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Mussack V, Wittmann G, Pfaffl MW. Comparing small urinary extracellular vesicle purification methods with a view to RNA sequencing-Enabling robust and non-invasive biomarker research. Biomol Detect Quantif 2019; 17:100089. [PMID: 31194192 PMCID: PMC6554496 DOI: 10.1016/j.bdq.2019.100089] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 04/10/2019] [Indexed: 01/10/2023]
Abstract
Small extracellular vesicles (EVs) are 50–200 nm sized mediators in intercellular communication that reflect both physiological and pathophysiological changes of their parental cells. Thus, EVs hold great potential for biomarker detection. However, reliable purification methods for the downstream screening of the microRNA (miRNA) cargo carried within urinary EVs by small RNA sequencing have yet to be established. To address this knowledge gap, RNA extracted from human urinary EVs obtained by five different urinary EV purification methods (spin column chromatography, immunoaffinity, membrane affinity, precipitation and ultracentrifugation combined with density gradient) was analyzed by small RNA sequencing. Urinary EVs were further characterized by nanoparticle tracking analysis, Western blot analysis and transmission electron microscopy. Comprehensive EV characterization established significant method-dependent differences in size and concentration as well as variances in protein composition of isolated vesicles. Even though all purification methods captured enough total RNA to allow small RNA sequencing, method-dependent differences were also observed with respect to library sizes, mapping distributions, number of miRNA reads and diversity of transcripts. Whereas EVs obtained by immunoaffinity yielded the purest subset of small EVs, highly comparable with results attained by ultracentrifugation combined with density gradient, precipitation and membrane affinity, sample purification by spin column chromatography indicated a tendency to isolate different subtypes of small EVs, which might also carry a distinct subset of miRNAs. Based on our results, different EV purification methods seem to preferentially isolate different subtypes of EVs with varying efficiencies. As a consequence, sequencing experiments and resulting miRNA profiles were also affected. Hence, the selection of a specific EV isolation method has to satisfy the respective research question and should be well considered. In strict adherence with the MISEV (minimal information for studies of extracellular vesicles) guidelines, the importance of a combined evaluation of biophysical and proteomic EV characteristics alongside transcriptomic results was clearly demonstrated in this present study.
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Key Words
- A, spin column chromatography
- ANOVA, analysis of variance
- Ago2, argonaute-2 protein
- B, immunoaffinity
- Biomarker
- C, membrane affinity
- D, precipitation
- DGE, differential gene expression
- DTT, dithiothreitol
- E, ultracentrifugation combined with density gradient
- EV(s), extracellular vesicle(s)
- Extracellular vesicles
- FM, fluorescent mode
- Human
- MISEV, minimal information for studies of extracellular vesicles
- NTA, nanoparticle tracking analysis
- PC, principal component
- RIN, RNA integrity number
- RNA-Seq, RNA sequencing
- SM, scattering mode
- Small RNA sequencing
- TEM, transmission electron microscopy
- UCrea, urinary creatinine
- Urine
- mIgG, murine immunoglobulin G
- mRNA, messenger RNA
- miRNA, microRNA
- microRNA
- nm, nanometer(s)
- nt, nucleotide(s)
- rRNA, ribosomal RNA
- snRNA, small nuclear RNA
- snoRNA, small nucleolar RNA
- tRNA, transfer RNA
- uEVs, urinary extracellular vesicles
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Affiliation(s)
- Veronika Mussack
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Georg Wittmann
- Department for Transfusion Medicine, Cell therapeutics and Haemostaseology, University Hospital LMU, Marchioninistraße 15, 81377, Munich, Germany
| | - Michael W Pfaffl
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
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Wang N, Ahmed S, Haqqi TM. Genomic structure and functional characterization of the promoter region of human IkappaB kinase-related kinase IKKi/IKKvarepsilon gene. Gene 2005; 353:118-33. [PMID: 15939554 PMCID: PMC1266289 DOI: 10.1016/j.gene.2005.04.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Revised: 03/18/2005] [Accepted: 04/07/2005] [Indexed: 12/24/2022]
Abstract
