robust curriculum focusing on enzyme function prediction that is suitable for implementation in a wide variety of academic settings. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):498-505, 2019.
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Affiliation(s)
- Rebecca Roberts
- Department of Biology, Ursinus College, Collegeville, Pennsylvania
| | - Bonnie Hall
- Department of Chemistry, Grand View University, Des Moines, Iowa
| | - Colette Daubner
- Department of Biological Sciences, St. Mary's University, San Antonio, Texas
| | - Anya Goodman
- Department of Chemistry and Biochemistry, Cal Poly San Luis Obispo, San Luis Obispo, California
| | - Michael Pikaart
- Department of Chemistry and Biochemistry, Hope College, Holland, Michigan
| | - Arthur Sikora
- Department of Chemistry and Physics, Nova Southeastern University, Fort Lauderdale, Florida
| | - Paul Craig
- Head School of Chemistry & Materials Science, Rochester Institute of Technology, Rochester, New York
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77
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Agarwal S, Cho TY. Biochemical and structural characterization of a novel cooperative binding mode by Pit-1 with CATT repeats in the macrophage migration inhibitory factor promoter. Nucleic Acids Res 2019; 46:929-941. [PMID: 29186613 PMCID: PMC5778499 DOI: 10.1093/nar/gkx1183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/14/2017] [Indexed: 12/25/2022] Open
Abstract
Overexpression of the proinflammatory cytokine macrophage migration inhibitory factor (MIF) is linked to a number of autoimmune diseases and cancer. MIF production has been correlated to the number of CATT repeats in a microsatellite region upstream of the MIF gene. We have characterized the interaction of pituitary-specific positive transcription factor 1 (Pit-1) with a portion of the MIF promoter region flanking a microsatellite polymorphism (-794 CATT5-8). Using fluorescence anisotropy, we quantified tight complex formation between Pit-1 and an oligonucleotide consisting of eight consecutive CATT repeats (8xCATT) with an apparent Kd of 35 nM. Using competition experiments we found a 23 base pair oligonucleotide with 4xCATT repeats to be the minimum DNA sequence necessary for high affinity interaction with Pit-1. The stoichiometry of the Pit-1 DNA interaction was determined to be 2:1 and binding is cooperative in nature. We subsequently structurally characterized the complex and discovered a completely novel binding mode for Pit-1 in contrast to previously described Pit-1 complex structures. The affinity of Pit-1 for the CATT target sequence was found to be highly dependent on cooperativity. This work lays the groundwork for understanding transcriptional regulation of MIF and pursuing Pit-1 as a therapeutic target to treat MIF-mediated inflammatory disorders.
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Affiliation(s)
- Sorabh Agarwal
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Thomas Yoonsang Cho
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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78
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Human DEF6 deficiency underlies an immunodeficiency syndrome with systemic autoimmunity and aberrant CTLA-4 homeostasis. Nat Commun 2019; 10:3106. [PMID: 31308374 PMCID: PMC6629652 DOI: 10.1038/s41467-019-10812-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/29/2019] [Indexed: 12/15/2022] Open
Abstract
Immune responses need to be controlled tightly to prevent autoimmune diseases, yet underlying molecular mechanisms remain partially understood. Here, we identify biallelic mutations in three patients from two unrelated families in differentially expressed in FDCP6 homolog (DEF6) as the molecular cause of an inborn error of immunity with systemic autoimmunity. Patient T cells exhibit impaired regulation of CTLA-4 surface trafficking associated with reduced functional CTLA-4 availability, which is replicated in DEF6-knockout Jurkat cells. Mechanistically, we identify the small GTPase RAB11 as an interactor of the guanine nucleotide exchange factor DEF6, and find disrupted binding of mutant DEF6 to RAB11 as well as reduced RAB11+CTLA-4+ vesicles in DEF6-mutated cells. One of the patients has been treated with CTLA-4-Ig and achieved sustained remission. Collectively, we uncover DEF6 as player in immune homeostasis ensuring availability of the checkpoint protein CTLA-4 at T-cell surface, identifying a potential target for autoimmune and/or cancer therapy. CTLA-4 is critical for balancing protective immunity with self-tolerance. Here the authors identify homozygous DEF6 mutations in patients with severe autoimmunity, one of which received and responds to CTLA-4-Ig, and show that DEF6 is crucial for CTLA-4 cell surface trafficking and immune regulatory function.
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79
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Coscia F, Lengyel E, Duraiswamy J, Ashcroft B, Bassani-Sternberg M, Wierer M, Johnson A, Wroblewski K, Montag A, Yamada SD, López-Méndez B, Nilsson J, Mund A, Mann M, Curtis M. Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer. Cell 2019; 175:159-170.e16. [PMID: 30241606 DOI: 10.1016/j.cell.2018.08.065] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/23/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Most high-grade serous ovarian cancer (HGSOC) patients develop resistance to platinum-based chemotherapy and recur, but 15% remain disease free over a decade. To discover drivers of long-term survival, we quantitatively analyzed the proteomes of platinum-resistant and -sensitive HGSOC patients from minute amounts of formalin-fixed, paraffin-embedded tumors. This revealed cancer/testis antigen 45 (CT45) as an independent prognostic factor associated with a doubling of disease-free survival in advanced-stage HGSOC. Phospho- and interaction proteomics tied CT45 to DNA damage pathways through direct interaction with the PP4 phosphatase complex. In vitro, CT45 regulated PP4 activity, and its high expression led to increased DNA damage and platinum sensitivity. CT45-derived HLA class I peptides, identified by immunopeptidomics, activate patient-derived cytotoxic T cells and promote tumor cell killing. This study highlights the power of clinical cancer proteomics to identify targets for chemo- and immunotherapy and illuminate their biological roles.
