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Marshall CR, Farrow MA, Djambazova KV, Spraggins JM. Untangling Alzheimer's disease with spatial multi-omics: a brief review. Front Aging Neurosci 2023; 15:1150512. [PMID: 37533766 PMCID: PMC10390637 DOI: 10.3389/fnagi.2023.1150512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of neurological dementia, specified by extracellular β-amyloid plaque deposition, neurofibrillary tangles, and cognitive impairment. AD-associated pathologies like cerebral amyloid angiopathy (CAA) are also affiliated with cognitive impairment and have overlapping molecular drivers, including amyloid buildup. Discerning the complexity of these neurological disorders remains a significant challenge, and the spatiomolecular relationships between pathogenic features of AD and AD-associated pathologies remain poorly understood. This review highlights recent developments in spatial omics, including profiling and molecular imaging methods, and how they are applied to AD. These emerging technologies aim to characterize the relationship between how specific cell types and tissue features are organized in combination with mapping molecular distributions to provide a systems biology view of the tissue microenvironment around these neuropathologies. As spatial omics methods achieve greater resolution and improved molecular coverage, they are enabling deeper characterization of the molecular drivers of AD, leading to new possibilities for the prediction, diagnosis, and mitigation of this debilitating disease.
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Affiliation(s)
- Cody R. Marshall
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Melissa A. Farrow
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Jeffrey M. Spraggins
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
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2
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Farrow MA, Chumber NM, Bloch SC, King M, Moton-Melancon K, Shupe J, Washington MK, Spiller BW, Lacy DB. Small Molecule Inhibitor Screen Reveals Calcium Channel Signaling as a Mechanistic Mediator of Clostridium difficile TcdB-Induced Necrosis. ACS Chem Biol 2020; 15:1212-1221. [PMID: 31909964 DOI: 10.1021/acschembio.9b00906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clostridioides difficile is the leading cause of nosocomial diarrhea in the United States. The primary virulence factors are two homologous glucosyltransferase toxins, TcdA and TcdB, that inactivate host Rho-family GTPases. The glucosyltransferase activity has been linked to a "cytopathic" disruption of the actin cytoskeleton and contributes to the disruption of tight junctions and the production of pro-inflammatory cytokines. TcdB is also a potent cytotoxin that causes epithelium necrotic damage through an NADPH oxidase (NOX)-dependent mechanism. We conducted a small molecule screen to identify compounds that confer protection against TcdB-induced necrosis. We identified an enrichment of "hit compounds" with a dihydropyridine (DHP) core which led to the discovery of a key early stage calcium signal that serves as a mechanistic link between TcdB-induced NOX activation and reactive oxygen species (ROS) production. Disruption of TcdB-induced calcium signaling (with both DHP and non-DHP molecules) is sufficient to ablate ROS production and prevent subsequent necrosis in cells and in a mouse model of intoxication.
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Affiliation(s)
- Melissa A. Farrow
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - Nicole M. Chumber
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - Sarah C. Bloch
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - McKenzie King
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - Kaycei Moton-Melancon
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - John Shupe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - Mary K. Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - Benjamin W. Spiller
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - D. Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, A4116A Medical Center North, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
- The Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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3
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Palmer LD, Jordan AT, Maloney KN, Farrow MA, Gutierrez DB, Gant-Branum R, Burns WJ, Romer CE, Tsui T, Allen JL, Beavers WN, Nei YW, Sherrod SD, Lacy DB, Norris JL, McLean JA, Caprioli RM, Skaar EP. Zinc intoxication induces ferroptosis in A549 human lung cells. Metallomics 2020; 11:982-993. [PMID: 30968088 DOI: 10.1039/c8mt00360b] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Zinc (Zn) is an essential trace metal required for all forms of life, but is toxic at high concentrations. While the toxic effects of high levels of Zn are well documented, the mechanism of cell death appears to vary based on the study and concentration of Zn. Zn has been proposed as an anti-cancer treatment against non-small cell lung cancer (NSCLC). The goal of this analysis was to determine the effects of Zn on metabolism and cell death in A549 cells. Here, high throughput multi-omics analysis identified the molecular effects of Zn intoxication on the proteome, metabolome, and transcriptome of A549 human NSCLC cells after 5 min to 24 h of Zn exposure. Multi-omics analysis combined with additional experimental evidence suggests Zn intoxication induces ferroptosis, an iron and lipid peroxidation-dependent programmed cell death, demonstrating the utility of multi-omics analysis to identify cellular response to intoxicants.