The inducible IkappaB kinase (IKKi/IKKepsilon) is a recently described serine-threonine kinase that activates the transcription factors NFkappaB, interferon regulatory factor-3 (IRF3) and CCAAA/enhancer-binding protein (C/EBPdelta). Several inflammatory agents have been shown to induce the expression of the IKKi gene in macrophages and other cell types but the mechanism is unknown. We have found that the IKKi expression was constitutive in human chondrocytes from OA cartilage and a human chondrocytic cell line C28/I2 but was up-regulated by the inflammatory cytokines TNFalpha or IL-1betain an NFkappaB-dependent manner. To understand the constitutive and inducible expression of the IKKi gene we localized the transcription start site (TSS), cloned and sequenced a 2 kb genomic DNA fragment 5' of the TSS and characterized the putative promoter region (PPR), and identified the motifs therein that are required for basal and cytokine-induced IKKi gene promoter activity. We found that IKKi core promoter was TATA-less and by using PCR generated deletion mutants of the PPR we found that the cis-elements responsible for basal transcriptional activity were located between -51 and -100 bp upstream of the TSS while the cytokine response elements were located distally between -501 and -1000 bp upstream of the TSS. The DNA region containing the cytokine response elements had two kappaB sites as the most relevant regulatory motifs. The results of site-directed mutagenesis revealed that the kappaB site located between -833 and -847 bp upstream of the TSS was biologically functional and required for cytokine-induced IKKi promoter activity in human chondrocytes and HeLa cells. The silence of the other kappaB site (-816/-802) was positional, rather than sequence-specific. Over-expression of NFkappaB p65 mimics the TNFalpha-induced activation of the IKKi promoter. Also the gel shift assay suggested that NFkappaB p65 is responsible for activation of the IKKi promoter. These data for the first time characterize the promoter region and provide further insights into the transcriptional regulation of IKKi in human chondrocytes and other cell types.
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Key Words
- ikki/ikkɛ promoter
- cis-acting element
- transcriptional regulation
- nfκb, chondrocyte
- 5’-race, 5’-rapid amplification of cdna ends
- actd, actinomycin d
- bp, base pair(s)
- bre, tfiib responsive element
- chx, cycloheximide
- dpe, downstream promoter element
- emsa, electrophoretic mobility shift assay
- emssa, electrophoretic mobility supershift assay
- iκb, inhibitor of nfκb
- ikki/ikkɛ, inducible iκb kinase
- il, interleukin
- inr, initiator
- nfκb, nuclear factor kappa b
- nt, nucleotide(s)
- ppr, putative promoter region
- rt-pcr, reverse transcriptase-polymerase chain reaction
- seap, secreted form of human placental alkaline phosphatase
- tbp, tata-binding protein
- tnf, tumor necrosis factor
- tss, transcription start site
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Affiliation(s)
| | | | - Tariq M. Haqqi
- Division of Rheumatic Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 U. S. A
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Abstract
A mouse acetyl-CoA transporter (Acatn) cDNA was isolated by PCR cloning. Mouse Acatn exhibited 92% homology with human sequence on the basis of amino-acid sequence. The predicted gene product of Acatn is a 61 kDa hydrophobic protein with six to 10 transmembrane domains. Transfection of mouse Acatn cDNA into HeLa/GT3+ cells resulted in significant increase in the amount of 9-O-acetylated gangliosides, suggesting that Acatn does play an important role in the acetylation of gangliosides. Northern blot analysis of Acatn mRNA suggested that transcript of Acatn is widely distributed in various adult tissues. Expression of Acatn was found to be developmentally regulated, with high expression levels during early embryonic stages, and then there was a subsequent decrease in expression levels in the later embryonic stages.
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Key Words
- dorsal root ganglia
- embryonic development
- o-acetylated gangliosides
- cdna, dna complementary to mrna
- pcr, polymerase chain reaction
- acatn, acetyl-coa transporter
- acatn, gene encoding acatn
- mab, monoclonal antibody
- nt, nucleotide(s)
- ed, embryonic day
- dig, digoxigenin
- gapdh, glyceraldehyde-3-phosphate dehydrogenase
- gd3, neuacα(2-8)neuacα(2-3)galβ(1-4)glcβ(1-1′)cer
- gt3, neuacα(2-8)neuacα(2-8)neuacα(2-3)galβ(1-4) glcβ(1-1′)cer
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Abstract
SHFV is a member of a new virus family which includes the genus arterivirus. We have cloned and sequenced 6,314 nt from the 3' end of the SHFV genome. This sequence encompasses nine complete ORFs which is three additional ORFs as compared to the other arteriviruses. We have numbered these ORFs 2a, 2b, 3, 4, 5, 6, 7, 8 and 9. At the 5' end of this sequence is a partial ORF (ORF 1b) of 1590 nt and at the 3' end is a poly(A) tract preceded by a 76 nt noncoding region. The coding capacity for each of the SHFV ORFs as well as the potential mass, pI and number of N-linked glycosylation sites for each of the encoded peptides was determined.
