Academic literature on the topic 'ER-targeting sequence coding region'
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Journal articles on the topic "ER-targeting sequence coding region"
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Nordholm, Johan, Jeanne Petitou, Henrik Östbye, Diogo V. da Silva, Dan Dou, Hao Wang, and Robert Daniels. "Translational regulation of viral secretory proteins by the 5′ coding regions and a viral RNA-binding protein." Journal of Cell Biology 216, no. 8 (July 10, 2017): 2283–93. http://dx.doi.org/10.1083/jcb.201702102.
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A primary function of 5′ regions in many secretory protein mRNAs is to encode an endoplasmic reticulum (ER) targeting sequence. In this study, we show how the regions coding for the ER-targeting sequences of the influenza glycoproteins NA and HA also function as translational regulatory elements that are controlled by the viral RNA-binding protein (RBP) NS1. The translational increase depends on the nucleotide composition and 5′ positioning of the ER-targeting sequence coding regions and is facilitated by the RNA-binding domain of NS1, which can associate with ER membranes. Inserting the ER-targeting sequence coding region of NA into different 5′ UTRs confirmed that NS1 can promote the translation of secretory protein mRNAs based on the nucleotides within this region rather than the resulting amino acids. By analyzing human protein mRNA sequences, we found evidence that this mechanism of using 5′ coding regions and particular RBPs to achieve gene-specific regulation may extend to human-secreted proteins.
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Kuroki, K., R. Russnak, and D. Ganem. "Novel N-terminal amino acid sequence required for retention of a hepatitis B virus glycoprotein in the endoplasmic reticulum." Molecular and Cellular Biology 9, no. 10 (October 1989): 4459–66. http://dx.doi.org/10.1128/mcb.9.10.4459.
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The preS1 surface glycoprotein of hepatitis B virus is targeted to the endoplasmic reticulum (ER) and is retained in this organelle when expressed in the absence of other viral gene products. The protein is also acylated at its N terminus with myristic acid. Sequences responsible for its ER retention have been identified through examination of mutants bearing lesions in the preS1 coding region. These studies reveal that such sequences map to the N terminus of the molecule, between residues 6 and 19. Molecules in which this region was present remained in the ER; those in which it had been deleted were secreted from the cell. Although all deletions which allowed efficient secretion also impaired acylation of the polypeptide, myristylation alone was not sufficient for ER retention: point mutations which eliminated myristylation did not lead to secretion. These data indicate that an essential element for ER retention resides in a 14-amino-acid sequence that is unrelated to previously described ER retention signals.
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Kuroki, K., R. Russnak, and D. Ganem. "Novel N-terminal amino acid sequence required for retention of a hepatitis B virus glycoprotein in the endoplasmic reticulum." Molecular and Cellular Biology 9, no. 10 (October 1989): 4459–66. http://dx.doi.org/10.1128/mcb.9.10.4459-4466.1989.
Full textAbstract:
The preS1 surface glycoprotein of hepatitis B virus is targeted to the endoplasmic reticulum (ER) and is retained in this organelle when expressed in the absence of other viral gene products. The protein is also acylated at its N terminus with myristic acid. Sequences responsible for its ER retention have been identified through examination of mutants bearing lesions in the preS1 coding region. These studies reveal that such sequences map to the N terminus of the molecule, between residues 6 and 19. Molecules in which this region was present remained in the ER; those in which it had been deleted were secreted from the cell. Although all deletions which allowed efficient secretion also impaired acylation of the polypeptide, myristylation alone was not sufficient for ER retention: point mutations which eliminated myristylation did not lead to secretion. These data indicate that an essential element for ER retention resides in a 14-amino-acid sequence that is unrelated to previously described ER retention signals.
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Krönke, Jan, Ralf Kittler, Frank Buchholz, Marc P. Windisch, Thomas Pietschmann, Ralf Bartenschlager, and Michael Frese. "Alternative Approaches for Efficient Inhibition of Hepatitis C Virus RNA Replication by Small Interfering RNAs." Journal of Virology 78, no. 7 (April 1, 2004): 3436–46. http://dx.doi.org/10.1128/jvi.78.7.3436-3446.2004.