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Affiliation(s)
- Lauren D Palmer
- Vanderbilt Institute for Infection, Immunology and Inflammation and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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4
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Gutierrez DB, Gant-Branum RL, Romer CE, Farrow MA, Allen JL, Dahal N, Nei YW, Codreanu SG, Jordan AT, Palmer LD, Sherrod SD, McLean JA, Skaar EP, Norris JL, Caprioli RM. An Integrated, High-Throughput Strategy for Multiomic Systems Level Analysis. J Proteome Res 2018; 17:3396-3408. [PMID: 30114907 DOI: 10.1021/acs.jproteome.8b00302] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteomics, metabolomics, and transcriptomics generate comprehensive data sets, and current biocomputational capabilities allow their efficient integration for systems biology analysis. Published multiomics studies cover methodological advances as well as applications to biological questions. However, few studies have focused on the development of a high-throughput, unified sample preparation approach to complement high-throughput omic analytics. This report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, sample preparation for multi-omics technologies (SPOT), provides equivalent performance to typical individual omic preparation methods but greatly enhances throughput and minimizes the resources required for multiomic experiments. SPOT was applied to a multiomics time course experiment for zinc-treated HL-60 cells. The data reveal Zn effects on NRF2 antioxidant and NFkappaB signaling. High-throughput approaches such as these are critical for the acquisition of temporally resolved, multicondition, large multiomic data sets such as those necessary to assess complex clinical and biological concerns. Ultimately, this type of approach will provide an expanded understanding of challenging scientific questions across many fields.
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5
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Norris JL, Farrow MA, Gutierrez DB, Palmer LD, Muszynski N, Sherrod SD, Pino JC, Allen JL, Spraggins JM, Lubbock ALR, Jordan A, Burns W, Poland JC, Romer C, Manier ML, Nei YW, Prentice BM, Rose KL, Hill S, Van de Plas R, Tsui T, Braman NM, Keller MR, Rutherford SA, Lobdell N, Lopez CF, Lacy DB, McLean JA, Wikswo JP, Skaar EP, Caprioli RM. Integrated, High-Throughput, Multiomics Platform Enables Data-Driven Construction of Cellular Responses and Reveals Global Drug Mechanisms of Action. J Proteome Res 2017; 16:1364-1375. [PMID: 28088864 DOI: 10.1021/acs.jproteome.6b01004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An understanding of how cells respond to perturbation is essential for biological applications; however, most approaches for profiling cellular response are limited in scope to pre-established targets. Global analysis of molecular mechanism will advance our understanding of the complex networks constituting cellular perturbation and lead to advancements in areas, such as infectious disease pathogenesis, developmental biology, pathophysiology, pharmacology, and toxicology. We have developed a high-throughput multiomics platform for comprehensive, de novo characterization of cellular mechanisms of action. Platform validation using cisplatin as a test compound demonstrates quantification of over 10 000 unique, significant molecular changes in less than 30 days. These data provide excellent coverage of known cisplatin-induced molecular changes and previously unrecognized insights into cisplatin resistance. This proof-of-principle study demonstrates the value of this platform as a resource to understand complex cellular responses in a high-throughput manner.
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Affiliation(s)
| | | | | | | | | | - Stacy D Sherrod
- Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | | | | | | | | | | | | | - James C Poland
- Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | | | | | | | | | | | | | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology , Delft 2628 CD, The Netherlands
| | | | - Nathaniel M Braman
- Biomedical Engineering, Vanderbilt University School of Engineering , Nashville, Tennessee 37235, United States
| | - M Ray Keller
- Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | | | | | - Carlos F Lopez
- Biomedical Engineering, Vanderbilt University School of Engineering , Nashville, Tennessee 37235, United States
| | | | - John A McLean
- Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - John P Wikswo
- Biomedical Engineering, Vanderbilt University School of Engineering , Nashville, Tennessee 37235, United States
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6
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Chumbler NM, Rutherford SA, Zhang Z, Farrow MA, Lisher JP, Farquhar E, Giedroc DP, Spiller BW, Melnyk RA, Lacy DB. Crystal structure of Clostridium difficile toxin A. Nat Microbiol 2016; 1:15002. [PMID: 27571750 PMCID: PMC4976693 DOI: 10.1038/nmicrobiol.2015.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/18/2015] [Indexed: 02/04/2023]
Abstract
Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics.