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Affiliation(s)
- Fabian Coscia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA.
| | | | - Bradley Ashcroft
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Michal Bassani-Sternberg
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alyssa Johnson
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Kristen Wroblewski
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Anthony Montag
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - S Diane Yamada
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Blanca López-Méndez
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andreas Mund
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Marion Curtis
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
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80
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Ricketts MD, Dasgupta N, Fan J, Han J, Gerace M, Tang Y, Black BE, Adams PD, Marmorstein R. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity. J Biol Chem 2019; 294:9239-9259. [PMID: 31040182 DOI: 10.1074/jbc.ra119.007480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/01/2019] [Indexed: 02/04/2023] Open
Abstract
The HIRA histone chaperone complex is composed of the proteins HIRA, UBN1, and CABIN1 and cooperates with the histone chaperone ASF1a to specifically bind and deposit H3.3/H4 into chromatin. We recently reported that the UBN1 Hpc2-related domain (HRD) specifically binds to H3.3/H4 over H3.1/H4. However, the mechanism for HIRA complex deposition of H3.3/H4 into nucleosomes remains unclear. Here, we characterize a central region of UBN1 (UBN1 middle domain) that is evolutionarily conserved and predicted to have helical secondary structure. We report that the UBN1 middle domain has dimer formation activity and binds to H3/H4 in a manner that does not discriminate between H3.1 and H3.3. We additionally identify a nearby DNA-binding domain in UBN1, located between the UBN1 HRD and middle domain, which binds DNA through electrostatic contacts involving several conserved lysine residues. Together, these observations suggest a mechanism for HIRA-mediated H3.3/H4 deposition whereby UBN1 associates with DNA and dimerizes to mediate formation of an (H3.3/H4)2 heterotetramer prior to chromatin deposition.
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Affiliation(s)
- M Daniel Ricketts
- From the Department of Biochemistry and Biophysics and.,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Nirmalya Dasgupta
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Jiayi Fan
- From the Department of Biochemistry and Biophysics and
| | - Joseph Han
- From the Department of Biochemistry and Biophysics and.,the Department of Chemistry Graduate Group and
| | - Morgan Gerace
- From the Department of Biochemistry and Biophysics and
| | - Yong Tang
- the Wistar Institute, Philadelphia, Pennsylvania 19104, and
| | - Ben E Black
- From the Department of Biochemistry and Biophysics and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Peter D Adams
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Ronen Marmorstein
- From the Department of Biochemistry and Biophysics and .,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,the Department of Chemistry Graduate Group and.,the Wistar Institute, Philadelphia, Pennsylvania 19104, and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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81
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Bromodomain inhibition of the coactivators CBP/EP300 facilitate cellular reprogramming. Nat Chem Biol 2019; 15:519-528. [PMID: 30962627 DOI: 10.1038/s41589-019-0264-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/27/2019] [Indexed: 01/09/2023]
Abstract
Silencing of the somatic cell type-specific genes is a critical yet poorly understood step in reprogramming. To uncover pathways that maintain cell identity, we performed a reprogramming screen using inhibitors of chromatin factors. Here, we identify acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators CREB (cyclic-AMP response element binding protein) binding protein (CBP) and E1A binding protein of 300 kDa (EP300) as potent enhancers of reprogramming. These inhibitors accelerate reprogramming, are critical during its early stages and, when combined with DOT1L inhibition, enable efficient derivation of human induced pluripotent stem cells (iPSCs) with OCT4 and SOX2. In contrast, catalytic inhibition of CBP/EP300 prevents iPSC formation, suggesting distinct functions for different coactivator domains in reprogramming. CBP/EP300 bromodomain inhibition decreases somatic-specific gene expression, histone H3 lysine 27 acetylation (H3K27Ac) and chromatin accessibility at target promoters and enhancers. The master mesenchymal transcription factor PRRX1 is one such functionally important target of CBP/EP300 bromodomain inhibition. Collectively, these results show that CBP/EP300 bromodomains sustain cell-type-specific gene expression and maintain cell identity.