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Key Words
- arterivirus
- genome organization
- 3′ genes
- a, adenosine
- bcv, bovine coronavirus
- eav, equine arteritis virus
- kb, kilobase(s)
- ldv, lactate dehydrogenase-elevating virus
- mhv, mouse hepatitis virus
- nt, nucleotide(s)
- orf, open reading frame
- prrsv, porcine reproductive and respiratory syndrome virus
- sgrna(s), subgenomic mrna(s)
- shfv, simian hemorrhagic fever virus.
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Affiliation(s)
| | | | - Elmer K Godeny
- Corresponding author. Tel.: +1 504 3463304; fax: +1 504 3465715; e-mail:
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Abstract
We have previously reported the nucleotide sequences of gene 2 (spike (S) protein gene), gene 6 (nucleocapsid (N) protein gene), and the 3' end untranslated region of a novel avian infectious bronchitis virus (IBV) strain, CU-T2 [Jia et al. (1995) Arch. Virol. 140, 259 271]. In the present report we describe the sequences of the remaining genes of this strain (gene 3, 4 and 5) with the exception of gene 1 (RNA polymerase gene). Gene 3 contained three open reading frames (ORFs), 3a, 3b and 3c of 174, 195 and 282 nucleotides (nt), respectively. Gene 4 (membrane (M) protein gene) consisted of 749 nt with a single ORF of 687 nt. Gene 5 contained two ORFs, 5a and 5b, with 198 and 249 nt, respectively. Thus, in total, there were 7349 nt from the 5' end of S protein gene to the 3' end of the CU-T2 genome. The overall nt sequence homologies between gene 3, 4, and 5 of CU-T2 and those of other strains were between 84.1-90.8%, 85.8-88.8% and 90.4 96.4%, respectively. The predicted amino acid (aa) sequence homologies revealed that gene 3b and 5b were more conserved than 3a, 3c and 5a. Each individual gene of CU-T2 strain (with the exception of the RNA polymerase gene) had a different level of homology with the homologous gene of other strains, suggesting that the evolution of IBV strains in general has been a complex, and as yet, poorly understood process.
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Key Words
- coronaviridae
- coronavirus
- ibv
- virus evolution
- cloning
- recombinant dna
- membrane protein gene
- small membrane protein gene
- aa, amino acid(s)
- ark, arkansas
- bp, base pair(s)
- escherichia coli (e. coli)
- ibv, infectious bronchitis virus
- kb, kilobase(s) or 1000 bp
- m, membrane
- mass, massachusetts
- n, nucleocapsid
- nt, nucleotide(s)
- oligo, oligodeoxyribonucleotide
- orf, open reading frame(s)
- s, spike
- sm, small membrane
- utr, untranslated region.
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Affiliation(s)
| | - Syed A Naqi
- Corresponding author. Tel. +1 607 2534045; Fax +1 607 2533369; e-mail:
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Huh C, Nagle JW, Kozak CA, Abrahamson M, Karlsson S. Structural organization, expression and chromosomal mapping of the mouse cystatin-C-encoding gene (Cst3). Gene 1995; 152:221-6. [PMID: 7835704 PMCID: PMC7173308 DOI: 10.1016/0378-1119(94)00728-b] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/1994] [Revised: 05/23/1994] [Accepted: 10/17/1994] [Indexed: 01/27/2023]
Abstract
Cystatin C (CstC) is a potent cysteine-proteinase inhibitor. The structure of the mouse CstC-encoding gene (Cst3) was examined by sequencing a 6.1-kb genomic DNA containing the entire gene, as well as 0.9 kb of 5' flanking and 1.7 kb of its 3' flanking region. The sequence revealed that the overall organization of the gene is very similar to those of the genes encoding human CstC and other type-2 Cst, with two introns at positions identical to those in the human gene. The promoter area does not contain typical TATA or CAAT boxes. Two copies of a Sp1-binding motif, GGGCGG, are present in the 5' flanking region within 300 bp upstream from the initiation codon. A hexa-nucleotide, TGTTCT, which is a core sequence of the androgen-responsive element (ARE), is found in the promoter region. This region also contains a 21-nucleotide sequence, 5'-AGACTAGCAGCTGACTGAAGC, which contains two potential binding sites for the transcription factor, AP-1. The mouse Cst3 mRNA was detected in all of thirteen tissues examined by Northern blot analysis. Cst3 was mapped in the mouse to a position on distal chromosome 2.