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Affiliation(s)
- Nicole M. Chumbler
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Stacey A. Rutherford
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Zhifen Zhang
- Department of Biochemistry, University of Toronto and the Molecular Structure & Function Research Institute at The Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
| | - Melissa A. Farrow
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - John P. Lisher
- Interdisciplinary Graduate Program in Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Erik Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences, National Synchrotron Light Source, Building 725, Brookhaven National Laboratory, New York 11973, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Benjamin W. Spiller
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA
| | - Roman A. Melnyk
- Department of Biochemistry, University of Toronto and the Molecular Structure & Function Research Institute at The Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
| | - D. Borden Lacy
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, USA
- The Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37212, USA
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7
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Wang X, Yamamoto Y, Wilson LH, Zhang T, Howitt BE, Farrow MA, Kern F, Ning G, Hong Y, Khor CC, Chevalier B, Bertrand D, Wu L, Nagarajan N, Sylvester FA, Hyams JS, Devers T, Bronson R, Lacy DB, Ho KY, Crum CP, McKeon F, Xian W. Cloning and variation of ground state intestinal stem cells. Nature 2015; 522:173-8. [PMID: 26040716 PMCID: PMC4853906 DOI: 10.1038/nature14484] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/14/2015] [Indexed: 12/18/2022]
Abstract
Stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia collectively resist cloning in their elemental states. Here we demonstrate the cloning and propagation of highly clonogenic, “ground state” stem cells of the human intestine and colon. We show that derived stem cell pedigrees sustain limited copy number and sequence variation despite extensive serial passaging and display exquisitely precise, cell-autonomous commitment to epithelial differentiation consistent with their origins along the intestinal tract. This developmentally patterned and epigenetically maintained commitment of stem cells likely enforces the functional specificity of the adult intestinal tract. Using clonally-derived colonic epithelia, we show that toxins A or B of the enteric pathogen C. difficile recapitulate the salient features of pseudomembranous colitis. The stability of the epigenetic commitment programs of these stem cells, coupled with their unlimited replicative expansion and maintained clonogenicity, suggests certain advantages for their use in disease modeling and regenerative medicine.
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Affiliation(s)
- Xia Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Yusuke Yamamoto
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Lane H Wilson
- 1] The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA [2] Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
| | - Ting Zhang
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02118, USA
| | - Melissa A Farrow
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Florian Kern
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Gang Ning
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Yue Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Chiea Chuen Khor
- 1] Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore [2] Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
| | - Benoit Chevalier
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Denis Bertrand
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Lingyan Wu
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore
| | - Francisco A Sylvester
- Department of Pediatrics, Division of Gastroenterology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut 06106, USA
| | - Thomas Devers
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
| | - Roderick Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - D Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Khek Yu Ho
- Department of Medicine, National University of Singapore, 119228 Singapore
| | - Christopher P Crum
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02118, USA
| | - Frank McKeon
- 1] The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA [2] Genome Institute of Singapore, Agency for Science, Technology and Research, 138672 Singapore [3] Department of Medicine, National University of Singapore, 119228 Singapore [4] Multiclonal Therapeutics, Inc., Farmington, Connecticut 06032, USA
| | - Wa Xian
- 1] The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA [2] Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06032, USA [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02118, USA [4] Department of Medicine, National University of Singapore, 119228 Singapore [5] Multiclonal Therapeutics, Inc., Farmington, Connecticut 06032, USA
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Chumbler NM, Farrow MA, Lapierre LA, Franklin JL, Haslam D, Goldenring JR, Lacy DB. Clostridium difficile Toxin B causes epithelial cell necrosis through an autoprocessing-independent mechanism. PLoS Pathog 2012; 8:e1003072. [PMID: 23236283 PMCID: PMC3516567 DOI: 10.1371/journal.ppat.1003072] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 10/22/2012] [Indexed: 01/21/2023] Open