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82
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Haldeman JM, Conway AE, Arlotto ME, Slentz DH, Muoio DM, Becker TC, Newgard CB. Creation of versatile cloning platforms for transgene expression and dCas9-based epigenome editing. Nucleic Acids Res 2019; 47:e23. [PMID: 30590691 PMCID: PMC6393299 DOI: 10.1093/nar/gky1286] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 12/11/2018] [Accepted: 12/16/2018] [Indexed: 01/09/2023] Open
Abstract
Genetic manipulation via transgene overexpression, RNAi, or Cas9-based methods is central to biomedical research. Unfortunately, use of these tools is often limited by vector options. We have created a modular platform (pMVP) that allows a gene of interest to be studied in the context of an array of promoters, epitope tags, conditional expression modalities, and fluorescent reporters, packaged in 35 custom destination vectors, including adenovirus, lentivirus, PiggyBac transposon, and Sleeping Beauty transposon, in aggregate >108,000 vector permutations. We also used pMVP to build an epigenetic engineering platform, pMAGIC, that packages multiple gRNAs and either Sa-dCas9 or x-dCas9(3.7) fused to one of five epigenetic modifiers. Importantly, via its compatibility with adenoviral vectors, pMAGIC uniquely enables use of dCas9/LSD1 fusions to interrogate enhancers within primary cells. To demonstrate this, we used pMAGIC to target Sa-dCas9/LSD1 and modify the epigenetic status of a conserved enhancer, resulting in altered expression of the homeobox transcription factor PDX1 and its target genes in pancreatic islets and insulinoma cells. In sum, the pMVP and pMAGIC systems empower researchers to rapidly generate purpose-built, customized vectors for manipulation of gene expression, including via targeted epigenetic modification of regulatory elements in a broad range of disease-relevant cell types.
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Affiliation(s)
- Jonathan M Haldeman
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA
| | - Amanda E Conway
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Michelle E Arlotto
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Dorothy H Slentz
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Deborah M Muoio
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27701, USA
| | - Thomas C Becker
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27701, USA
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83
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Luoma LM, Berry FB. Molecular analysis of NPAS3 functional domains and variants. BMC Mol Biol 2018; 19:14. [PMID: 30509165 PMCID: PMC6276216 DOI: 10.1186/s12867-018-0117-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/26/2018] [Indexed: 12/14/2022] Open
Abstract
Background NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as well as a marked reduction in neurogenesis in the adult mouse hippocampus. This neurogenic deficit, alongside the reduction in cortical interneuron number, likely contributes to the behavioral and cognitive alterations observed in Npas3 knockout mice. Although loss of Npas3 has been found to affect proliferation and apoptosis, the molecular function of NPAS3 is largely uncharacterized outside of predictions based on its high homology to bHLH–PAS transcription factors. Here we set out to characterize NPAS3 as a transcription factor, and to confirm whether NPAS3 acts as predicted for a Class 1 bHLH–PAS family member. Results Through these studies we have experimentally demonstrated that NPAS3 behaves as a true transcription factor, capable of gene regulation through direct association with DNA. NPAS3 and ARNT are confirmed to directly interact in human cells through both bHLH and PAS dimerization domains. The C-terminus of NPAS3 was found to contain a functional transactivation domain. Further, the NPAS3::ARNT heterodimer was shown to directly regulate the expression of VGF and TXNIP through binding of their proximal promoters. Finally, we assessed the effects of three human variants of NPAS3 on gene regulatory function and do not observe significant deficits. Conclusions NPAS3 is a true transcription factor capable of regulating expression of target genes through their promoters by directly cooperating with ARNT. The tested human variants of NPAS3 require further characterization to identify their effects on NPAS3 expression and function in the individuals that carry them. These data enhance our understanding of the molecular function of NPAS3 and the mechanism by which it contributes to normal and abnormal neurodevelopment and neural function. Electronic supplementary material The online version of this article (10.1186/s12867-018-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leiah M Luoma
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Fred B Berry
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada. .,Department of Surgery, 3002D Li Ka Shing Centre, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains. Nat Commun 2018; 9:3520. [PMID: 30166540 PMCID: PMC6117352 DOI: 10.1038/s41467-018-06034-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022] Open
Abstract
Human estrogen receptor alpha (hERα) is a hormone-responsive nuclear receptor (NR) involved in cell growth and survival that contains both a DNA-binding domain (DBD) and a ligand-binding domain (LBD). Functionally relevant inter-domain interactions between the DBD and LBD have been observed in several other NRs, but for hERα, the detailed structural architecture of the complex is unknown. By utilizing integrated complementary techniques of small-angle X-ray scattering, hydroxyl radical protein footprinting and computational modeling, here we report an asymmetric L-shaped “boot” structure of the multidomain hERα and identify the specific sites on each domain at the domain interface involved in DBD–LBD interactions. We demonstrate the functional role of the proposed DBD–LBD domain interface through site-specific mutagenesis altering the hERα interfacial structure and allosteric signaling. The L-shaped structure of hERα is a distinctive DBD–LBD organization of NR complexes and more importantly, reveals a signaling mechanism mediated by inter-domain crosstalk that regulates this receptor’s allosteric function. The human estrogen receptor alpha (hERα) is a hormone-responsive transcription factor. Here the authors combine small-angle X-ray scattering, hydroxyl radical protein footprinting and computational modeling and show that multidomain hERα adopts an L-shaped boot-like architecture revealing a cross-talk between its DNA-binding domain and Ligand-binding domain.
