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Автор: Grafiati
Опубліковано: 7 липня 2024
Оновлено: 7 липня 2024

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1

Rziha, Hanns-Joachim, Mathias Büttner, Melanie Müller, Ferdinand Salomon, Alena Reguzova, Dominic Laible, and Ralf Amann. "Genomic Characterization of Orf Virus Strain D1701-V (Parapoxvirus) and Development of Novel Sites for Multiple Transgene Expression." Viruses 11, no. 2 (January 30, 2019): 127. http://dx.doi.org/10.3390/v11020127.

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The Orf virus (ORFV; Parapoxvirus) strain D1701 with an attenuated phenotype and excellent immunogenic capacity is successfully used for the generation of recombinant vaccines against different viral infections. Adaption for growth in Vero cells was accompanied by additional major genomic changes resulting in ORFV strain variant D1701-V. In this study, restriction enzyme mapping, blot hybridization and DNA sequencing of the deleted region s (A, AT and D) in comparison to the predecessor strain D1701-B revealed the loss of 7 open reading frames (ORF008, ORF101, ORF102, ORF114, ORF115, ORF116, ORF117). The suitability of deletion site D for expression of foreign genes is demonstrated using novel synthetic early promoter eP1 and eP2. Comparison of promoter strength showed that the original vegf-e promoter Pv as well as promoter eP2 display an up to 11-fold stronger expression than promoter eP1, irrespective of the insertion site. Successful integration and expression of the fluorescent marker genes is demonstrated by gene- and insertion-site specific PCR assays, fluorescence microscopy and flow cytometry. For the first time ORFV recombinants are generated simultaneously expressing transgenes in two different insertion loci. That allows production of polyvalent vaccines containing several antigens against one or different pathogens in a single vectored ORFV vaccine.
2

Tang, Ruizhe, Liqun Lu, Beiyang Wang, Jiao Yu, and Hao Wang. "Identification of the Immediate-Early Genes of Cyprinid Herpesvirus 2." Viruses 12, no. 9 (September 7, 2020): 994. http://dx.doi.org/10.3390/v12090994.

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Cyprinid herpesvirus 2 (CyHV-2), which infects goldfish and crucian carp causing high mortality, is an emerging viral pathogen worldwide. The genome of CyHV-2 is large and comprises double-stranded DNA, including several genes similar to cyprinid herpesvirus 1, ictalurid herpesvirus-1, cyprinid herpesvirus 3, and ranid herpesvirus-1. Genes of DNA viruses are expressed in three temporal phases: immediate-early (IE), early (E), and late (L) genes. Viral IE genes initiate transcription as soon as the virus enters the host, without viral DNA replication. IE gene products enable the efficient expression of E and L genes or regulate the host to initiate virus replication. In the present study, five IE genes of CyHV-2 were identified, including open reading frame (ORF)54, ORF121, ORF141, ORF147, and ORF155. Time course analysis and reverse transcription polymerase chain reaction confirmed five IE genes, thirty-four E genes, and thirty-nine L genes. In addition, all 150 ORFs identified in the CyHV-2 genome are transcribed, and are expressed in chronological order, similar to other herpesviruses. This study is the first to identify the IE genes of CyHV-2, which will provide more information for viral molecular characterization.
3

Gong, Min, Jianping Jin, and Linda A. Guarino. "Mapping of ORF121, a Factor That Activates Baculovirus Early Gene Expression." Virology 244, no. 2 (May 1998): 495–503. http://dx.doi.org/10.1006/viro.1998.9116.

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4

Che, Xibing, Mike Reichelt, Marvin H. Sommer, Jaya Rajamani, Leigh Zerboni, and Ann M. Arvin. "Functions of the ORF9-to-ORF12 Gene Cluster in Varicella-Zoster Virus Replication and in the Pathogenesis of Skin Infection." Journal of Virology 82, no. 12 (April 9, 2008): 5825–34. http://dx.doi.org/10.1128/jvi.00303-08.

