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Journal articles on the topic 'ORF2 protein'

Author: Grafiati

Published: 15 June 2024

Last updated: 31 July 2025

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1

Tsai, Chi-Wei, Margaret G. Redinbaugh, Kristen J. Willie, Sharon Reed, Michael Goodin, and Saskia A. Hogenhout. "Complete Genome Sequence and In Planta Subcellular Localization of Maize Fine Streak Virus Proteins." Journal of Virology 79, no. 9 (2005): 5304–14. http://dx.doi.org/10.1128/jvi.79.9.5304-5314.2005.

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ABSTRACT The genome of the nucleorhabdovirus maize fine streak virus (MFSV) consists of 13,782 nucleotides of nonsegmented, negative-sense, single-stranded RNA. The antigenomic strand consisted of seven open reading frames (ORFs), and transcripts of all ORFs were detected in infected plants. ORF1, ORF6, and ORF7 had significant similarities to the nucleocapsid protein (N), glycoprotein (G), and polymerase (L) genes of other rhabdoviruses, respectively, whereas the ORF2, ORF3, ORF4, and ORF5 proteins had no significant similarities. The N (ORF1), ORF4, and ORF5 proteins localized to nuclei, con

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2

Kondo, Hideki, Takanori Maeda, Yukio Shirako, and Tetsuo Tamada. "Orchid fleck virus is a rhabdovirus with an unusual bipartite genome." Journal of General Virology 87, no. 8 (2006): 2413–21. http://dx.doi.org/10.1099/vir.0.81811-0.

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Orchid fleck virus (OFV) has an unusual bipartite negative-sense RNA genome with clear sequence similarities to those of nucleorhabdoviruses. The OFV genome consists of two single-stranded RNA molecules, RNA1 and RNA2 that are 6413 and 6001 nt long, respectively, with open reading frame (ORF) information in the complementary sense. RNA1 encodes 49 (ORF1), 26 (ORF2), 38 (ORF3), 20 (ORF4) and 61 kDa (ORF5) proteins, and RNA2 encodes a single protein of 212 kDa (ORF6). ORF1, ORF5 and ORF6 proteins had significant similarities (21–38 % identity) to the nucleocapsid protein (N), glycoprotein (G) an

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3

Melzer, M. J., A. V. Karasev, D. M. Sether, and J. S. Hu. "Nucleotide sequence, genome organization and phylogenetic analysis of pineapple mealybug wilt-associated virus-2." Journal of General Virology 82, no. 1 (2001): 1–7. http://dx.doi.org/10.1099/0022-1317-82-1-1.

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The genome of pineapple mealybug wilt-associated closterovirus-2 (PMWaV-2) was cloned from double-stranded RNA isolated from diseased pineapple and its sequence determined. The 3′-terminal 14861 nt of the single-stranded RNA genome contains ten open reading frames (ORFs) which, from 5′ to 3′, potentially encode a >204 kDa polyprotein containing papain-like protease, methyltransferase and helicase domains (ORF1a), a 65 kDa RNA-dependent RNA polymerase (ORF1b), a 5 kDa hydrophobic protein (ORF2), a 59 kDa heat shock protein 70 homologue (ORF3), a 46 kDa protein (ORF4), a 34 kDa coat protein (

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4

Li, Jiapeng, Xiaoyin Wu, Hui Liu, et al. "Identification and Molecular Characterization of a Novel Carlavirus Infecting Chrysanthemum morifolium in China." Viruses 15, no. 4 (2023): 1029. http://dx.doi.org/10.3390/v15041029.

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Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, China. The genome sequence of CiCV1-CN was 8795 nucleotides (nt) in length, with a 68-nt 5′-untranslated region (UTR) and a 76-nt 3′-UTR, which contained six predicted open reading frames (ORFs) that encode six corresponding proteins of various sizes. Phylogenetic analyses based on

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5

Shafat, Zoya. "Sequence to structural analysis of ORF5 protein in Norway rat Hepatitis E Virus." Bioinformation 18, no. 1 (2022): 19–25. http://dx.doi.org/10.6026/97320630018019.

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Hepatitis E virus (HEV) is a major causative agent of acute hepatitis in developing countries. The Norway rat HEV genome consists of six open reading frames (ORFs), i.e., ORF1, ORF2, ORF3, ORF4, ORF5 and ORF6. The additional reading frame encoded protein ORF5 is attributed to life cycle of rat HEV. The ORFF5 protein’s function remains undetermined. Therefore, it is of interest to analyze the ORF5 protein for its physiochemical properties, primary structure, secondary structure, tertiary structure and functional characteristics using bioinformatics tools. Analysis of the ORF5 protein revealed i

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Shafat, Zoya. "Intrinsically disordered regions in the rodent hepevirus proteome." Bioinformation 18, no. 2 (2022): 111–18. http://dx.doi.org/10.6026/97320630018111.

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Hepatitis E virus (HEV) is the causative agent of Hepatitis E infections across the world. Intrinsically disordered protein regions (IDPRs) or intrinsically disordered proteins (IDPs) are regions or proteins that are characterized by lack of definite structure. These IDPRs or IDPs play significant roles in a wide range of biological processes, such as cell cycle regulation, control of signaling pathways, etc. IDPR/IDP in proteins is associated with the virus’s pathogenicity and infectivity. The prevalence of IDPR/IDP in rat HEV proteome remains undetermined. Hence, we examined the unstructured

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Garcia, Miguel, Madalena Pimentel та José Moniz-Pereira. "Expression of Mycobacteriophage Ms6 Lysis Genes Is Driven by Two σ70-Like Promoters and Is Dependent on a Transcription Termination Signal Present in the Leader RNA". Journal of Bacteriology 184, № 11 (2002): 3034–43. http://dx.doi.org/10.1128/jb.184.11.3034-3043.2002.