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Key Words
- recombinant genomic dna
- gene mapping
- exon
- intron
- promoter sequence
- proteinase inhibitor
- multigene family
- aa, amino acid(s)
- are, androgen-responsive element(s)
- bp, base pair(s)
- chr, chromosome
- cst, cystatin(s)
- cst3, gene (dna) encoding cstc
- cstl, gene (dna) encoding cstsn
- cst2, gene (dna) encoding cstsa
- cst4, gene (dna) encoding cstd
- hccaa, hereditary cstc amyloid angiopathy
- kb, kilobase(s) or 1000 bp
- nt, nucleotide(s)
- rflp, restriction-fragment length polymorphism
- w, a or t
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Affiliation(s)
- Changgoo Huh
- Molecular and Medical Genetics Section, Developmental and Metabolic Neurolology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - James W. Nagle
- Neurogenetic Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA. Tel. (1-301) 496-8801
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Tel. (1-301) 496-0972
| | - Magnus Abrahamson
- Department of Clinical Chemistry, University Hospital, S-221 85 Lund, Sweden. Tel. (46-46) 173-445
| | - Stefan Karlsson
- Molecular and Medical Genetics Section, Developmental and Metabolic Neurolology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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Der Vartanian M, Méchin MC, Jaffeux B, Bertin Y, Félix I, Gaillard-Martinie B. Permissible peptide insertions surrounding the signal peptide-mature protein junction of the ClpG prepilin: CS31A fimbriae of Escherichia coli as carriers of foreign sequences. Gene 1994; 148:23-32. [PMID: 7523252 PMCID: PMC7131889 DOI: 10.1016/0378-1119(94)90229-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The clpG gene, expressing the Escherichia coli major CS31A fimbrial subunit ClpG, was subjected to random mutagenesis by insertion of an EcoRI linker and a kanamycin-resistance (KmR) cassette into the multiple newly generated EcoRI sites. The KmR gene was then excised by PstI, which left a 48-bp linker representing the heterologous sequence. The same procedure was followed to introduce a synthetic oligodeoxyribonucleotide (oligo) corresponding to epitope C from the spike protein S from the porcine transmissible gastroenteritis coronavirus (TGEV). Nine insertion/deletion mutants (indels) that contained long foreign peptides variously located around the ClpG signal peptide (SP) processing site were characterized. A striking feature of this study is the variety of amino acid (aa) insertions in the ClpG prepilin that have little or no effect on CS31A fimbria biogenesis. These 'permissive' sites tolerate inserts of 18 or 19 aa and accept sequences of different natures in view of their aa composition, charge and hydrophobicity. The results obtained here are also interesting in light of the high level of aa sequence conservation seen in the SP and N-terminal domains of the ClpG-related subunits. The structure-function relationship of the ClpG SP is discussed. The TGEV-C epitope fused to the N-terminal end of the mature ClpG protein was cell-surface exposed, as observed on immuno-electron microscopy. Therefore, the CS31A fimbria seems to be a potent tool for the presentation of foreign antigenic determinants or the production of heterologous polypeptides in E. coli.