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85
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Wozniak KL, Phelps WA, Tembo M, Lee MT, Carlson AE. The TMEM16A channel mediates the fast polyspermy block in Xenopus laevis. J Gen Physiol 2018; 150:1249-1259. [PMID: 30012842 PMCID: PMC6122928 DOI: 10.1085/jgp.201812071] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/12/2018] [Indexed: 12/03/2022] Open
Abstract
In their preceding paper, Wozniak et al. show that fertilization increases intracellular Ca2+ in Xenopus laevis eggs by activating an IP3 signaling cascade. Here, they reveal that Ca2+ subsequently opens the Cl− channel TMEM16A to allow Cl− efflux, cell depolarization, and fast block to polyspermy. In externally fertilizing animals, such as sea urchins and frogs, prolonged depolarization of the egg immediately after fertilization inhibits the entry of additional sperm—a phenomenon known as the fast block to polyspermy. In the African clawed frog Xenopus laevis, this depolarization is driven by Ca2+-activated Cl− efflux. Although the prominent Ca2+-activated Cl− currents generated in immature X. laevis oocytes are mediated by X. laevis transmembrane protein 16a (xTMEM16A) channels, little is known about the channels that contribute to the fast block in mature eggs. Moreover, the gamete undergoes a gross transformation as it develops from an immature oocyte into a fertilization-competent egg. Here, we report the results of our approach to identify the Ca2+-activated Cl− channel that triggers the fast block. By querying published proteomic and RNA-sequencing data, we identify two Ca2+-activated Cl− channels expressed in fertilization-competent X. laevis eggs: xTMEM16A and X. laevis bestrophin 2A (xBEST2A). By exogenously expressing xTMEM16A and xBEST2A in axolotl cells lacking endogenous Ca2+-activated currents, we characterize the effect of inhibitors on currents mediated by these channels. None of the inhibitors tested block xBEST2A currents specifically. However, 2-(4-chloro-2-methylphenoxy)-N-[(2-methoxyphenyl)methylideneamino]-acetamide (Ani9) and N-((4-methoxy)-2-naphthyl)-5-nitroanthranilic acid (MONNA) each reduce xTMEM16A currents by more than 70% while only nominally inhibiting those generated by xBEST2A. Using whole-cell recordings during fertilization, we find that Ani9 and MONNA effectively diminish fertilization-evoked depolarizations. Additionally, these inhibitors lead to increased polyspermy in X. laevis embryos. These results indicate that fertilization activates TMEM16A channels in X. laevis eggs and induces the earliest known event triggered by fertilization: the fast block to polyspermy.
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Affiliation(s)
| | - Wesley A Phelps
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Maiwase Tembo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Miler T Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Anne E Carlson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
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86
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White PJ, McGarrah RW, Grimsrud PA, Tso SC, Yang WH, Haldeman JM, Grenier-Larouche T, An J, Lapworth AL, Astapova I, Hannou SA, George T, Arlotto M, Olson LB, Lai M, Zhang GF, Ilkayeva O, Herman MA, Wynn RM, Chuang DT, Newgard CB. The BCKDH Kinase and Phosphatase Integrate BCAA and Lipid Metabolism via Regulation of ATP-Citrate Lyase. Cell Metab 2018; 27:1281-1293.e7. [PMID: 29779826 PMCID: PMC5990471 DOI: 10.1016/j.cmet.2018.04.015] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/27/2018] [Accepted: 04/13/2018] [Indexed: 12/16/2022]
Abstract
Branched-chain amino acids (BCAA) are strongly associated with dysregulated glucose and lipid metabolism, but the underlying mechanisms are poorly understood. We report that inhibition of the kinase (BDK) or overexpression of the phosphatase (PPM1K) that regulates branched-chain ketoacid dehydrogenase (BCKDH), the committed step of BCAA catabolism, lowers circulating BCAA, reduces hepatic steatosis, and improves glucose tolerance in the absence of weight loss in Zucker fatty rats. Phosphoproteomics analysis identified ATP-citrate lyase (ACL) as an alternate substrate of BDK and PPM1K. Hepatic overexpression of BDK increased ACL phosphorylation and activated de novo lipogenesis. BDK and PPM1K transcript levels were increased and repressed, respectively, in response to fructose feeding or expression of the ChREBP-β transcription factor. These studies identify BDK and PPM1K as a ChREBP-regulated node that integrates BCAA and lipid metabolism. Moreover, manipulation of the BDK:PPM1K ratio relieves key metabolic disease phenotypes in a genetic model of severe obesity.
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Affiliation(s)
- Phillip J White
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Robert W McGarrah
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Paul A Grimsrud
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Shih-Chia Tso
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wen-Hsuan Yang
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Jonathan M Haldeman
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Thomas Grenier-Larouche
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Jie An
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Amanda L Lapworth
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Inna Astapova
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Sarah A Hannou
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Tabitha George
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Michelle Arlotto
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Lyra B Olson
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Michelle Lai
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Guo-Fang Zhang
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Mark A Herman
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA; Departments of Medicine and Pharmacology & Cancer Biology, Durham, NC 27701, USA.