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ABSTRACT The gene cluster composed of varicella-zoster virus (VZV) open reading frame 9 (ORF9) to ORF12 encodes four putative tegument proteins and is highly conserved in most alphaherpesviruses. In these experiments, the genes within this cluster were deleted from the VZV parent Oka (POKA) individually or in combination, and the consequences for VZV replication were evaluated with cultured cells in vitro and with human skin xenografts in SCID mice in vivo. As has been reported for ORF10, ORF11 and ORF12 were dispensable for VZV replication in melanoma and human embryonic fibroblast cells. In contrast, deletion of ORF9 was incompatible with the recovery of infectious virus. ORF9 localized to the virion tegument and formed complexes with glycoprotein E, which is an essential protein, in VZV-infected cells. Recombinants lacking ORF10 and ORF11 (POKAΔ10/11), ORF11 and ORF12 (POKAΔ11/12), or ORF10, ORF11 and ORF12 (POKAΔ10/11/12) were viable in cultured cells. Their growth kinetics did not differ from those of POKA, and nucleocapsid formation and virion assembly were not disrupted. In addition, these deletion mutants showed no differences compared to POKA in infectivity levels for primary human tonsil T cells. Deletion of ORF12 had no effect on skin infection, whereas replication of POKAΔ11, POKAΔ10/11, and POKAΔ11/12 was severely reduced, and no virus was recovered from skin xenografts inoculated with POKAΔ10/11/12. These results indicate that with the exception of ORF9, the individual genes within the ORF9-to-ORF12 gene cluster are dispensable and can be deleted simultaneously without any apparent effect on VZV replication in vitro but that the ORF10-to-ORF12 cluster is essential for VZV virulence in skin in vivo.
5

Kessler, Peter S., Carrine Blank, and John A. Leigh. "The nif Gene Operon of the Methanogenic Archaeon Methanococcus maripaludis." Journal of Bacteriology 180, no. 6 (March 15, 1998): 1504–11. http://dx.doi.org/10.1128/jb.180.6.1504-1511.1998.

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ABSTRACT Nitrogen fixation occurs in two domains, Archaea andBacteria. We have characterized a nif(nitrogen fixation) gene cluster in the methanogenic archaeonMethanococcus maripaludis. Sequence analysis revealed eight genes, six with sequence similarity to known nif genes and two with sequence similarity to glnB. The gene order,nifH, ORF105 (similar to glnB),ORF121 (similar to glnB), nifD,nifK, nifE, nifN, andnifX, was the same as that found in part in other diazotrophic methanogens and except for the presence of theglnB-like genes, also resembled the order found in many members of the Bacteria. Using transposon insertion mutagenesis, we determined that an 8-kb region required for nitrogen fixation corresponded to the nif gene cluster. Northern analysis revealed the presence of either a single 7.6-kbnif mRNA transcript or 10 smaller mRNA species containing portions of the large transcript. Polar effects of transposon insertions demonstrated that all of these mRNAs arose from a single promoter region, where transcription initiated 80 bp 5′ tonifH. Distinctive features of the nif gene cluster include the presence of the six primary nif genes in a single operon, the placement of the two glnB-like genes within the cluster, the apparent physical separation of the cluster from any other nif genes that might be in the genome, the fragmentation pattern of the mRNA, and the regulation of expression by a repression mechanism described previously. Our study and others with methanogenic archaea reporting multiple mRNAs arising from gene clusters with only a single putative promoter sequence suggest that mRNA processing following transcription may be a common occurrence in methanogens.
6

Gao, Wa, Lupin Zhao, Yihua Zheng, Kaixuan Wu, Feiyang Xu, Hao Wang, Liqun Lu, and Yousheng Jiang. "Generation and application of a monoclonal antibody specific for the ORF121 of cyprinid herpesvirus 2." Journal of Fish Diseases 45, no. 3 (December 6, 2021): 387–94. http://dx.doi.org/10.1111/jfd.13566.

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7

Kolosov, A. V., V. A. Ternovoy, A. N. Shvalov, A. A. Moiseeva, A. S. Safatov, and V. N. Mikheev. "ADAPTATION OF THE CORN EARWORM SINGLE NUCLEOCAPCIDE NUCLEOPOLYHEDROVIRUS (HELICOVERPA ZEA SNPV) FOR THE CONTROL OF THE COTTON BOLLWORM (HELICOVERPA ARMIGERA) POPULATION." Problems of Virology, Russian journal 62, no. 3 (June 20, 2017): 134–37. http://dx.doi.org/10.18821/0507-4088-2017-62-3-134-137.

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Helicoverpa zea (Boddie, 1850) (Hz) single nucleocapcide nucleopolyhedrovirus (SNPV) was adapted to the cotton bollworm (Helicoverpa armigera, (Hübner, 1805) (Ha)) by five blind passages on larvae. The full genomic sequence of the resulting strain HS-18 has been determined (GenBank acc. №: KJ004000.1). Biological activity of the HS-18 strain is higher than the activity of all other Russian strains of NPV, as far as cotton bollworm strain HearSNPV-G4. HS-18-infected caterpillars at the 3-rd and 4-th ages died much faster than those infected with HearSNPV-G4 strain. A major difference of HS-18 genome is an 18 bp repeat in the RING-finger ORF that confirms high variability of this region. Three other insertions and seven base substitutions were observed earlier, while six base substitutions are new. Mutations are located at ORF42, lef-9, ORF58, VP39, PIF-4, P48, SOD, ORF111, ORF129 and ORF138 genes. Among all nucleotide mutation only one is synonymous. Thus we suppose the selective pressure to the virus. The resulting strain HS-18 is recommended as a biopesticide for controlling the number of cotton bollworm in cotton fields.
8

Martínez-Costa, Oscar H., Angel J. Martín-Triana, Eduardo Martínez, Miguel A. Fernández-Moreno, and Francisco Malpartida. "An Additional Regulatory Gene for Actinorhodin Production in Streptomyces lividans Involves a LysR-Type Transcriptional Regulator." Journal of Bacteriology 181, no. 14 (1999): 4353–64. http://dx.doi.org/10.1128/jb.181.14.4353-4364.1999.