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Key Words
- recombinant dna
- random mutagenesis
- signal sequence
- genetic fusions
- hybrid protein secretion
- chaperone
- transmissible gastroenteritis virus
- epitope
- antigen display
- pilin
- a, absorbance (1 cm)
- aa, amino acid(s)
- ab, antibody (ies)
- ap, ampicillin
- bp, base pair(s)
- clpg, major cs31a fimbrial subunit
- cmm, chloramphenicol
- dnase i, bovine pancreatic deoxyribonuclease
- dntp, deoxynucleotide triphosphate
- em, electron microscopy
- igg, immunoglobulin g
- indel, insertion/deletion mutant
- iptg, isopropyl-β-d-thiogalactopyranoside
- kb, kilobase(s) or 1000 bp
- km, kanamycin
- mab, monoclonal ab
- mcs, multiple cloning site(s)
- nt, nucleotide(s)
- oligo, oligodeoxyribonucleotide
- pa, polyacrylamide
- pab, polyclonal ab
- page, pa-gel electrophoresis
- pbs, 0.14 m nacl/2.7 mm kcl/1.8 mm kh2po4/10 mm na2 · hpo4 ph 7.2
- polik, klenow (large) fragment of e. coli dna polymerase i
- r, resistance/resistant
- sds, sodium dodecyl sulfate
- sp, signal peptide
- tgev, transmissible gastroenteritis virus
- wt, wild type
- x, any aa
- ::, novel junction (fusion or insertion)
- [ ], denotes plasmid-carrier state
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Affiliation(s)
- M Der Vartanian
- Laboratoire de Microbiologie, Centre de Recherches de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
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Abstract
The biliary glycoprotein (BGP)-encoding gene is a member of the human carcinoembryonic antigen (CEA) gene family. We have now cloned several mouse Bgp cDNAs from an outbred CDR-1 mouse colon cDNA library, as well as by reverse transcription-PCR amplification of colon RNA. The distinguishing features of the deduced Bgp protein isoforms are found in the two divergent N-terminal domains, the highly conserved internal C2-set immunoglobulin domains, and an intracytoplasmic domain of either 10 or 73 amino acids (aa). The cDNA structures suggest that these mRNAs are produced through alternative splicing of a Bgp gene and the usage of multiple transcriptional terminators. The Bgp deduced aa sequences are highly homologous to several well characterized rat hepatocyte proteins such as the cell CAM105/ecto-ATPase/pp120/HA4 proteins. Oligodeoxyribonucleotide probes representing the various cDNA isoform domains revealed predominant transcripts of 1.8, 3.1 and 4.0 kb on Northern analyses of mouse colon RNA; some of these bands are actually composed of several co-migrating transcripts. The transcripts encoding the long intracytoplasmic-tailed Bgp proteins are expressed at one-tenth the relative abundance of the shorter-tailed species. We have previously demonstrated that several mouse Bgp cDNAs, when transfected into eukaryotic cells, express BGP proteins at the cell surface and function in vitro as cell adhesion molecules, much like their human and rat counterparts. The expression of the many Bgp isoforms at the surface of epithelial cells, such as colon, suggests that these proteins play a determinant role, through self- or heterologous contact, in renewal and/or differentiation of their epithelia.
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Key Words
- carcinoembryonic antigen gene family member
- reverse transcription and polymerase chain amplification
- mouse hepatitis virus receptor
- adhesion molecule
- aa, amino acid(s)
- bgp, biliary glycoprotein
- bgp, mouse biliary glycoprotein
- bgpx, gene isoforms encoding mouse bgps (replaces mmcgm to conform with mouse genome nomenclature
- x is assigned by order of characterization)
- bp, base pair(s)
- cd, complement determining
- cea, carcinoembryonic antigen
- cgm, cea-related gene family member
- cyt, intracytoplasmic tail
- icam-1, intercellular adhesion molecule 1
- ig, immunoglobulin
- kb, kilobase(s) or 1000 bp
- mhv, mouse hepatitis virus
- mhvr, mhv receptor
- nca, nonspecific cross-reacting antigen
- nt, nucleotide(s)
- oligo, oligodeoxyribonucleotide
- orf, open reading frame
- pcr, polymerase chain reaction
- psg, pregnancy-specific glycoprotein
- 5′ or 3′utr, 5′ or 3′ untranslated region
- rit, oligo specific for cyt in the antisense orientation
- rt, reverse transcription
- tm, transmembrane
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Affiliation(s)
- K McCuaig
- McGill Cancer Centre, McGill University, Montreal, Québec, Canada
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Abstract
A 50-nucleotide (nt) untranslated region (coding gap sequence) that interrupts the amino acid coding sequence in T4 gene 60, plus an additional 5 nt upstream and another 3 nt downstream from the gap sequence, shows unusual folding patterns according to RNA structure prediction. A predicted highly stable and significant hairpin structure in the 5' half of the gap sequence and a plausible tertiary structural element computed in the 3' part of the gap sequence seem significant by statistical tests on the wild-type (wt) sequence. This feature is absent in insertion, deletion and substitution variants of the gap sequence, in which template activities are markedly lower than that of the wt. The proposed feature is consistent with currently available data showing that the translational bypass of the coding gap is correlated with a stop codon involved in a stem-loop structure folded in the gap sequence. We suggest that the role of this segment in 'ribosomal bypass' of a portion of the mRNA sequence is a property of its special folded structure.