Abstract
Clostridium difficile is the most common cause of antibiotic-associated nosocomial infection in the United States. C. difficile secretes two homologous toxins, TcdA and TcdB, which are responsible for the symptoms of C. difficile associated disease. The mechanism of toxin action includes an autoprocessing event where a cysteine protease domain (CPD) releases a glucosyltransferase domain (GTD) into the cytosol. The GTD acts to modify and inactivate Rho-family GTPases. The presumed importance of autoprocessing in toxicity, and the apparent specificity of the CPD active site make it, potentially, an attractive target for small molecule drug discovery. In the course of exploring this potential, we have discovered that both wild-type TcdB and TcdB mutants with impaired autoprocessing or glucosyltransferase activities are able to induce rapid, necrotic cell death in HeLa and Caco-2 epithelial cell lines. The concentrations required to induce this phenotype correlate with pathology in a porcine colonic explant model of epithelial damage. We conclude that autoprocessing and GTD release is not required for epithelial cell necrosis and that targeting the autoprocessing activity of TcdB for the development of novel therapeutics will not prevent the colonic tissue damage that occurs in C. difficile – associated disease. Clostridium difficile is an anaerobic spore-forming bacterium that infects the human colon and causes diarrhea, pseudomembranous colitis, and toxic megacolon. Most people that develop disease symptoms have undergone antibiotic treatment, which alters the normal gut flora and allows C. difficile to flourish. C. difficile secretes two toxins, TcdA and TcdB, that are responsible for the fluid secretion, inflammation, and colonic tissue damage associated with disease. The emergence of hypervirulent strains of C. difficile that are linked to increased morbidity and mortality highlights the need for new therapeutic strategies. One strategy is to inhibit the function of the toxins, thereby decreasing damage to the colon while the patient clears the infection with antibiotics. Toxin function is thought to depend on an autoprocessing event that releases a catalytic ‘effector’ portion of the toxin into the host cell. In the course of trying to identify small molecules that would inhibit such a function, we found that TcdB induces a rapid necrosis in epithelial cells that is not dependent on autoprocessing. The physiological relevance of this observation is confirmed in colonic explants and suggests that inhibiting TcdB autoprocessing will not prevent the colonic tissue damage observed in C. difficile associated diseases.
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Affiliation(s)
- Nicole M. Chumbler
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Melissa A. Farrow
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Lynne A. Lapierre
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jeffrey L. Franklin
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology and the Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - David Haslam
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James R. Goldenring
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology and the Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - D. Borden Lacy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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9
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Pruitt RN, Chumbler NM, Rutherford SA, Farrow MA, Friedman DB, Spiller B, Lacy DB. Structural determinants of Clostridium difficile toxin A glucosyltransferase activity. J Biol Chem 2012; 287:8013-20. [PMID: 22267739 DOI: 10.1074/jbc.m111.298414] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.
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Affiliation(s)
- Rory N Pruitt
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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10
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Abstract
The human cytidine deaminase APOBEC3G (A3G) is an innate restriction factor that inhibits human immunodeficiency virus, type 1 (HIV-1) replication. Regulation of A3G gene expression plays an important role in this suppression. Currently, an understanding of the mechanism of this gene regulation is largely unknown. Here, we have identified and characterized a TATA-less core promoter with an NFAT/IRF-4 composite binding site that confers cell type-specific transcriptional regulation. We found that A3G expression is critically dependent on NFATc1/NFATc2 and IRF-4. When either NFATc1 or NFATc2 and IRF-4 were co-expressed, A3G promoter activity was observed in cells that normally lack A3G expression and expression was not detected in the presence of the individual factors. This induced A3G expression allowed normally permissive CEMss cells to adopt a nonpermissive state, able to resist an HIV-1Δvif challenge. This represents the first reporting of manipulating the restrictive state of a cell type via gene regulation. Identification of NFAT and IRF family members as critical regulators of A3G expression offers important insight into the transcriptional control mechanisms that regulate innate immune responses and identifies specific targets for therapeutic intervention aimed at effectively boosting our natural immunity, in the form of a host defensive factor, against HIV-1.