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ABSTRACT A mycobacteriophage Ms6 strong promoter region (Plys ) was isolated by using transcriptional fusions with the lacZ reporter gene. Two tandem σ70-like promoter sequences (P1 and P2) were found in this region. DNA sequencing of the promoter downstream region revealed a 214-bp leader sequence followed by five adjacent coding regions of 231 bp (ORF1), 1,152 bp (ORF2), 996 bp (ORF3), 231 bp (ORF4), and 372 (ORF5). ORF1 has the potential to encode a 77-amino-acid protein which revealed similarity to mycobacteriophage TM4 gp90, a predicted protein with unknown function. ORF2 encodes a 384-am

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Kiatpapan, Pornpimon, Yoshiteru Hashimoto, Hisako Nakamura, et al. "Characterization of pRGO1, a Plasmid from Propionibacterium acidipropionici, and Its Use for Development of a Host-Vector System in Propionibacteria." Applied and Environmental Microbiology 66, no. 11 (2000): 4688–95. http://dx.doi.org/10.1128/aem.66.11.4688-4695.2000.

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ABSTRACT The complete nucleotide sequence of pRGO1, a cryptic plasmid fromPropionibacterium acidipropionici E214, was determined. pRGO1 is 6,868 bp long, and its G+C content is 65.0%. Frame analysis of the sequence revealed six open reading frames, which were designated Orf1 to Orf6. The deduced amino acid sequences of Orf1 and Orf2 showed extensive similarities to an initiator of plasmid replication, the Rep protein, of various plasmids of gram-positive bacteria. The amino acid sequence of the putative translation product of orf3 exhibited a high degree of similarity to the amino acid sequenc

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Shimizu, Takeo, Hiroshi Kinoshita, and Takuya Nihira. "Identification and In Vivo Functional Analysis by Gene Disruption of ctnA, an Activator Gene Involved in Citrinin Biosynthesis in Monascus purpureus." Applied and Environmental Microbiology 73, no. 16 (2007): 5097–103. http://dx.doi.org/10.1128/aem.01979-06.

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ABSTRACT Citrinin, a secondary fungal metabolite of polyketide origin, is moderately nephrotoxic to vertebrates, including humans. From the red-pigment producer Monascus purpureus, a 21-kbp region flanking pksCT, which encodes citrinin polyketide synthase, was cloned. Four open reading frames (ORFs) (orf1, orf2, orf3, and orf4) in the 5′-flanking region and one ORF (orf5) in the 3′-flanking region were identified in the vicinity of pksCT. orf1 to orf5 encode a homolog of a dehydrogenase (similarity, 46%), a regulator (similarity, 38%), an oxygenase (similarity, 41%), an oxidoreductase (similar

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10

Surjit, Milan, Shahid Jameel, and Sunil K. Lal. "The ORF2 Protein of Hepatitis E Virus Binds the 5′ Region of Viral RNA." Journal of Virology 78, no. 1 (2004): 320–28. http://dx.doi.org/10.1128/jvi.78.1.320-328.2004.

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ABSTRACT Hepatitis E virus (HEV) is a major human pathogen in much of the developing world. It is a plus-strand RNA virus with a 7.2-kb polyadenylated genome consisting of three open reading frames, ORF1, ORF2, and ORF3. Of these, ORF2 encodes the major capsid protein of the virus and ORF3 encodes a small protein of unknown function. Using the yeast three-hybrid system and traditional biochemical techniques, we have studied the RNA binding activities of ORF2 and ORF3, two proteins encoded in the 3′ structural part of the genome. Since the genomic RNA from HEV has been postulated to contain sec

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Thomas, Darby L., Jerome Schaack, Hannes Vogel, and Ronald Javier. "Several E4 Region Functions Influence Mammary Tumorigenesis by Human Adenovirus Type 9." Journal of Virology 75, no. 2 (2001): 557–68. http://dx.doi.org/10.1128/jvi.75.2.557-568.2001.

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ABSTRACT Among oncogenic adenoviruses, human adenovirus type 9 (Ad9) is unique in eliciting exclusively estrogen-dependent mammary tumors in rats and in not requiring viral E1 region transforming genes for tumorigenicity. Instead, studies with hybrid viruses generated between Ad9 and the closely related nontumorigenic virus Ad26 have roughly localized an Ad9 oncogenic determinant(s) to a segment of the viral E4 region containing open reading frame 1 (E4-ORF1), E4-ORF2, and part of E4-ORF3. Although subsequent findings have shown that E4-ORF1 codes for an oncoprotein essential for tumorigenesis

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12

Lymanska, О. Yu. "Comparative analysis of the open reading frames protein genes of genotype 4 Hepatitis E virus in swine and wild boar." Journal for Veterinary Medicine, Biotechnology and Biosafety 9, no. 1-2 (2023): 12–19. http://dx.doi.org/10.36016/jvmbbs-2023-9-1-2-3.

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The goal of this study was to determine the molecular diversity of the open reading frames (ORFs) ORF1, ORF2, ORF3 protein genes from full-length genomes of genotype 4 hepatitis E virus (HEV) from pigs and wild boars at protein and gene level. Statistical technique Shannon entropy was used for mutational analysis of ORF1–ORF3 protein genes to identify amino acid substitutions in the HEV 4 sequences isolated from pigs and wild boars that were most susceptible to mutations. Gene selective pressure for genes was estimated using Tajima’s neutrality test. The ORF regions of 11 swine and 11 wild boa

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13

Alves-Freitas, Dione M. T., Bruna Pinheiro-Lima, Josias C. Faria, Cristiano Lacorte, Simone G. Ribeiro, and Fernando L. Melo. "Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line." Viruses 11, no. 1 (2019): 90. http://dx.doi.org/10.3390/v11010090.