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Affiliation(s)
- Le Shu-Yun
- Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis Centers, National Cancer Institute, NIH, Frederick, MD 21702, USA
- Correspondence to: Dr. S.-Y. Le, Laboratory of Mathematical Biol., DCBDC, NCI, NIH, Bldg. 469, Rm. 151, Frederick, MD 21702, USA. Tel. (301)846-5576; Fax (301)846-5598.
| | - Chen Jih-Hsiang
- Biomedical Supercomputing Center, Program Resources Inc., DynCorp, NCI/FCRDC, Frederick, MD 21702, USA. Tel. (301)846-5773
| | - Jacob V. Maizel
- Laboratory of Mathematical Biology, Division of Cancer Biology and Diagnosis Centers, National Cancer Institute, NIH, Frederick, MD 21702, USA
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Trirawatanapong T, Chandran B, Putnak R, Padmanabhan R. Mapping of a region of dengue virus type-2 glycoprotein required for binding by a neutralizing monoclonal antibody. Gene X 1992; 116:139-50. [PMID: 1634111 PMCID: PMC7125935 DOI: 10.1016/0378-1119(92)90509-n] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Envelope glycoprotein E of flaviviruses is exposed at the surface of the virion, and is responsible for eliciting a neutralizing antibody (Ab) response, as well as protective immunity in the host. In this report, we describe a method for the fine mapping of a linear sequence of the E protein of dengue virus type-2 (DEN-2), recognized by a type-specific and neutralizing monoclonal Ab (mAb), 3H5. First, an Escherichia coli expression vector containing a heat-inducible lambda pL promoter was used to synthesize several truncated, and near-full length E polypeptides. Reactivities of these polypeptides with polyclonal mouse hyperimmune sera, as well as the 3H5 mAb revealed the location of the 3H5-binding site to be within a region of 166 amino acids (aa) between aa 255 and 422. For fine mapping, a series of targeted deletions were made inframe within this region using the polymerase chain reaction (PCR). The hydrophilicity pattern of this region was used as a guide to systematically delete the regions encoding the various groups of surface aa residues within the context of a near-full-length E polypeptide by using PCR. The 3H5-binding site was thus precisely mapped to a region encoding 12 aa (between aa 386 and 397). A synthetic peptide containing this sequence was able to bind to the 3H5 mAb specifically, as shown by enzyme-linked immunosorbent assay. In addition, we show that rabbit Abs raised against the synthetic peptide of 12 aa were able to bind to the authentic E protein, and to neutralize DEN-2 virus in a plaque reduction assay.