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Noguchi K, Dincman TA, Dalton AC, Howley BV, McCall BJ, Mohanty BK, Howe PH. Interleukin-like EMT inducer (ILEI) promotes melanoma invasiveness and is transcriptionally up-regulated by upstream stimulatory factor-1 (USF-1). J Biol Chem 2018; 293:11401-11414. [PMID: 29871931 PMCID: PMC6065179 DOI: 10.1074/jbc.ra118.003616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/22/2018] [Indexed: 12/25/2022] Open
Abstract
Interleukin-like EMT inducer (ILEI, FAM3C) is a secreted factor that contributes to the epithelial-to-mesenchymal transition (EMT), a cell-biological process that confers metastatic properties to a tumor cell. However, very little is known about how ILEI is regulated. Here we demonstrate that ILEI is an in vivo regulator of melanoma invasiveness and is transcriptionally up-regulated by the upstream stimulatory factor-1 (USF-1), an E-box-binding, basic-helix-loop-helix family transcription factor. shRNA-mediated knockdown of ILEI in melanoma cell lines attenuated lung colonization but not primary tumor formation. We also identified the mechanism underlying ILEI transcriptional regulation, which was through a direct interaction of USF-1 with the ILEI promoter. Of note, stimulation of endogenous USF-1 by UV-mediated activation increased ILEI expression, whereas shRNA-mediated USF-1 knockdown decreased ILEI gene transcription. Finally, we report that knocking down USF-1 decreases tumor cell migration. In summary, our work reveals that ILEI contributes to melanoma cell invasiveness in vivo without affecting primary tumor growth and is transcriptionally up-regulated by USF-1.
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Affiliation(s)
- Ken Noguchi
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Toros A Dincman
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425; Division of Hematology and Oncology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Annamarie C Dalton
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Breege V Howley
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Buckley J McCall
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Bidyut K Mohanty
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, College of Medicine, Charleston, South Carolina 29425; Hollings Cancer Center, Charleston, South Carolina 29425.
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88
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Ritt M, Sivaramakrishnan S. Engaging myosin VI tunes motility, morphology and identity in endocytosis. Traffic 2018; 19:10.1111/tra.12583. [PMID: 29869361 PMCID: PMC6437008 DOI: 10.1111/tra.12583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 12/14/2022]
Abstract
While unconventional myosins interact with different stages of the endocytic pathway, they are ascribed a transport function that is secondary to the protein complexes that control organelle identity. Endosomes are subject to a dynamic, continuous flux of proteins that control their characteristic properties, including their motility within the cell. Efforts to describe the changes in identity of this compartment have largely focused on the adaptors present on the compartment and not on the motile properties of the compartment itself. In this study, we use a combination of optogenetic and chemical-dimerization strategies to target exogenous myosin VI to early endosomes, and probe its influence on organelle motility, morphology and identity. Our analysis across timescales suggests a model wherein the artificial engagement of myosin VI motility on early endosomes restricts microtubule-based motion, followed by morphological changes characterized by the rapid condensation and disintegration of organelles, ultimately leading to the enhanced overlap of markers that demarcate endosomal compartments. Together, our findings show that synthetic engagement of myosin VI motility is sufficient to alter organelle homeostasis in the endocytic pathway.
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Affiliation(s)
- Michael Ritt
- Department of Genetics, Cell and Developmental Biology, University of Minnesota, Minneapolis, Minnesota
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell and Developmental Biology, University of Minnesota, Minneapolis, Minnesota
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89
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Stopschinski BE, Holmes BB, Miller GM, Manon VA, Vaquer-Alicea J, Prueitt WL, Hsieh-Wilson LC, Diamond MI. Specific glycosaminoglycan chain length and sulfation patterns are required for cell uptake of tau versus α-synuclein and β-amyloid aggregates. J Biol Chem 2018; 293:10826-10840. [PMID: 29752409 DOI: 10.1074/jbc.ra117.000378] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/07/2018] [Indexed: 12/21/2022] Open
Abstract
Transcellular propagation of protein aggregate "seeds" has been proposed to mediate the progression of neurodegenerative diseases in tauopathies and α-synucleinopathies. We previously reported that tau and α-synuclein aggregates bind heparan sulfate proteoglycans (HSPGs) on the cell surface, promoting cellular uptake and intracellular seeding. However, the specificity and binding mode of these protein aggregates to HSPGs remain unknown. Here, we measured direct interaction with modified heparins to determine the size and sulfation requirements for tau, α-synuclein, and β-amyloid (Aβ) aggregate binding to glycosaminoglycans (GAGs). Varying the GAG length and sulfation patterns, we next conducted competition studies with heparin derivatives in cell-based assays. Tau aggregates required a precise GAG architecture with defined sulfate moieties in the N- and 6-O-positions, whereas the binding of α-synuclein and Aβ aggregates was less stringent. To determine the genes required for aggregate uptake, we used CRISPR/Cas9 to individually knock out the major genes of the HSPG synthesis pathway in HEK293T cells. Knockouts of the extension enzymes exostosin 1 (EXT1), exostosin 2 (EXT2), and exostosin-like 3 (EXTL3), as well as N-sulfotransferase (NDST1) or 6-O-sulfotransferase (HS6ST2) significantly reduced tau uptake, consistent with our biochemical findings, and knockouts of EXT1, EXT2, EXTL3, or NDST1, but not HS6ST2 reduced α-synuclein uptake. In summary, tau aggregates display specific interactions with HSPGs that depend on GAG length and sulfate moiety position, whereas α-synuclein and Aβ aggregates exhibit more flexible interactions with HSPGs. These principles may inform the development of mechanism-based therapies to block transcellular propagation of amyloid protein-based pathologies.