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ABSTRACT Persistent infection with hepatitis C virus (HCV) is a leading cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. It has recently been shown that HCV RNA replication is susceptible to small interfering RNAs (siRNAs), but the antiviral activity of siRNAs depends very much on their complementarity to the target sequence. Thus, the high degree of sequence diversity between different HCV genotypes and the rapid evolution of new quasispecies is a major problem in the development of siRNA-based gene therapies. For this study, we developed two alternative strategies to overcome these obstacles. In one approach, we used endoribonuclease-prepared siRNAs (esiRNAs) to simultaneously target multiple sites of the viral genome. We show that esiRNAs directed against various regions of the HCV coding sequence as well as the 5′ nontranslated region (5′ NTR) efficiently block the replication of subgenomic and genomic HCV replicons. In an alternative approach, we generated pseudotyped retroviruses encoding short hairpin RNAs (shRNAs). A total of 12 shRNAs, most of them targeting highly conserved sequence motifs within the 5′ NTR or the early core coding region, were analyzed for their antiviral activities. After the transduction of Huh-7 cells containing a subgenomic HCV replicon, we found that all shRNAs targeting sequences in domain IV or nearby coding sequences blocked viral replication. In contrast, only one of seven shRNAs targeting sequences in domain II or III had a similar degree of antiviral activity, indicating that large sections of the NTRs are resistant to RNA interference. Moreover, we show that naive Huh-7 cells that stably expressed certain 5′ NTR-specific shRNAs were largely resistant to a challenge with HCV replicons. These results demonstrate that the retroviral transduction of HCV-specific shRNAs provides a new possibility for antiviral intervention.
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Skach, W. R., L. B. Shi, M. C. Calayag, A. Frigeri, V. R. Lingappa, and A. S. Verkman. "Biogenesis and transmembrane topology of the CHIP28 water channel at the endoplasmic reticulum." Journal of Cell Biology 125, no. 4 (May 15, 1994): 803–15. http://dx.doi.org/10.1083/jcb.125.4.803.
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CHIP28 is a 28-kD hydrophobic integral membrane protein that functions as a water channel in erythrocytes and renal tubule epithelial cell membranes. We examined the transmembrane topology of CHIP28 in the ER by engineering a reporter of translocation (derived from bovine prolactin) into nine sequential sites in the CHIP28 coding region. The resulting chimeras were expressed in Xenopus oocytes, and the topology of the reporter with respect to the ER membrane was determined by protease sensitivity. We found that although hydropathy analysis predicted up to seven potential transmembrane regions, CHIP28 spanned the membrane only four times. Two putative transmembrane helices, residues 52-68 and 143-157, reside on the lumenal and cytosolic surfaces of the ER membrane, respectively. Topology derived from these chimeric proteins was supported by cell-free translation of five truncated CHIP28 cDNAs, by N-linked glycosylation at an engineered consensus site in native CHIP28 (residue His69), and by epitope tagging of the CHIP28 amino terminus. Defined protein chimeras were used to identify internal sequences that direct events of CHIP28 topogenesis. A signal sequence located within the first 52 residues initiated nascent chain translocation into the ER lumen. A stop transfer sequence located in the hydrophobic region from residues 90-120 terminated ongoing translocation. A second internal signal sequence, residues 155-186, reinitiated translocation of a COOH-terminal domain (residues 186-210) into the ER lumen. Integration of the nascent chain into the ER membrane occurred after synthesis of 107 residues and required the presence of two membrane-spanning regions. From this data, we propose a structural model for CHIP28 at the ER membrane in which four membrane-spanning alpha-helices form a central aqueous channel through the lipid bilayer and create a pathway for water transport.