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Affiliation(s)
- Melissa A Farrow
- Department of Biology, College of the Holy Cross, Worcester, Massachusetts 01610, USA
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11
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Bellin RM, Bruno MK, Farrow MA. Purification and characterization of Taq polymerase: A 9-week biochemistry laboratory project for undergraduate students. Biochem Mol Biol Educ 2010; 38:11-16. [PMID: 21567784 DOI: 10.1002/bmb.20352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We have developed a 9-week undergraduate laboratory series focused on the purification and characterization of Thermus aquaticus DNA polymerase (Taq). Our aim was to provide undergraduate biochemistry students with a full-semester continuing project simulating a research-like experience, while having each week's procedure focus on a single learning goal. The laboratory series has been taught for the past 7 years, and survey-based assessment of the effectiveness of the laboratory series was completed during the 2006 and 2007 fall semesters. Statistical analysis of the survey results demonstrate that the laboratory series is very effective in teaching students the theory and practice of protein purification and analysis while also demonstrating positive results in more broad areas of scientific skill and knowledge. Amongst the findings, the largest reported increases in knowledge were related to students' understanding of how patent law relates to laboratory science, a topic of great importance to modern researchers that is readily discussed in relation to Taq polymerase. Overall, this laboratory series proves to be a very effective component in the curricula of undergraduate biology and chemistry majors and may be an appropriate laboratory experience for undergraduates.
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Affiliation(s)
- Robert M Bellin
- Department of Biology, College of the Holy Cross, Worcester, Massachusetts 01610.
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Abstract
It is now 26 years after the first published report on HIV, and the global epidemic continues unabated, with estimates of over 33 million people currently infected, worldwide. Development of targeted therapies aimed at perturbing the HIV life cycle can be achieved only with a detailed comprehension of the dynamics of virus-host interactions within the cell. One such critical virus-host interaction is the recently elucidated interplay between the viral Vif protein and the innate immune defense molecule Apobec3G. Apobec3G potently suppresses HIV replication, but Vif can alleviate this inhibition, rescuing viral infectivity. Early work describing the characterization of Vif and the cloning and identification of Apobec3G as an antiviral are discussed. Recent advances detailing the mechanisms of the Vif-Apobec3G regulatory circuit and our nascent understanding of Apobec3G endogenous function are also presented. Collectively, these studies have shed light on potential novel therapeutic strategies aimed at exploiting Apobec3G antiviral function to abrogate HIV replication.
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Affiliation(s)
- Melissa A Farrow
- College of the Holy Cross, Department of Biology, 1 College Street, Worcester, MA 01610, USA.
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13
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Sanchez-Merino V, Farrow MA, Brewster F, Somasundaran M, Luzuriaga K. Identification and characterization of HIV-1 CD8+ T cell escape variants with impaired fitness. J Infect Dis 2008; 197:300-8. [PMID: 18177249 DOI: 10.1086/524845] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
In this study, amino acid sequence variation in human immunodeficiency virus (HIV)-1 Gag CD8(+) T cell epitopes was examined in untreated mother-infant pairs. Several HIV-1 CD8(+) T cell escape variants were identified within maternal plasma viral p17 and p24 sequences that were either not detected or did not persist in the plasma of their non-HLA-matched HIV-1-infected infants. Viruses constructed with each of these mutations demonstrated reduced viral replication in vitro and reduced expression of p17 and p24 proteins compared with wild type. Reduced recognition of the variant sequences compared with wild-type sequence was also demonstrated by enzyme-linked immunospot assays. Nontransmission or reversion after transmission was thus associated with reduced viral fitness cost in vivo. Better understanding of the balance between CD8(+) T cell selective pressures and viral fitness cost may facilitate the identification of optimal viral sequences for inclusion in HIV-1 vaccines.
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Affiliation(s)
- Victor Sanchez-Merino
- Department of Pediatrics and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Farrow MA, Somasundaran M, Zhang C, Gabuzda D, Sullivan JL, Greenough TC. Nuclear localization of HIV type 1 Vif isolated from a long-term asymptomatic individual and potential role in virus attenuation. AIDS Res Hum Retroviruses 2005; 21:565-74. [PMID: 15989462 DOI: 10.1089/aid.2005.21.565] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent reports have determined that HIV-1 Vif counteracts an innate antiviral cellular factor, Apobec3G. However, the function of Vif during HIV-1 pathogenesis remains poorly understood. To gain a better understanding of Vif function, the viral isolate from an HIV-1-infected long-term nonprogressor (LTNP) that displayed a Vif-mutant replication phenotype was studied. This LTNP has been infected since before 1983 and has no HIV-related disease in the absence of antiretroviral therapy. From separate samples, obtained on more than one study visit, virus grew in cocultures of LTNP cells with Vif-complementing T cell lines, but not the parental T cell lines. An unusual amino acid motif (KKRK) was found in the Vif sequence at positions 90 to 93. Since this motif commonly functions as a nuclear localization sequence, experiments were performed to determine the ability of this KKRK motif to mediate nuclear localization of Vif. Wild-type Vif displayed a predominantly cytoplasmic distribution. In contrast, the KKRK Vif showed a predominantly nuclear localization. The effect of the KKRK mutation on virus production and infectivity was also studied. The KKRK motif that mislocalizes Vif to the nucleus also reduces viral replication and infectivity in nonpermissive cells. Our data highlight the importance of Vif in HIV-1 pathogenesis and also provide a unique tool to investigate the interaction of Vif and Apobec3G.