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Affiliation(s)
- Barbara E Stopschinski
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,the Department of Neurology, RWTH University Aachen, D-52074 Aachen, Germany
| | - Brandon B Holmes
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,the Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri 63110, and
| | - Gregory M Miller
- the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Victor A Manon
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Jaime Vaquer-Alicea
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - William L Prueitt
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Linda C Hsieh-Wilson
- the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Marc I Diamond
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390,
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90
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Roos A, Dhruv HD, Peng S, Inge LJ, Tuncali S, Pineda M, Millard N, Mayo Z, Eschbacher JM, Loftus JC, Winkles JA, Tran NL. EGFRvIII-Stat5 Signaling Enhances Glioblastoma Cell Migration and Survival. Mol Cancer Res 2018; 16:1185-1195. [PMID: 29724813 DOI: 10.1158/1541-7786.mcr-18-0125] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/22/2018] [Accepted: 04/19/2018] [Indexed: 01/27/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common brain malignancies in adults. Most GBM patients succumb to the disease less than 1 year after diagnosis due to the highly invasive nature of the tumor, which prevents complete surgical resection and gives rise to tumor recurrence. The invasive phenotype also confers radioresistant and chemoresistant properties to the tumor cells; therefore, there is a critical need to develop new therapeutics that target drivers of GBM invasion. Amplification of EGFR is observed in over 50% of GBM tumors, of which half concurrently overexpress the variant EGFRvIII, and expression of both receptors confers a worse prognosis. EGFR and EGFRvIII cooperate to promote tumor progression and invasion, in part, through activation of the Stat signaling pathway. Here, it is reported that EGFRvIII activates Stat5 and GBM invasion by inducing the expression of a previously established mediator of glioma cell invasion and survival: fibroblast growth factor-inducible 14 (Fn14). EGFRvIII-mediated induction of Fn14 expression is Stat5 dependent and requires activation of Src, whereas EGFR regulation of Fn14 is dependent upon Src-MEK/ERK-Stat3 activation. Notably, treatment of EGFRvIII-expressing GBM cells with the FDA-approved Stat5 inhibitor pimozide blocked Stat5 phosphorylation, Fn14 expression, and cell migration and survival. Because EGFR inhibitors display limited therapeutic efficacy in GBM patients, the EGFRvIII-Stat5-Fn14 signaling pathway represents a node of vulnerability in the invasive GBM cell populations.Implications: Targeting critical effectors in the EGFRvIII-Stat5-Fn14 pathway may limit GBM tumor dispersion, mitigate therapeutic resistance, and increase survival. Mol Cancer Res; 16(7); 1185-95. ©2018 AACR.
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Affiliation(s)
- Alison Roos
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Landon J Inge
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona
| | - Serdar Tuncali
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Michael Pineda
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Nghia Millard
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Zachary Mayo
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jennifer M Eschbacher
- Department of Neuropathology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona
| | - Joseph C Loftus
- Department of Biochemistry and Molecular Biology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Jeffrey A Winkles
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland
| | - Nhan L Tran
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona.
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Radha R, Arumugam N, Gummadi SN. Glutaminase free l-asparaginase from Vibrio cholerae: Heterologous expression, purification and biochemical characterization. Int J Biol Macromol 2018; 111:129-138. [DOI: 10.1016/j.ijbiomac.2017.12.165] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/20/2017] [Accepted: 12/30/2017] [Indexed: 11/26/2022]
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Palanirajan SK, Sivagnanam U, Murugan S, Gummadi SN. In vitro reconstitution and biochemical characterization of human phospholipid scramblase 3: phospholipid specificity and metal ion binding studies. Biol Chem 2018; 399:361-374. [DOI: 10.1515/hsz-2017-0309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 01/11/2023]
Abstract
AbstractHuman phospholipid scramblase 3 (hPLSCR3) is a single pass transmembrane protein that plays a vital role in fat metabolism, mitochondrial function, structure, maintenance and apoptosis. The mechanism of action of scramblases remains still unknown, and the role of scramblases in phospholipid translocation is heavily debated. hPLSCR3 is the only member of scramblase family localized to mitochondria and is involved in cardiolipin translocation at the mitochondrial membrane. Direct biochemical evidence of phospholipid translocation by hPLSCR3 is yet to be reported. Functional assay in synthetic proteoliposomes upon Ca2+and Mg2+revealed that, apart from cardiolipin, recombinant hPLSCR3 translocates aminophospholipids such as NBD-PE and NBD-PS but not neutral phospholipids. Point mutation in hPLSCR3 (F258V) resulted in decreased Ca2+binding affinity. Functional assay with F258V-hPLSCR3 led to ~50% loss in scramblase activity in the presence of Ca2+and Mg2+. Metal ion-induced conformational changes were monitored by intrinsic tryptophan fluorescence, circular dichroism, surface hydrophobicity changes and aggregation studies. Our results revealed that Ca2+and Mg2+bind to hPLSCR3 and trigger conformational changes mediated by aggregation. In summary, we suggest that the metal ion-induced conformational change and the aggregation of the protein are essential for the phospholipid translocation by hPLSCR3.