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ZHANG, WEI, ALLISON HUGHES, GRIER WILT, and STEPHEN J. KNABEL. "The BAX PCR Assay for Screening Listeria monocytogenes Targets a Partial Putative Gene lmo2234." Journal of Food Protection 67, no. 7 (July 1, 2004): 1507–11. http://dx.doi.org/10.4315/0362-028x-67.7.1507.
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The BAX PCR for screening Listeria monocytogenes is a commercial PCR assay for specifically targeting L. monocytogenes, a foodborne pathogen that can contaminate a variety of foods and cause a potentially fatal disease, listeriosis, among high-risk populations. The high specificity (>98%) of this PCR assay is achieved by targeting a species-specific genomic region (∼400 bp) presumably found only in L. monocytogenes. In this study, the identity of the BAX PCR–targeted genomic region was determined by using PCR cloning, DNA sequencing, and basic local alignment search tool (BLAST) analysis of the amplicon sequences of an L. monocytogenes serotype 1/2a strain. BLAST analysis identified the BAX PCR amplicon (GenBank accession no. AY364605) as a 423-bp genomic region between nucleotides 224,409 and 224,831 in the genome of L. monocytogenes (serotype 1/2a strain EGD-e), including a 145-bp noncoding region and a 278-bp partial coding sequence of a putative gene, lmo2234. The translated amino acid sequence (92 amino acids) of this partial coding region is highly conserved between L. monocytogenes and Listeria innocua (93% homology). Reverse-position-specific BLAST analysis identified a conserved domain in Lmo2234 that was similar (95.3% aligned, E value = 9E−18) to the consensus amino acid sequence of sugar phosphate isomerases/epimerases (National Center for Biotechnology Information conserved domain database accession no. COG 1082.1, IolE), indicating that Lmo2234 might be involved in bacterial carbohydrate transport and metabolism.
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Berger, Irving Joseph, Dirce Maria Carraro, Ralph Bock, Ricardo Antunes Azevedo, and Helaine Carrer. "Cloning and sequence analysis of tomato cpDNA fragments: towards developing homologous chloroplast transformation vectors." Brazilian Journal of Plant Physiology 17, no. 2 (June 2005): 239–46. http://dx.doi.org/10.1590/s1677-04202005000200007.
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With the view of developing chloroplast transformation vectors based on homologous targeting regions for tomato (Lycopersicon esculentum L.), plastid DNA fragments of tomato cv. IAC-Santa Clara were cloned and analyzed. Isolation and cloning of PstI/SalI chloroplast fragments into the pBlueScript vectors yielded the plasmids pIJB1 and pIJB2 with cpDNA fragments of 8.6 kb and 6.4 kb, respectively. DNA sequencing and computer analyses revealed that the tomato sequences cloned display from 93 to 100 % of identity to the respective fragments in tobacco, which is more pronounced in coding regions. The intergenic spacers are somewhat less conserved suggesting that evolutionary divergences occurred mainly in these putative non-coding regions. The most remarkable difference found is a 437 bp sequence present in tobacco chloroplast genome in the intergenic region of the genes trnE and trnT but completely absent in the tomato chloroplast DNA. Analysis of restriction enzyme digestion patterns revealed several unique restriction sites in the intergenic spacer regions suggesting potential utility of these sequences in species-specific vector construction for tomato chloroplast transformation.
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Obrepalska-Steplowska, Aleksandra, Marta Budziszewska, and Henryk Pospieszny. "Complete nucleotide sequence of a Polish strain of Peanut stunt virus (PSV-P) that is related to but not a typical member of subgroup I." Acta Biochimica Polonica 55, no. 4 (December 16, 2008): 731–39. http://dx.doi.org/10.18388/abp.2008_3034.