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Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frame

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14

Ruiz-García, Ana Belén, Thierry Candresse, José Malagón, et al. "Olive Leaf Mottling Virus: A New Member of the Genus Olivavirus." Plants 13, no. 16 (2024): 2290. http://dx.doi.org/10.3390/plants13162290.

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Studies of the virome of olive trees with symptoms of leaf mottling by high-throughput sequencing (HTS) revealed the presence of a new virus. Full coding genome sequences of two isolates were determined and consisted of a single RNA segment of 16,516 nt and 16,489, respectively. The genomic organization contained 10 open reading frames (ORFs) from 5′ to 3′: ORF1a, ORF1b (RdRp), ORF2 (p22), ORF3 (p7), ORF4 (HSP70h), ORF5 (HSP90h), ORF6 (CP), ORF7 (p19), ORF8 (p12), ORF9 (p23) and ORF10 (p9). Phylogenetic analyses clustered this virus in the genus Olivavirus, family Closteroviridae, with the clo

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15

Gaur, Arti, and William R. Green. "Role of a Cytotoxic-T-Lymphocyte Epitope-Defined, Alternative gag Open Reading Frame in the Pathogenesis of a Murine Retrovirus-Induced Immunodeficiency Syndrome." Journal of Virology 79, no. 7 (2005): 4308–15. http://dx.doi.org/10.1128/jvi.79.7.4308-4315.2005.

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ABSTRACT LP-BM5 murine leukemia virus-infected C57BL/6 mice develop profound immunodeficiency and B-cell lymphomas. The LP-BM5 complex contains a mixture of defective (BM5def) and replication-competent helper viruses among which BM5def is the primary causative agent of disease. The BM5def primary open reading frame (ORF1) encodes the single gag precursor protein (Pr60 gag ). Our lab has recently demonstrated that a novel immunodominant cytotoxic-T-lymphocyte (CTL) epitope (SYNTGRFPPL) is expressed from a +1-nucleotide translational open reading frame of BM5def during the course of normal retro

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16

Basim, Huseyin, Gerald V. Minsavage, Robert E. Stall, Jaw-Fen Wang, Savita Shanker, and Jeffrey B. Jones. "Characterization of a Unique Chromosomal Copper Resistance Gene Cluster from Xanthomonas campestris pv. vesicatoria." Applied and Environmental Microbiology 71, no. 12 (2005): 8284–91. http://dx.doi.org/10.1128/aem.71.12.8284-8291.2005.

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ABSTRACT We characterized the copper resistance genes in strain XvP26 of Xanthomonas campestris pv. vesicatoria, which was originally isolated from a pepper plant in Taiwan. The copper resistance genes were localized to a 7,652-bp region which, based on pulsed-field gel electrophoresis and Southern hybridization, was determined to be located on the chromosome. These genes hybridized only weakly, as determined by Southern analysis, to other copper resistance genes in Xanthomonas and Pseudomonas strains. We identified five open reading frames (ORFs) whose products exhibited high levels of amino

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17

Zhang, Yun-Ping, Jerry K. Uyemoto, Deborah A. Golino, and Adib Rowhani. "Nucleotide Sequence and RT-PCR Detection of a Virus Associated with Grapevine Rupestris Stem-Pitting Disease." Phytopathology® 88, no. 11 (1998): 1231–37. http://dx.doi.org/10.1094/phyto.1998.88.11.1231.

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Grapevine rupestris stem pitting (RSP) is a graft-transmissible disease of unknown etiology. We have characterized a virus associated with this disease. The entire genomic sequence (GenBank accession number AF026278) consisted of 8,725 nucleotides excluding a poly(A) tail. Six open reading frames (ORF) were found. ORF1 potentially encodes a polypeptide with a methyltransferase domain, a papain-like proteinase domain, a helicase domain, and a RNA-dependent RNA polymerase domain; ORF2, ORF3, and ORF4 compose a triple-gene block; ORF5 encodes a coat protein; and ORF6 is located near the 3′ end wi

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18

Mahé, Dominique, Philippe Blanchard, Catherine Truong, et al. "Differential recognition of ORF2 protein from type 1 and type 2 porcine circoviruses and identification of immunorelevant epitopes." Microbiology 81, no. 7 (2000): 1815–24. http://dx.doi.org/10.1099/0022-1317-81-7-1815.

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Two types of porcine circovirus (PCV) have been isolated and are referred to as PCV1 and PCV2. PCV1 represents an apathogenic virus, whereas PCV2 is associated with post-weaning multisystemic wasting syndrome. The two PCVs are related, since they display about 70% identity based on nucleotide sequences. In order to discriminate between common and type-specific antigens, an immunocytological approach was used following transfections with cloned circovirus DNAs, as well as recombinant proteins expressed by either baculovirus or plasmid vectors. The ORF1-encoded proteins in the two viruses were s

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Göbel, Markus, Kerstin Kassel-Cati, Eberhard Schmidt, and Walter Reineke. "Degradation of Aromatics and Chloroaromatics by Pseudomonas sp. Strain B13: Cloning, Characterization, and Analysis of Sequences Encoding 3-Oxoadipate:Succinyl-Coenzyme A (CoA) Transferase and 3-Oxoadipyl-CoA Thiolase." Journal of Bacteriology 184, no. 1 (2002): 216–23. http://dx.doi.org/10.1128/jb.184.1.216-223.2002.