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93
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Wijesuriya TM, De Ceuninck L, Masschaele D, Sanderson MR, Carias KV, Tavernier J, Wevrick R. The Prader-Willi syndrome proteins MAGEL2 and necdin regulate leptin receptor cell surface abundance through ubiquitination pathways. Hum Mol Genet 2018; 26:4215-4230. [PMID: 28973533 DOI: 10.1093/hmg/ddx311] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
In Prader-Willi syndrome (PWS), obesity is caused by the disruption of appetite-controlling pathways in the brain. Two PWS candidate genes encode MAGEL2 and necdin, related melanoma antigen proteins that assemble into ubiquitination complexes. Mice lacking Magel2 are obese and lack leptin sensitivity in hypothalamic pro-opiomelanocortin neurons, suggesting dysregulation of leptin receptor (LepR) activity. Hypothalamus from Magel2-null mice had less LepR and altered levels of ubiquitin pathway proteins that regulate LepR processing (Rnf41, Usp8, and Stam1). MAGEL2 increased the cell surface abundance of LepR and decreased their degradation. LepR interacts with necdin, which interacts with MAGEL2, which complexes with RNF41 and USP8. Mutations in the MAGE homology domain of MAGEL2 suppress RNF41 stabilization and prevent the MAGEL2-mediated increase of cell surface LepR. Thus, MAGEL2 and necdin together control LepR sorting and degradation through a dynamic ubiquitin-dependent pathway. Loss of MAGEL2 and necdin may uncouple LepR from ubiquitination pathways, providing a cellular mechanism for obesity in PWS.
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Affiliation(s)
| | - Leentje De Ceuninck
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Delphine Masschaele
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Matthea R Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton T6G 2H7, Canada
| | | | - Jan Tavernier
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton T6G 2H7, Canada
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94
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Hansen DT, Craciunescu FM, Fromme P, Johnston SA, Sykes KF. Generation of High-Specificity Antibodies against Membrane Proteins Using DNA-Gold Micronanoplexes for Gene Gun Immunization. ACTA ACUST UNITED AC 2018. [PMID: 29516482 DOI: 10.1002/cpps.50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Membrane proteins are the molecular interface of the cell and its environs; however, studies of membrane proteins are highly technically challenging, mainly due to instability of the isolated protein. Towards the production of antibodies that recognize properly folded and stabilized forms of membrane protein antigen, we describe a DNA-based immunization method for mice that expresses the antigen in the membranes of dendritic cells, thus allowing direct presentation to the immune system. This genetic immunization approach employs a highly efficient method of biolistic delivery based on DNA-gold micronanoplexes, which are complexes of micron-sized gold particles that allow dermal penetration and nanometer-sized gold particles that provide a higher surface area for DNA binding than micron gold alone. In contrast to antibodies derived from immunizations with detergent-solubilized protein or with protein fragments, antibodies from genetic immunization are expected to have a high capacity for binding conformational epitopes and for modulating membrane protein activity. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Debra T Hansen
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona
| | - Felicia M Craciunescu
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona
| | - Stephen A Johnston
- Biodesign Center for Innovations in Medicine, Arizona State University, Tempe, Arizona
| | - Kathryn F Sykes
- Biodesign Center for Innovations in Medicine, Arizona State University, Tempe, Arizona.,Current address: HealthTell, Inc, Chandler, Arizona
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95
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Zanini F, Pu SY, Bekerman E, Einav S, Quake SR. Single-cell transcriptional dynamics of flavivirus infection. eLife 2018; 7:32942. [PMID: 29451494 PMCID: PMC5826272 DOI: 10.7554/elife.32942] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/08/2018] [Indexed: 12/25/2022] Open
Abstract
Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage and shock or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.