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The sequence of a 4.8-kbp DNA fragment adjacent to the right-hand end of the actinorhodin biosynthetic (act) cluster downstream of actVB-orf6 from Streptomyces coelicolor A3(2) reveals six complete open reading frames, namedorf7 to orf12. The deduced amino acid sequences from orf7, orf10, and orf11 show significant similarities with the following products in the databases: a putative protein from the S. coelicolor SCP3 plasmid, LysR-type transcriptional regulators, and proteins belonging to the family of short-chain dehydrogenases/reductases, respectively. The deduced product of orf8 reveals low similarities with several methyltransferases from different sources, whileorf9 and orf12 products show no similarities with other known proteins. Disruptions of orf10 andorf11 genes in S. coelicolor appear to have no significant effect on the production of actinorhodin. Nevertheless, disruption or deletion of orf10 in Streptomyces lividans causes actinorhodin overproduction. The introduction of extra copies of orf10 and orf11 genes in anS. coelicolor actIII mutant restores the ability to produce actinorhodin. Transcriptional analysis and DNA footprinting indicate that Orf10 represses its own transcription and regulatesorf11 transcription, expression of which might require the presence of an unknown inducer. No DNA target for Orf10 protein was found within the act cluster.
9

Tan, Yeping, Dennis K. Bideshi, Jeffrey J. Johnson, Yves Bigot, and Brian A. Federici. "Proteomic analysis of the Spodoptera frugiperda ascovirus 1a virion reveals 21 proteins." Journal of General Virology 90, no. 2 (February 1, 2009): 359–65. http://dx.doi.org/10.1099/vir.0.005934-0.

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The Spodoptera frugiperda ascovirus 1a (SfAV-1a) is a double-stranded DNA virus that attacks lepidopteran larvae, in which it produces enveloped virions with complex symmetry which have an average diameter of 130 nm and length of 400 nm. Here, we report identification of 21 SfAV-1a-encoded proteins that occur in the virion, as determined by nano-liquid chromatography/tandem mass spectrometry. These included a helicase (ORF009), nuclease (ORF075), ATPase (ORF047), serine/threonine-like protein kinase (ORF064), inhibitor of apoptosis-like protein (ORF015), thiol oxidoreductase-like protein (ORF061), CTD phosphatase (ORF109), major capsid protein (ORF041) and a highly basic protein, P64 (ORF048). The latter two were the most abundant. Apart from ascoviruses, the closest orthologues were found in iridoviruses, providing further evidence that ascoviruses evolved from invertebrate iridoviruses. These results establish a foundation for investigating how ascovirus virion proteins interact to form their complex asymmetrical structure, as well as for elucidating the mechanisms involved in SfAV-1a virion morphogenesis.
10

Li, Ping, Shanghai Yong, Xin Zhou, and Jiayin Shen. "Characterization of a New Temperate Escherichia coli Phage vB_EcoP_ZX5 and Its Regulatory Protein." Pathogens 11, no. 12 (November 30, 2022): 1445. http://dx.doi.org/10.3390/pathogens11121445.

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The study of the interaction between temperate phages and bacteria is vital to understand their role in the development of human diseases. In this study, a novel temperate Escherichia coli phage, vB_EcoP_ZX5, with a genome size of 39,565 bp, was isolated from human fecal samples. It has a short tail and belongs to the genus Uetakevirus and the family Podoviridae. Phage vB_EcoP_ZX5 encodes three lysogeny-related proteins (ORF12, ORF21, and ORF4) and can be integrated into the 3′-end of guaA of its host E. coli YO1 for stable transmission to offspring bacteria. Phage vB_EcoP_ZX5 in lysogenized E. coli YO1+ was induced spontaneously, with a free phage titer of 107 PFU/mL. The integration of vB_EcoP_ZX5 had no significant effect on growth, biofilm, environmental stress response, antibiotic sensitivity, adherence to HeLa cells, and virulence of E. coli YO1. The ORF4 anti-repressor, ORF12 integrase, and ORF21 repressors that affect the lytic–lysogenic cycle of vB_EcoP_ZX5 were verified by protein overexpression. We could tell from changes of the number of total phages and the transcription level of phage genes that repressor protein is the key determinant of lytic-to-lysogenic conversion, and anti-repressor protein promotes the conversion from lysogenic cycle to lytic cycle.
11