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ABSTRACT 3-Oxoadipate:succinyl-coenzyme A (CoA) transferase and 3-oxoadipyl-CoA thiolase carry out the ultimate steps in the conversion of benzoate and 3-chlorobenzoate to tricarboxylic acid cycle intermediates in bacteria utilizing the 3-oxoadipate pathway. This report describes the characterization of DNA fragments with the overall length of 5.9 kb from Pseudomonas sp. strain B13 that encode these enzymes. DNA sequence analysis revealed five open reading frames (ORFs) plus an incomplete one. ORF1, of unknown function, has a length of 414 bp. ORF2 (catI) encodes a polypeptide of 282 amino aci

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20

Graff, Judith, Hanh Nguyen, Claro Yu, et al. "The Open Reading Frame 3 Gene of Hepatitis E Virus Contains a cis-Reactive Element and Encodes a Protein Required for Infection of Macaques." Journal of Virology 79, no. 11 (2005): 6680–89. http://dx.doi.org/10.1128/jvi.79.11.6680-6689.2005.

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ABSTRACT An infectious cDNA clone of hepatitis E virus was mutated in order to prevent synthesis of either open reading frame 2 (ORF2) protein or ORF3 protein. HuH-7 cells transfected with an ORF2-null mutant produced ORF3, and those transfected with an ORF3-null mutant produced ORF2. Silent mutations introduced into a highly conserved nucleotide sequence in the ORF3 coding region eliminated the synthesis of both ORF2 and ORF3 proteins, suggesting that it comprised a cis-reactive element. A mutant that was not able to produce ORF3 protein did not produce a detectable infection in rhesus macaqu

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Martínez-Guinó, Laura, Maria Ballester, Joaquim Segalés, and Tuija Kekarainen. "Expression profile and subcellular localization of Torque teno sus virus proteins." Journal of General Virology 92, no. 10 (2011): 2446–57. http://dx.doi.org/10.1099/vir.0.033134-0.

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In the present study, the expression, generation and subcellular localization of Torque teno sus virus (TTSuV) proteins were characterized into two genetically distinct TTSuV species (TTSuV1 and TTSuV2). Following transfection of three TTSuV1 and TTSuV2 full-length ORF (ORF1, ORF2 and ORF3) expression constructs into porcine kidney cells, alternative splice variants encoding new TTSuV protein isoforms were identified for the first time. Proteins encoded from ORF1 and ORF3 were localized in the nucleoli of porcine kidney cells and that of ORF2 in the cytoplasm and nucleus excluding the nucleoli

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Hervouet, Kévin, Martin Ferrié, Maliki Ankavay, et al. "An Arginine-Rich Motif in the ORF2 capsid protein regulates the hepatitis E virus lifecycle and interactions with the host cell." PLOS Pathogens 18, no. 8 (2022): e1010798. http://dx.doi.org/10.1371/journal.ppat.1010798.

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Hepatitis E virus (HEV) infection is the most common cause of acute viral hepatitis worldwide. Hepatitis E is usually asymptomatic and self-limiting but it can become chronic in immunocompromised patients and is associated with increased fulminant hepatic failure and mortality rates in pregnant women. HEV genome encodes three proteins including the ORF2 protein that is the viral capsid protein. Interestingly, HEV produces 3 isoforms of the ORF2 capsid protein which are partitioned in different subcellular compartments and perform distinct functions in the HEV lifecycle. Notably, the infectious

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Li, Tong, Massoud Kheir Khah, Snjezana Slavnic, Ingegerd Johansson, and Nicklas Strömberg. "Different Type 1 Fimbrial Genes and Tropisms of Commensal and Potentially Pathogenic Actinomyces spp. with Different Salivary Acidic Proline-Rich Protein and Statherin Ligand Specificities." Infection and Immunity 69, no. 12 (2001): 7224–33. http://dx.doi.org/10.1128/iai.69.12.7224-7233.2001.

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ABSTRACT Actinomyces spp. exhibit type 1 fimbria-mediated adhesion to salivary acidic proline-rich proteins (PRPs) and statherin ligands. Actinomyces spp. with different animal and tissue origins belong to three major adhesion types as relates to ligand specificity and type 1 fimbria genes. (i) In preferential acidic-PRP binding, strains of Actinomyces naeslundiigenospecies 1 and 2 from human and monkey mouths displayed at least three ligand specificities characterized by preferential acidic-PRP binding. Slot blot DNA hybridization showed seven highly conserved type 1 fimbria genes (orf1- to -

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Ralfs, Philipp, Eduardo Salinas, Charuta Ambardekar, et al. "Contribution of soluble ORF2 viral protein to viral replication and host immune response during acute Hepatitis E virus infection." Journal of Immunology 206, no. 1_Supplement (2021): 20.34. http://dx.doi.org/10.4049/jimmunol.206.supp.20.34.

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Abstract The hepatitis E virus (HEV) is a small, positive-stranded RNA virus that is a major cause of acute viral hepatitis globally. Acute HEV infection is typically asymptomatic and resolves within 8–10 weeks. HEV encodes 2 forms of capsid protein. A cytoplasmic form (ORF2c) is essential for virion structure. A secreted glycosylated form (ORF2s) accumulates at high titer in serum and can mask anti-ORF2 neutralizing antibodies. Here, we explored the contribution of ORF2s to HEV replicative fitness in vivo, and its role in generating anti-ORF2 antibodies (Abs). Rhesus Macaques (RM) were challe

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Xu, Zhi, Mahmoud E. Khalifa, Rebekah A. Frampton, et al. "Characterization of a Novel Double-Stranded RNA Virus from Phytophthora pluvialis in New Zealand." Viruses 14, no. 2 (2022): 247. http://dx.doi.org/10.3390/v14020247.