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Affiliation(s)
- Fabio Zanini
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Szu-Yuan Pu
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Elena Bekerman
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Shirit Einav
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Applied Physics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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96
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Ballister ER, Rodgers J, Martial F, Lucas RJ. A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling. BMC Biol 2018; 16:10. [PMID: 29338718 PMCID: PMC5771134 DOI: 10.1186/s12915-017-0475-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/18/2017] [Indexed: 11/10/2022] Open
Abstract
Background Animal opsins are light-sensitive G-protein-coupled receptors (GPCRs) that enable optogenetic control over the major heterotrimeric G-protein signaling pathways in animal cells. As such, opsins have potential applications in both biomedical research and therapy. Selecting the opsin with the best balance of activity and selectivity for a given application requires knowing their ability to couple to a full range of relevant Gα subunits. We present the GsX assay, a set of tools based on chimeric Gs subunits that transduce coupling of opsins to diverse G proteins into increases in cAMP levels, measured with a real-time reporter in living cells. We use this assay to compare coupling to Gi/o/t across a panel of natural and chimeric opsins selected for potential application in gene therapy for retinal degeneration. Results Of the opsins tested, wild-type human rod opsin had the highest activity for chimeric Gs proxies for Gi and Gt (Gsi and Gst) and was matched in Go proxy (Gso) activity only by a human rod opsin/scallop opsin chimera. Rod opsin drove roughly equivalent responses via Gsi, Gso, and Gst, while cone opsins showed much lower activities with Gso than Gsi or Gst, and a human rod opsin/amphioxus opsin chimera demonstrated higher activity with Gso than with Gsi or Gst. We failed to detect activity for opsin chimeras bearing three intracellular fragments of mGluR6, and observed unexpectedly complex response profiles for scallop and amphioxus opsins thought to be specialized for Go. Conclusions These results identify rod opsin as the most potent non-selective Gi/o/t-coupled opsin, long-wave sensitive cone opsin as the best for selectively activating Gi/t over Go, and a rod opsin/amphioxus opsin chimera as the best choice for selectively activating Go over Gi/t. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0475-2) contains supplementary material, which is available to authorized users.
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97
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Yamagishi Y, Abe H. Actin assembly mediated by a nucleation promoting factor WASH is involved in MTOC–TMA formation during
Xenopus
oocyte maturation. Cytoskeleton (Hoboken) 2018; 75:131-143. [DOI: 10.1002/cm.21428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Yuka Yamagishi
- Department of Nanobiology, Graduate School of Advanced Integration ScienceChiba University Chiba263‐8522 Japan
| | - Hiroshi Abe
- Department of Nanobiology, Graduate School of Advanced Integration ScienceChiba University Chiba263‐8522 Japan
- Department of Biology, Graduate School of ScienceChiba UniversityChiba, 263‐8522 Japan
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98
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Gandomkar S, Dennig A, Dordic A, Hammerer L, Pickl M, Haas T, Hall M, Faber K. Biocatalytic Oxidative Cascade for the Conversion of Fatty Acids into α-Ketoacids via Internal H 2 O 2 Recycling. Angew Chem Int Ed Engl 2018; 57:427-430. [PMID: 29125663 PMCID: PMC5768024 DOI: 10.1002/anie.201710227] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 11/18/2022]
Abstract
The functionalization of bio-based chemicals is essential to allow valorization of natural carbon sources. An atom-efficient biocatalytic oxidative cascade was developed for the conversion of saturated fatty acids to α-ketoacids. Employment of P450 monooxygenase in the peroxygenase mode for regioselective α-hydroxylation of fatty acids combined with enantioselective oxidation by α-hydroxyacid oxidase(s) resulted in internal recycling of the oxidant H2 O2 , thus minimizing degradation of ketoacid product and maximizing biocatalyst lifetime. The O2 -dependent cascade relies on catalytic amounts of H2 O2 and releases water as sole by-product. Octanoic acid was converted under mild conditions in aqueous buffer to 2-oxooctanoic acid in a simultaneous one-pot two-step cascade in up to >99 % conversion without accumulation of hydroxyacid intermediate. Scale-up allowed isolation of final product in 91 % yield and the cascade was applied to fatty acids of various chain lengths (C6:0 to C10:0).
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Affiliation(s)
- Somayyeh Gandomkar
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Alexander Dennig
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Andela Dordic
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
- Austrian Center of Industrial Biotechnology c/oDepartment of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Lucas Hammerer
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
- Austrian Center of Industrial Biotechnology c/oDepartment of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Mathias Pickl
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Thomas Haas
- CreavisEvonik Industries, Bau 1420Paul Baumann Strasse 145772MarlGermany
| | - Mélanie Hall
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Department of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
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99
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Abstract
In this review, we describe how the interplay among science, technology and community interests contributed to the evolution of four structural biology data resources. We present the method by which data deposited by scientists are prepared for worldwide distribution, and argue that data archiving in a trusted repository must be an integral part of any scientific investigation.
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Affiliation(s)
- Helen M. Berman
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Catherine L. Lawson
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Brinda Vallat
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Margaret J. Gabanyi
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
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100
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Gandomkar S, Dennig A, Dordic A, Hammerer L, Pickl M, Haas T, Hall M, Faber K. Eine biokatalytische oxidative Kaskade für die Umsetzung von Fettsäuren zu α-Ketosäuren mit interner H2
O2
-Regeneration. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Somayyeh Gandomkar
- Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
| | - Alexander Dennig
- Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
| | - Andela Dordic
- Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
- Austrian Center of Industrial Biotechnology c/o; Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
| | - Lucas Hammerer
- Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
- Austrian Center of Industrial Biotechnology c/o; Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
| | - Mathias Pickl
- Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
| | - Thomas Haas
- Creavis; Evonik Industries, Bau 1420; Paul Baumann Straße 1 45772 Marl Deutschland
| | - Mélanie Hall
- Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
| | - Kurt Faber
- Institut für Chemie; Universität Graz; Heinrichstraße 28 8010 Graz Österreich
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