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Key Words
- recombinant dna
- λ pl promoter
- expression in escherichia coli
- epitope mapping
- pcr
- deletion mutagenesis
- mab
- synthetic peptide antigen
- a, absorbance
- aa, amino acid(s)
- ap, ampicillin
- bp, base pair(s)
- c, capsid protein
- cdna, dna complementary to rna
- den-2, dengue virus type 2
- dmem, dulbecco's modified eagle's medium
- doc, deoxycholate
- e, envelope protein
- elisa, enzyme-linked immunosorbent assay
- hi, hemagglutination-inhibition
- hmaf, hyperimmune mouse ascitic fluid containing polyclonal antibodies against a mixture of den-2 antigens
- hplc, high-performance liquid chromatography
- hsv-2, herpes simplex virus type 2
- je, japanese encephalitis virus
- kb, kilobase(s) or 1000 bp
- klh, keyhole limpet hemocyanin
- lb, luria-bertani (medium)
- m, membrane protein
- mab, monoclonal antibody
- mbs, m-maleimidobenzoylsulfosuccinimide ester
- m.o.i., multiplicity of infection
- ngs-c, new guinea c strain
- nt, nucleotide(s)
- oligo, oligodeoxyribonucleotide
- orf, open reading frame
- pbs, phosphate-buffered saline (10 mm na phosphate,ph 7.2/150 mm nacl)
- polik, klenow (large) fragment of e. coli dna polymerase i
- pcr, polymerase chain reaction
- pfu, plaque forming units
- pmsf, phenylmethylsulfonyl fluoride
- prm, precursor to membrane protein
- prnt, plaque reduction neutralization test
- rbs, ribosome binding site
- sds, sodium dodecyl sulfate
- taq, thermus aquaticus yti
- tbe, tick-borne encephalitis
- wn, west nile virus
- yf, yellow fever virus
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Affiliation(s)
- T Trirawatanapong
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City 66103
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Zoltick PW, Leibowitz JL, DeVries JR, Weinstock GM, Weiss SR. A general method for the induction and screening of antisera for cDNA-encoded polypeptides: antibodies specific for a coronavirus putative polymerase-encoding gene. Gene 1989; 85:413-20. [PMID: 2560756 PMCID: PMC7127337 DOI: 10.1016/0378-1119(89)90434-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/1989] [Revised: 06/29/1989] [Accepted: 06/30/1989] [Indexed: 01/01/2023]
Abstract
A prokaryotic vector, pGE374, containing the recA and lacZ genes, out-of-frame, was used for the expression of cDNA derived from the putative polymerase-encoding gene of the coronavirus mouse hepatitis virus strain A59 (MHV-A59). The pGE374/viral recombinant vector generates a tripartite bacterial/viral protein composed of a segment of the RecA protein at the N terminus, the coronaviral sequences in the middle, and an enzymatically active beta-galactosidase at the C terminus. Rabbits immunized with such recombinant proteins generated antibodies to the MHV-A59 portion of the tripartite protein. Because the MHV-A59 polymerase proteins have been difficult to identify during infection, we used a novel method to demonstrate the viral specificity of the antiserum. The viral cDNA was excised from the expression vector, and transferred to a pGem vector, downstream from and in-frame with a portion of the cat gene. This construct contained a bacteriophage RNA polymerase promoter that enabled the cell-free synthesis of a fusion protein that was used to verify that antibodies were generated to the expressed viral DNA. This strategy was shown to successfully result in the specific generation of antibodies to the encoded information of the viral cDNA. Furthermore, this method has general applicability in the generation and characterization of antibodies directed against proteins encoded in cDNAs.
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Key Words
- recombinant dna
- open reading frame vector
- nonstructural viral proteins
- cell-free protein synthesis
- mouse hepatitis virus
- aa, amino acid(s)
- ap, ampicillin
- bp, base pair(s)
- βgal, β-galactosidase
- b/v, bacterial/viral (fusion protein)
- cat, cm acetyl transferase
- cat, gene encoding cat
- cdna, dna complementary to rna
- cm, chloramphenicol
- iptg, isopropyl-β-d-thiogalactopyranoside
- kb, kilobase(s) or 1000 bp
- mhv, mouse hepatitis virus
- moi, multiplicity of infection
- np40, nonidet p40
- nt, nucleotide(s)
- onpg, o-nitrophenyl-d-galactopyranoside
- orf, open reading frame
- page, polyacrylamide-gel electrophoresis
- pbs, 0.9% nacl/10mm na · phosphate ph 7.4
- pmsf, phenylmethylsulfonyl fluoride
- ripa buffer, 0.1 % sds/1 % np40/400 mm nacl/25 μg pmsf per ml/20 μg aprotinin per ml/10 mm na · phosphate ph 7.4
- sds, sodium dodecyl sulfate
- ts, 10 mm tris ph 7.4/10 mm nacl/1.5 mm mgcl2
- ts/p, ts with 20 μg pmsf/ml
- wt, wild type
- xgal, 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside
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Affiliation(s)
- P W Zoltick
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia 19104
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