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A new dsRNA virus from the oomycete Phytophthora pluvialis has been characterized and designated as Phytophthora pluvialis RNA virus 1 (PplRV1). The genome of the PplRV1 reference genome is 6742 bp that encodes two predicted open reading frames (ORFs). ORF1 and ORF2 overlap by a 47 nt “slippery” frameshift sequence. ORF1 encodes a putative protein of unknown function. ORF2 shows high similarity to the RNA-dependent RNA polymerase (RdRp) of other dsRNA viruses. Phylogenetic analysis of the putative PplRV1 RdRp and its most closely related viruses showed PplRV1 is distinct from other known virus

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Bertolotti-Ciarlet, Andrea, Sue E. Crawford, Anne M. Hutson, and Mary K. Estes. "The 3′ End of Norwalk Virus mRNA Contains Determinants That Regulate the Expression and Stability of the Viral Capsid Protein VP1: a Novel Function for the VP2 Protein." Journal of Virology 77, no. 21 (2003): 11603–15. http://dx.doi.org/10.1128/jvi.77.21.11603-11615.2003.

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ABSTRACT Norwalk virus (NV) is the prototype strain of a group of noncultivable human caliciviruses responsible for epidemic outbreaks of acute gastroenteritis. The capsid protein VP1 is synthesized from a subgenomic RNA that contains two open reading frames (ORFs), ORF2 and ORF3, and the 3′ untranslated region (UTR). ORF2 and ORF3 code for the capsid protein (VP1) and a small structural basic protein (VP2), respectively. We discovered that the yields of virus-like particles (VLPs) composed of VP1 are significantly reduced when this protein is expressed from ORF2 alone. To determine how the 3′

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Balak, O. K., and O. Yu Lymanska. "Structural analysis of open reading frames of bovine immunodeficiency virus proteins." Veterinary Medicine: inter-departmental subject scientific collection, no. 109 (September 27, 2023): 26–34. http://dx.doi.org/10.36016/vm-2023-109-5.

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The goal of this study was determining the structural organization peculiarities of the ORF2 and ORF3 proteins of the bovine immunodeficiency virus (BIV). Five ORFs were determined for two BIV isolates with complete genome using the ATGpr software, which permits effective prediction of translation initiation codons with nucleotide accuracy. Phyre2 software was used to predict, analyze the secondary structure and function of proteins. PONDR-FIT software was used to search for protein fragments in a disordered or natively unfolded state. Analysis of the amino acid composition of ORF2 and ORF3 pr

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Sadowy, Ewa, Anna Maasen, Marek Juszczuk, et al. "The ORF0 product of Potato leafroll virus is indispensable for virus accumulation." Journal of General Virology 82, no. 6 (2001): 1529–32. http://dx.doi.org/10.1099/0022-1317-82-6-1529.

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Using a cDNA expression cassette in combination with agroinoculation of potato leaf discs we have investigated the role the protein encoded by ORF0 of Potato leafroll virus (PLRV) and have shown its importance for virus accumulation. Two mutations introduced into ORF0 by site-directed mutagenesis prevented expression of the corresponding protein and completely abolished virus accumulation in plant cells. They did not, however, affect translation of ORF1 and ORF2. We therefore conclude that ORF0 of PLRV produces a protein essential for virus accumulation, a hitherto undescribed finding.

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Vakulenko, Yulia A., Artem V. Orlov, and Alexander N. Lukashev. "Patterns and Temporal Dynamics of Natural Recombination in Noroviruses." Viruses 15, no. 2 (2023): 372. http://dx.doi.org/10.3390/v15020372.

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Noroviruses infect a wide range of mammals and are the major cause of gastroenteritis in humans. Recombination at the junction of ORF1 encoding nonstructural proteins and ORF2 encoding major capsid protein VP1 is a well-known feature of noroviruses. Using all available complete norovirus sequences, we systematically analyzed patterns of natural recombination in the genus Norovirus both throughout the genome and across the genogroups. Recombination events between nonstructural (ORF1) and structural genomic regions (ORF2 and ORF3) were found in all analyzed genogroups of noroviruses, although re

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Silva, Gonçalo, Moritz Bömer, Ajith I. Rathnayake, et al. "Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing." Plants 8, no. 6 (2019): 167. http://dx.doi.org/10.3390/plants8060167.

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To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the

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Kojima, Kenji K., Takumi Matsumoto, and Haruhiko Fujiwara. "Eukaryotic Translational Coupling in UAAUG Stop-Start Codons for the Bicistronic RNA Translation of the Non-Long Terminal Repeat Retrotransposon SART1." Molecular and Cellular Biology 25, no. 17 (2005): 7675–86. http://dx.doi.org/10.1128/mcb.25.17.7675-7686.2005.

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ABSTRACT Most eukaryotic cellular mRNAs are monocistronic; however, many retroviruses and long terminal repeat (LTR) retrotransposons encode multiple proteins on a single RNA transcript using ribosomal frameshifting. Non-long terminal repeat (non-LTR) retrotransposons are considered the ancestor of LTR retrotransposons and retroviruses, but their translational mechanism of bicistronic RNA remains unknown. We used a baculovirus expression system to produce a large amount of the bicistronic RNA of SART1, a non-LTR retrotransposon of the silkworm, and were able to detect the second open reading f

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Salaipeth, Lakha, Sotaro Chiba, Ana Eusebio-Cope, Satoko Kanematsu, and Nobuhiro Suzuki. "Biological properties and expression strategy of rosellinia necatrix megabirnavirus 1 analysed in an experimental host, Cryphonectria parasitica." Journal of General Virology 95, no. 3 (2014): 740–50. http://dx.doi.org/10.1099/vir.0.058164-0.

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Rosellinia necatrix megabirnavirus 1 (RnMBV1) with a bipartite dsRNA genome (dsRNA1 and dsRNA2) confers hypovirulence to its natural host, the white root rot fungus, and is thus regarded as a potential virocontrol (biocontrol) agent. Each segment has two large ORFs: ORF1 and partially overlapping ORF2 on dsRNA1 encode the major capsid protein (CP) and RNA-dependent RNA polymerase (RdRp), whilst ORF3 and ORF4 on dsRNA2 encode polypeptides with unknown functions. Here, we report the biological and molecular characterization of this virus in the chestnut blight fungus, Cryphonectria parasitica, a

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Mazalovska, Milena, and J. Calvin Kouokam. "Progress in the Production of Virus-Like Particles for Vaccination against Hepatitis E Virus." Viruses 12, no. 8 (2020): 826. http://dx.doi.org/10.3390/v12080826.