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Affiliation(s)
- Melissa A Farrow
- Program in Molecular Medicine and Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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15
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Fàbrega C, Farrow MA, Mukhopadhyay B, de Crécy-Lagard V, Ortiz AR, Schimmel P. An aminoacyl tRNA synthetase whose sequence fits into neither of the two known classes. Nature 2001; 411:110-4. [PMID: 11333988 DOI: 10.1038/35075121] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aminoacyl transfer RNA synthetases catalyse the first step of protein synthesis and establish the rules of the genetic code through the aminoacylation of tRNAs. There is a distinct synthetase for each of the 20 amino acids and throughout evolution these enzymes have been divided into two classes of ten enzymes each. These classes are defined by the distinct architectures of their active sites, which are associated with specific and universal sequence motifs. Because the synthesis of aminoacyl-tRNAs containing each of the twenty amino acids is a universally conserved, essential reaction, the absence of a recognizable gene for cysteinyl tRNA synthetase in the genomes of Archae such as Methanococcus jannaschii and Methanobacterium thermoautotrophicum has been difficult to interpret. Here we describe a different cysteinyl-tRNA synthetase from M. jannaschii and Deinococcus radiodurans and its characterization in vitro and in vivo. This protein lacks the characteristic sequence motifs seen in the more than 700 known members of the two canonical classes of tRNA synthetase and may be of ancient origin. The existence of this protein contrasts with proposals that aminoacylation with cysteine in M. jannaschii is an auxiliary function of a canonical prolyl-tRNA synthetase.
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Affiliation(s)
- C Fàbrega
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Beckman Center, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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16
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Abstract
Aminoacyl-tRNA synthetases establish the rules of the genetic code by aminoacylation reactions. Occasional activation of the wrong amino acid can lead to errors of protein synthesis. For isoleucyl-tRNA synthetase, these errors are reduced by tRNA-dependent hydrolytic editing reactions that occur at a site 25 A from the active site. These reactions require that the misactivated amino acid be translocated from the active site to the center for editing. One mechanism describes translocation as requiring the mischarging of tRNA followed by a conformational change in the tRNA that moves the amino acid from one site to the other. Here a specific DNA aptamer is investigated. The aptamer can stimulate amino acid-specific editing but cannot be aminoacylated. Although the aptamer could in principle stimulate hydrolysis of a misactivated amino acid by an idiosyncratic mechanism, the aptamer is shown here to induce translocation and hydrolysis of misactivated aminoacyl adenylate at the same site as that seen with the tRNA cofactor. Thus, translocation to the site for editing does not require joining of the amino acid to the nucleic acid. Further experiments demonstrated that aptamer-induced editing is sensitive to aptamer sequence and that the aptamer is directed to a site other than the active site or tRNA binding site of the enzyme.
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Affiliation(s)
- M A Farrow
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Beckman Center, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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17
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Abstract
The high accuracy of the genetic code relies on the ability of tRNA synthetases to discriminate rigorously between closely similar amino acids. While the enzymes can detect differences between closely similar amino acids at an accuracy of about 1 part in 100-200, a finer discrimination requires the presence of the cognate tRNA. The role of the tRNA is to direct the misactivated amino acid to a distinct catalytic site for editing where hydrolysis occurs. Previous work showed that three nucleotides at the corner of the L-shaped tRNA were collectively required. Here we show that each of these nucleotides individually contributes to the efficiency of editing. However, all are dispensable for the chemical step of hydrolysis. Instead, these nucleotides are required for translocation of a misactivated amino acid from the active site to the center for editing.