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Peanut stunt virus (PSV) is a common legume pathogen present worldwide. It is also infectious for many other plants including peanut and some vegetables. Viruses of this species are classified at present into three subgroups based on their serology and nucleotide homology. Some of them may also carry an additional subviral element - satellite RNA. Analysis of the full genome sequence of a Polish strain - PSV-P - associated with satRNA was performed and showed that it may be classified as a derivative of the subgroup I sharing 83.9-87.9% nucleotide homology with other members of this subgroup. A comparative study of sequenced PSV strains indicates that PSV-P shows the highest identity level with PSV-ER or PSV-J depending on the region used for analysis. Phylogenetic analyses, on the other hand, have revealed that PSV-P is related to representatives of the subgroup I to the same degree, with the exception of the coat protein coding sequence where PSV-P is clustered together with PSV-ER.
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Bento, Miguel, Sónia Gomes Pereira, Wanda Viegas, and Manuela Silva. "Unravelling the hidden inter and intra-varietal diversity of durum wheat commercial varieties used in Portugal." Plant Genetic Resources: Characterization and Utilization 17, no. 04 (May 6, 2019): 386–89. http://dx.doi.org/10.1017/s1479262119000133.
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AbstractAssessing durum wheat genomic diversity is crucial in a changing environmental particularly in the Mediterranean region where it is largely used to produce pasta. Durum wheat varieties cultivated in Portugal and previously assessed regarding thermotolerance ability were screened for the variability of coding sequences associated with technological traits and repetitive sequences. As expected, reduced variability was observed regarding low molecular weight glutenin subunits (LMW-GS) but a specific LMW-GS allelic form associated with improved pasta-making characteristics was absent in one variety. Contrastingly, molecular markers targeting repetitive elements like microsatellites and retrotransposons – Inter Simple Sequence Repeat (ISSR) and Inter Retrotransposons Amplified Polymorphism (IRAP) – disclosed significant inter and intra-varietal diversity. This high level of polymorphism was revealed by the 20 distinct ISSR/IRAP concatenated profiles observed among the 23 individuals analysed. Interestingly, median joining networks and PCoA analysis grouped individuals of the same variety and clustered varieties accordingly with geographical origin. Globally, this work demonstrates that durum wheat breeding strategies induced selection pressure for some relevant coding sequences while maintaining high levels of genomic variability in non-coding regions enriched in repetitive sequences.
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Chun, Jongsik, Anwarul Huq, and Rita R. Colwell. "Analysis of 16S-23S rRNA Intergenic Spacer Regions of Vibrio cholerae and Vibrio mimicus." Applied and Environmental Microbiology 65, no. 5 (May 1, 1999): 2202–8. http://dx.doi.org/10.1128/aem.65.5.2202-2208.1999.
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ABSTRACT Vibrio cholerae identification based on molecular sequence data has been hampered by a lack of sequence variation from the closely related Vibrio mimicus. The two species share many genes coding for proteins, such as ctxAB, and show almost identical 16S DNA coding for rRNA (rDNA) sequences. Primers targeting conserved sequences flanking the 3′ end of the 16S and the 5′ end of the 23S rDNAs were used to amplify the 16S-23S rRNA intergenic spacer regions of V. cholerae and V. mimicus. Two major (ca. 580 and 500 bp) and one minor (ca. 750 bp) amplicons were consistently generated for both species, and their sequences were determined. The largest fragment contains three tRNA genes (tDNAs) coding for tRNAGlu, tRNALys, and tRNAVal, which has not previously been found in bacteria examined to date. The 580-bp amplicon contained tDNAIle and tDNAAla, whereas the 500-bp fragment had single tDNA coding either tRNAGlu or tRNAAla. Little variation, i.e., 0 to 0.4%, was found among V. cholerae O1 classical, O1 El Tor, and O139 epidemic strains. Slightly more variation was found against the non-O1/non-O139 serotypes (ca. 1% difference) and V. mimicus (2 to 3% difference). A pair of oligonucleotide primers were designed, based on the region differentiating all of V. cholerae strains from V. mimicus. The PCR system developed was subsequently evaluated by using representatives of V. cholerae from environmental and clinical sources, and of other taxa, including V. mimicus. This study provides the first molecular tool for identifying the species V. cholerae.
Dissertations / Theses on the topic "ER-targeting sequence coding region"
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Nordholm, Johan. "NA transmembrane domain : Amphiphilic drift to accommodate two functions." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-142051.