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Hepatitis E virus (HEV), a pathogen that causes acute viral hepatitis, is a small icosahedral, quasi-enveloped, positive ssRNA virus. Its genome has three open reading frames (ORFs), with ORF1 and ORF3 encoding for nonstructural and regulatory proteins, respectively, while ORF2 is translated into the structural, capsid protein. ORF2 is most widely used for vaccine development in viral hepatitis. Hepatitis E virus-like particles (VLPs) are potential vaccine candidates against HEV infection. VLPs are composed of capsid subunits mimicking the natural configuration of the native virus but lack the

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Nawagitgul, Porntippa, Igor Morozov, Steven R. Bolin, Perry A. Harms, Steven D. Sorden, and Prem S. Paul. "Open reading frame 2 of porcine circovirus type 2 encodes a major capsid protein." Journal of General Virology 81, no. 9 (2000): 2281–87. http://dx.doi.org/10.1099/0022-1317-81-9-2281.

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Porcine circovirus 2 (PCV2), a single-stranded DNA virus associated with post-weaning multisystemic wasting syndrome of swine, has two potential open reading frames, ORF1 and ORF2, greater than 600 nucleotides in length. ORF1 is predicted to encode a replication-associated protein (Rep) essential for replication of viral DNA, while ORF2 contains a conserved basic amino acid sequence at the N terminus resembling that of the major structural protein of chicken anaemia virus. Thus far, the structural protein(s) of PCV2 have not been identified. In this study, a viral structural protein of 30 kDa

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Hardy, Richard W., and Gail W. Wertz. "The Product of the Respiratory Syncytial Virus M2 Gene ORF1 Enhances Readthrough of Intergenic Junctions during Viral Transcription." Journal of Virology 72, no. 1 (1998): 520–26. http://dx.doi.org/10.1128/jvi.72.1.520-526.1998.

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ABSTRACT The mRNA encoding the M2 protein of respiratory syncytial (RS) virus contains two open reading frames (ORFs). ORF1 encodes the 22-kDa structural protein, M2, and ORF2 has the potential to encode a 10-kDa protein (90 amino acids). Using a vaccinia virus T7 expression system, we examined the RNA synthetic activities of mono- and dicistronic subgenomic replicons of RS virus by direct metabolic labeling of RNA in the presence and absence of the products of ORF1 and ORF2. In the absence of ORF1 and ORF2, the negative- and positive-sense products of genomic RNA replication and positive-sens

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Glass, Pamela J., Carl Q. Zeng, and Mary K. Estes. "Two Nonoverlapping Domains on the Norwalk Virus Open Reading Frame 3 (ORF3) Protein Are Involved in the Formation of the Phosphorylated 35K Protein and in ORF3-Capsid Protein Interactions." Journal of Virology 77, no. 6 (2003): 3569–77. http://dx.doi.org/10.1128/jvi.77.6.3569-3577.2003.

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ABSTRACT Expression of the Norwalk virus open reading frame 3 (ORF3) in Spodoptera frugiperda (Sf9) cells yields two major forms, the predicted 23,000-molecular-weight (23K) form and a larger 35K form. The 23K form is able to interact with the ORF2 capsid protein and be incorporated into virus-like particles. In this paper, we provide mass spectrometry evidence that both the 23K and 35K forms are composed only of the ORF3 protein. Two-dimensional gel electrophoresis and phosphatase treatment showed that the 35K form results solely from phosphorylation and that the 35K band is composed of sever

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Elsner, Andrea, Bernd Kreikemeyer, Andrea Braun-Kiewnick, Barbara Spellerberg, Bettina A. Buttaro, and Andreas Podbielski. "Involvement of Lsp, a Member of the LraI-Lipoprotein Family in Streptococcus pyogenes, in Eukaryotic Cell Adhesion and Internalization." Infection and Immunity 70, no. 9 (2002): 4859–69. http://dx.doi.org/10.1128/iai.70.9.4859-4869.2002.

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ABSTRACT Three open reading frames (ORFs) were identified by a genome walking strategy in the genomes of serotype M49 group A streptococcal (GAS) strains CS101 and 591. These ORFs were located between the mga core regulon and the dipeptide permease operon. The deduced amino acid (aa) sequences contained signature sequences indicative of a lipoprotein (306 aa), an intracellular protein (823 aa), and a secreted peptide (66 aa), respectively. ORF1 (named Lsp for lipoprotein of Streptococcus pyogenes) and ORF2 exhibited a high degree of homology to the lmb/ORF2 genes of S. agalactiae (B. Spellerbe

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Chuang, Duen-Yau, Ampaabeng G. Kyeremeh, Yuichi Gunji, Yoshiyuki Takahara, Yoshio Ehara, and Toshio Kikumoto. "Identification and Cloning of an Erwinia carotovorasubsp. carotovora Bacteriocin Regulator Gene by Insertional Mutagenesis." Journal of Bacteriology 181, no. 6 (1999): 1953–57. http://dx.doi.org/10.1128/jb.181.6.1953-1957.1999.