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Affiliation(s)
- M A Farrow
- The Skaggs Institute for Chemical Biology, Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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18
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Farrow MA, Aboul-ela F, Owen D, Karpeisky A, Beigelman L, Gait MJ. Site-specific cross-linking of amino acids in the basic region of human immunodeficiency virus type 1 Tat peptide to chemically modified TAR RNA duplexes. Biochemistry 1998; 37:3096-108. [PMID: 9485463 DOI: 10.1021/bi972695v] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Human Immunodeficiency Virus type 1 Tat protein interacts specifically with a U-rich bulge within an RNA stem-loop known as the trans-activation responsive region (TAR) that occurs in all viral transcripts. We have photochemically cross-linked to Tat peptide (37-72), a model TAR duplex substituted at U23 in the bulge by 4-thioU. We have identified the cross-linked amino acid as Arg55 in the basic region of the Tat peptide by use of a combination of proteolytic digestions and MALDI-TOF mass spectrometric analysis. The identification also required use of a synthetic Tat peptide containing a site-specific, uniformly 13C and 15N isotopically labeled arginine. We also describe a new chemical procedure for obtaining site-specific cross-links to Tat via the use of 2'-beta-alanyl U-substituted TAR and the amino-specific reagent dithiobis(succinimidyl propionate). U23-2'-functionalized TAR was shown to cross-link uniquely to Lys51 in the basic region of Tat, whereas other sites in the upper and lower stems of TAR (U35, U38, and U42) showed cross-linking only to the N-terminus of Tat peptide (37-72). U40 cross-linked to both Lys51 and the N-terminus of the peptide. The results help to establish a preliminary model of the binding of Tat peptide to the major groove of TAR RNA.
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Affiliation(s)
- M A Farrow
- Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 2QH, U.K
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19
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Naryshkin NA, Farrow MA, Ivanovskaya MG, Oretskaya TS, Shabarova ZA, Gait MJ. Chemical cross-linking of the human immunodeficiency virus type 1 Tat protein to synthetic models of the RNA recognition sequence TAR containing site-specific trisubstituted pyrophosphate analogues. Biochemistry 1997; 36:3496-505. [PMID: 9131999 DOI: 10.1021/bi962789p] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A chemical ligation procedure has been developed for the synthesis of oligoribonucleotides carrying a trisubstituted pyrophosphate (tsp) linkage in place of a single phosphodiester. Good yields of tsp were obtained when a single 2'-deoxynucleoside 5' to the tsp was used in the ligation reaction. A tsp linkage was found to be reasonably stable to hydrolysis but cleaved by treatment with ethylenediamine or lysine to give phosphoamidate adducts. A model human immunodeficiency virus type 1 (HIV-1) TAR RNA duplex containing an activated tsp was able to bind to HIV-1 Tat protein with only 3-fold reduced affinity and to a Tat peptide (residues 37-72) with identical affinity compared to that of an unmodified duplex. Tsps incorporated at sites previously identified as being in close proximity to Tat protein were able to cross-link to Tat peptide (37-72) to form a covalent phosphoamidate conjugate. Endopeptidase cleavage followed by MALDI-TOF (matrix-assisted laser desorption ionization time of flight) mass spectrometric analysis provided strong evidence that a TAR duplex containing a tsp replacing the phosphate at 38-39 had reacted specifically with Lys51 in the basic region of Tat peptide (37-72). The new chemical cross-linking method may be generally useful for identifying lysines in close proximity to phosphates in basic RNA-binding domains of proteins.
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MESH Headings
- Amino Acid Sequence
- Chromatography, High Pressure Liquid
- Cross-Linking Reagents/pharmacology
- Diphosphates/chemistry
- Diphosphates/metabolism
- Electrophoresis, Polyacrylamide Gel
- Gene Products, tat/chemical synthesis
- Gene Products, tat/metabolism
- HIV Long Terminal Repeat
- HIV-1
- Models, Chemical
- Molecular Sequence Data
- Oligonucleotides/chemical synthesis
- Oligonucleotides/chemistry
- Peptide Fragments/chemistry
- Peptide Fragments/metabolism
- RNA, Viral/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Templates, Genetic
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- N A Naryshkin
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, U.K
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