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Neuraminidase (NA) is one of two major antigens on the surface of influenza A viruses. It is comprised of a single N-terminal transmembrane domain (TMD), a stalk domain, and a C-terminal enzymatic head domain that cleaves sialic acid, most notably to release new particles from the host cell surface. NA is only enzymatically active as a homo-tetramer. However, it is not known which properties facilitate the oligomerization of NA during assembly. Our results show that, apart from anchoring the protein to the membrane, the NA TMD also contributes to the assembly process by keeping the stalk in a tetrameric conformation. The ability of the TMD to oligomerize is shown to be dependent on its amphiphilic characteristics that was largely conserved across the nine NA subtypes (N1-N9). Over time the NA TMDs in human H1N1 viruses were found to have become more amphiphilic, which correlated with stronger oligomerization. An old H1N1 virus with a more recent N1 TMD had impaired growth, but readily acquired compensatory mutations in the TMD to restore growth, by reverting the TMD oligomerization strength back to that of the old TMD, demonstrating a biological role of the TMD in folding and assembly. NA and the other viral proteins are spatially and temporally coordinated to achieve optimal viral production. By using a co-transfection analysis, the high AU-content in the NA and HA ER-targeting sequence coding regions (for NA TMD as well as the HA signal sequence) were found to inhibit their expression. The inhibition was alleviated by the early expressed influenza RNA-binding protein NS1, which promoted translation and showed enriched foci at the endoplasmic reticulum (ER). NS1, which expresses early during infection, is therefore likely the regulator of NA and HA to prevent premature expression. These results show that the NA TMD is under substantial selection pressure at both the nucleotide and amino acid level to accommodate its roles in ER-targeting, protein folding, and post-transcriptional regulation.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Accepted.
Conference papers on the topic "ER-targeting sequence coding region"
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Quertermous, T., J. M. Schnee, M. S. Runge, G. R. Matsueda, N. W. Hudson, J. G. Seidman, and E. Haber. "EXPRESSION OF A RECOMBINANT ANTIBODY-TARGETED THROMBOLYTIC MOLECULE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644616.
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We have recently shown that targeting tissue-type plasminogen activator (t-PA) by covalent linkage to a fibrin-specific monoclonal antibody (59D8) produces a more potent thrombolytic agent which also induces less fibrinogenolysis. A recombinant molecule encoding a t-PA-59D8 fusion protein was constructed to provide a ready source of this agent for further study, and to allow tailoring of the active moities for maximal activity. DNA sequence coding for the 59D8 heavy chain (HC) antigen combining site was cloned from a lambdaphage library by selection with a joining region probe. Gene segments coding for this cloned HC rearrangement, the amino portion of the mouse gamma 2b HC constant region, and the catalytic B chain of t-PA were joined in the pSV2-gpt expression vector. The desired coding sequence was confirmed by nucleotide sequence analysis. The construct was transfected by electroporation into 59D8 hybridoma HC loss variants. Transfectants were screened for antifibrin antibody activity. Positive clones were shown to produce mRNA which hybridized to the human t-PA gene in Northern blot analysis. Supernatants from 5 of these clones were subjected to affinity chromatography on a synthetic fibrin-like peptide-Sepharose column followed by a benzamidine-Sepharose column. Western blots of SDS polyacrylamide gels run under reducing conditions revealed binding to a 60 kd band by a monoclonal antihuman t-PA antibody, consistent with a 59D8 HC-t-PA fusion protein. Also, binding to a 25 kd band by goat anti-mouse Fab indicated the presence of 59D8 light chain. Affinity purified protein was shown to have amidolytic activity of similar potency to t-PA in a chromogenic substrate assay utilizing S-2288. Bifunctionality of the purified protein was demonstrated first by an assay which requires the protein to bind to immobilized fibrin and simultaneously exhibit activity in the S2288 assay, and second by simultaneous fibrin and iodinated anti-t-PA binding.