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ABSTRACT Avirulent Erwinia carotovora subsp.carotovora CGE234-M403 produces two types of bacteriocin. For the purpose of cloning the bacteriocin genes of strain CGE234M403, a spontaneous rifampin-resistant mutant of this strain, M-rif-11-2, was isolated. By Tn5 insertional mutagenesis using M-rif-11-2, a mutant, TM01A01, which produces the high-molecular-weight bacteriocin but not the low-molecular-weight bacteriocin was obtained. By thermal asymmetric interlaced PCR, the DNA sequence from the Tn5 insertion site and the DNA sequence of a contiguous 1,280-bp region were determined. One complete

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Yin, Xin, Dong Ying, Sébastien Lhomme, et al. "Origin, antigenicity, and function of a secreted form of ORF2 in hepatitis E virus infection." Proceedings of the National Academy of Sciences 115, no. 18 (2018): 4773–78. http://dx.doi.org/10.1073/pnas.1721345115.

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The enterically transmitted hepatitis E virus (HEV) adopts a unique strategy to exit cells by cloaking its capsid (encoded by the viral ORF2 gene) and circulating in the blood as “quasi-enveloped” particles. However, recent evidence suggests that the majority of the ORF2 protein present in the patient serum and supernatants of HEV-infected cell culture exists in a free form and is not associated with virus particles. The origin and biological functions of this secreted form of ORF2 (ORF2S) are unknown. Here we show that production of ORF2Sresults from translation initiated at the previously pr

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Oleksiewicz, M. B., A. Bøtner, and P. Normann. "Porcine B-cells recognize epitopes that are conserved between the structural proteins of American- and European-type porcine reproductive and respiratory syndrome virus." Journal of General Virology 83, no. 6 (2002): 1407–18. http://dx.doi.org/10.1099/0022-1317-83-6-1407.

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By selecting phage display libraries with immune sera from experimentally infected pigs, porcine B-cell epitopes in the open reading frame (ORF) 2, 3, 5 and 6 proteins of European-type porcine reproductive and respiratory syndrome virus (PRRSV) were identified. The sequences of all the epitopes were well conserved in European-type PRRSV and even between European- and American-type PRRSV. Accordingly, sera from pigs infected with American-type PRRSV cross-reacted with the European-type epitopes. Thus, this study showed, for the first time, the presence of highly conserved epitopes in the matrix

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Sasaya, Takahide, Shinnosuke Kusaba, Koichi Ishikawa, and Hiroki Koganezawa. "Nucleotide sequence of RNA2 of Lettuce big-vein virus and evidence for a possible transcription termination/initiation strategy similar to that of rhabdoviruses." Journal of General Virology 85, no. 9 (2004): 2709–17. http://dx.doi.org/10.1099/vir.0.80061-0.

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Lettuce big-vein virus (LBVV) is the type species of the genus Varicosavirus and is a two-segmented negative-sense single-stranded RNA virus. The larger LBVV genome segment (RNA1) consists of 6797 nt and encodes an L polymerase that resembles that of rhabdoviruses. Here, the nucleotide sequence of the second LBVV genome segment (RNA2) is reported. LBVV RNA2 consisted of 6081 nt and contained antisense information for five major ORFs: ORF1 (nt 210–1403 on the viral RNA), ORF2 (nt 1493–2494), ORF3 (nt 2617–3489), ORF4 (nt 3843–4337) and ORF5 (nt 4530–5636), which had coding capacities of 44, 36,

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Ilves, H., O. Kahre, and M. Speek. "Translation of the rat LINE bicistronic RNAs in vitro involves ribosomal reinitiation instead of frameshifting." Molecular and Cellular Biology 12, no. 9 (1992): 4242–48. http://dx.doi.org/10.1128/mcb.12.9.4242-4248.1992.

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The genomic structure of the rat LINE (L1Rn) DNA element contains two overlapping open reading frames (ORFs) and apparently has a potential to code for a DNA/RNA-binding protein (in ORF1) and a reverse transcriptase (in ORF2). We have characterized a 1,630-bp L1Rn cDNA clone encompassing the overlapping ORFs and a 600-bp genomic fragment derived from a full-length L1Rn member and containing the beginning of ORF1. These DNAs were used to restore in part the ORF1-ORF2 organization of L1Rn after being cloned into the pSP65 vector under the control of SP6 polymerase promoter. To test whether L1Rn

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Ilves, H., O. Kahre, and M. Speek. "Translation of the rat LINE bicistronic RNAs in vitro involves ribosomal reinitiation instead of frameshifting." Molecular and Cellular Biology 12, no. 9 (1992): 4242–48. http://dx.doi.org/10.1128/mcb.12.9.4242.

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The genomic structure of the rat LINE (L1Rn) DNA element contains two overlapping open reading frames (ORFs) and apparently has a potential to code for a DNA/RNA-binding protein (in ORF1) and a reverse transcriptase (in ORF2). We have characterized a 1,630-bp L1Rn cDNA clone encompassing the overlapping ORFs and a 600-bp genomic fragment derived from a full-length L1Rn member and containing the beginning of ORF1. These DNAs were used to restore in part the ORF1-ORF2 organization of L1Rn after being cloned into the pSP65 vector under the control of SP6 polymerase promoter. To test whether L1Rn

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Cowley, Jeff A., Lee C. Cadogan, Kirsten M. Spann, Nusra Sittidilokratna, and Peter J. Walker. "The Gene Encoding the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeus monodon Prawns Is Located Upstream of the Glycoprotein Gene." Journal of Virology 78, no. 16 (2004): 8935–41. http://dx.doi.org/10.1128/jvi.78.16.8935-8941.2004.

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ABSTRACT The ORF2 gene of Gill-associated virus (GAV) of Penaeus monodon prawns resides 93 nucleotides downstream of the ORF1a-ORF1b gene and encodes a 144-amino-acid hydrophilic polypeptide (15,998 Da; pI, 9.75) containing 20 basic (14%) and 13 acidic (9%) residues and 19 prolines (13%). Antiserum to a synthetic ORF2 peptide or an Escherichia coli-expressed glutathione S-transferase-ORF2 fusion protein detected a 20-kDa protein in infected lymphoid organ and gill tissues in Western blots. The GAV ORF2 fusion protein antiserum also cross-reacted with the p20 nucleoprotein in virions of the clo

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Llamas, María A., Juan L. Ramos, and José J. Rodríguez-Herva. "Transcriptional Organization of the Pseudomonas putida tol-oprL Genes." Journal of Bacteriology 185, no. 1 (2003): 184–95. http://dx.doi.org/10.1128/jb.185.1.184-195.2003.

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ABSTRACT Proteins of the Tol system play a key role in the maintenance of outer membrane integrity and cell morphology in gram-negative bacteria. In Pseudomonas putida, the seven genes, orf1, tolQ, tolR, tolA, tolB, oprL, and orf2, which encode the proteins of this complex, are clustered in a 5.8-kb region of chromosomal DNA. Analysis of polar mutations, reverse transcriptase PCR assays, and transcriptional fusion constructs with a promoterless lacZ gene revealed that the genes are arranged in two operons: orf1 tolQ tolR tolA tolB and oprL orf2. We were also able to find a transcript that was

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Robinson, D. N., and L. Cooley. "Examination of the function of two kelch proteins generated by stop codon suppression." Development 124, no. 7 (1997): 1405–17. http://dx.doi.org/10.1242/dev.124.7.1405.

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The Drosophila kelch gene produces a single transcript with a UGA stop codon separating two open reading frames (ORF1 and ORF2). From the transcript, 76 kDa ORF1 and 160 kDa full-length (ORF1 + ORF2) proteins are made. The expression of these two proteins is regulated in a tissue-specific manner causing the ratio of full-length to ORF1 protein to vary in different tissues. The only detected defect for kelch mutants is female sterility, and kelch protein is localized to the ovarian ring canals. kelch mutant ring canals are disorganized and have partly occluded lumens, causing a failure to trans

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Emerson, Suzanne U., Hanh T. Nguyen, Udana Torian, Danielle Burke, Ronald Engle, and Robert H. Purcell. "Release of Genotype 1 Hepatitis E Virus from Cultured Hepatoma and Polarized Intestinal Cells Depends on Open Reading Frame 3 Protein and Requires an Intact PXXP Motif." Journal of Virology 84, no. 18 (2010): 9059–69. http://dx.doi.org/10.1128/jvi.00593-10.

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ABSTRACT Hepatitis E virus genotype 1 strain Sar55 replicated in subcloned Caco-2 intestinal cells and Huh7 hepatoma cells that had been transfected with in vitro transcribed viral genomes, and hepatitis E virions were released into the culture medium of both cell lines. Virus egress from cells depended on open reading frame 3 (ORF3) protein, and a proline-rich sequence in ORF3 was important for egress from cultured cells and for infection of macaques. Both intracellular ORF3 protein accumulation and virus release occurred at the apical membrane of polarized Caco-2 cells. ORF3 protein and lipi

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Ichinose, Koji, Makoto Ozawa, Keiko Itou, Kanako Kunieda, and Yutaka Ebizuka. "Cloning, sequencing and heterologous expression of the medermycin biosynthetic gene cluster of Streptomyces sp. AM-7161: towards comparative analysis of the benzoisochromanequinone gene clusters." Microbiology 149, no. 7 (2003): 1633–45. http://dx.doi.org/10.1099/mic.0.26310-0.

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Medermycin is a Streptomyces aromatic C-glycoside antibiotic classified in the benzoisochromanequinones (BIQs), which presents several interesting biosynthetic problems concerning polyketide synthase (PKS), post-PKS tailoring and deoxysugar pathways. The biosynthetic gene cluster for medermycin (the med cluster) was cloned from Streptomyces sp. AM-7161. Completeness of the clone was proved by the heterologous expression of a cosmid carrying the entire med cluster in Streptomyces coelicolor CH999 to produce medermycin. The DNA sequence of the cosmid (36 202 bp) revealed 34 complete ORFs, with a

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Sunna, Anwar, Moreland D. Gibbs, Charles W. J. Chin, Peter J. Nelson та Peter L. Bergquist. "A Gene Encoding a Novel Multidomain β-1,4-Mannanase from Caldibacillus cellulovorans and Action of the Recombinant Enzyme on Kraft Pulp". Applied and Environmental Microbiology 66, № 2 (2000): 664–70. http://dx.doi.org/10.1128/aem.66.2.664-670.2000.

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ABSTRACT Genomic walking PCR was used to obtained a 4,567-bp nucleotide sequence from Caldibacillus cellulovorans. Analysis of this sequence revealed that there were three open reading frames, designated ORF1, ORF2, and ORF3. Incomplete ORF1 encoded a putative C-terminal cellulose-binding domain (CBD) homologous to members of CBD family IIIb, while putative ORF3 encoded a protein of unknown function. The putative ManA protein encoded by complete manA ORF2 was an enzyme with a novel multidomain structure and was composed of four domains in the following order: a putative N-terminal domain (D1)

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Kaiser, William J., Yasmin Chaudhry, Stanislav V. Sosnovtsev, and Ian G. Goodfellow. "Analysis of protein–protein interactions in the feline calicivirus replication complex." Journal of General Virology 87, no. 2 (2006): 363–68. http://dx.doi.org/10.1099/vir.0.81456-0.

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Caliciviruses are a major cause of gastroenteritis in humans and cause a wide variety of other diseases in animals. Here, the characterization of protein–protein interactions between the individual proteins of Feline calicivirus (FCV), a model system for other members of the family Caliciviridae, is reported. Using the yeast two-hybrid system combined with a number of other approaches, it is demonstrated that the p32 protein (the picornavirus 2B analogue) of FCV interacts with p39 (2C), p30 (3A) and p76 (3CD). The FCV protease/RNA polymerase (ProPol) p76 was found to form homo-oligomers, as we

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