Li, Rongfeng, Nusrat Khaleeli, and Craig A. Townsend. "Expansion of the Clavulanic Acid Gene Cluster: Identification and In Vivo Functional Analysis of Three New Genes Required for Biosynthesis of Clavulanic Acid by Streptomyces clavuligerus." Journal of Bacteriology 182, no. 14 (July 15, 2000): 4087–95. http://dx.doi.org/10.1128/jb.182.14.4087-4095.2000.

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ABSTRACT Clavulanic acid is a potent inhibitor of β-lactamase enzymes and is of demonstrated value in the treatment of infections by β-lactam-resistant bacteria. Previously, it was thought that eight contiguous genes within the genome of the producing strainStreptomyces clavuligerus were sufficient for clavulanic acid biosynthesis, because they allowed production of the antibiotic in a heterologous host (K. A. Aidoo, A. S. Paradkar, D. C. Alexander, and S. E. Jensen, p. 219–236, In V. P. Gullo et al., ed., Development in industrial microbiology series, 1993). In contrast, we report the identification of three new genes, orf10 (cyp), orf11(fd), and orf12, that are required for clavulanic acid biosynthesis as indicated by gene replacement andtrans-complementation analysis in S. clavuligerus. These genes are contained within a 3.4-kb DNA fragment located directly downstream of orf9(cad) in the clavulanic acid cluster. While theorf10 (cyp) and orf11(fd) proteins show homologies to other knownCYP-150 cytochrome P-450 and [3Fe-4S] ferredoxin enzymes and may be responsible for an oxidative reaction late in the pathway, the protein encoded by orf12 shows no significant similarity to any known protein. The results of this study extend the biosynthetic gene cluster for clavulanic acid and attest to the importance of analyzing biosynthetic genes in the context of their natural host. Potential functional roles for these proteins are proposed.
12

Köhler, Thilo, Javier Fernandez Alvarez, and Shigeaki Harayama. "Regulation of therpoN, ORF102 and ORF154 genes inPseudomonas putida." FEMS Microbiology Letters 115, no. 2-3 (January 1994): 177–84. http://dx.doi.org/10.1111/j.1574-6968.1994.tb06634.x.

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13

Wu, Yueh-Lung, Carol P. Wu, Song-Tay Lee, Han Tang, Chi-Hua Chang, Hong-Hwa Chen, and Yu-Chan Chao. "The Early Gene hhi1 Reactivates Heliothis zea Nudivirus 1 in Latently Infected Cells." Journal of Virology 84, no. 2 (November 4, 2009): 1057–65. http://dx.doi.org/10.1128/jvi.01548-09.

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ABSTRACT Heliothis zea nudivirus 1 (HzNV-1), previously known as Hz-1 virus, is an insect virus able to establish both productive and latent infections in several lepidopteran insect cells. Here, we have cloned and characterized one of the HzNV-1 early genes, hhi1, which maps to the HindIII-I fragment of the viral genome. During the productive viral infection, a 6.2-kb hhi1 transcript was detectable as early as 0.5 h postinfection (hpi). The level of transcript reached a maximum at 2 hpi and gradually decreased after 4 hpi. The transcript was not detectable during the latent phase of viral infection. Upon cycloheximide treatment, much higher levels of hhi1 transcript were detected throughout the productive viral infection cycle, suggesting that newly synthesized proteins are not needed for the expression of hhi1. Nevertheless, viral coinfection can further stimulate the expression of transfected hhi1 promoter in a plasmid. Transient hhi1 expression in latently infected cells resulted in a significant increase in virus titer and viral DNA propagation, suggesting that hhi1 plays a critical role in viral reactivation. Additional experiments showed that six early genes, which possibly function in transcription or DNA replication, were activated in the latent cells upon hhi1 transfection. Among these six genes, orf90 and orf121 expression could be induced by hhi1 alone without the need for other viral genes. Our discovery should be useful for future mechanistic study of the switches of latent/productive HzNV-1 viral infections.
14

Takeuchi, Ippei, Keita Osada, Aa Haeruman Azam, Hiroaki Asakawa, Kazuhiko Miyanaga, and Yasunori Tanji. "The Presence of Two Receptor-Binding Proteins Contributes to the Wide Host Range of Staphylococcal Twort-Like Phages." Applied and Environmental Microbiology 82, no. 19 (July 15, 2016): 5763–74. http://dx.doi.org/10.1128/aem.01385-16.

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ABSTRACTThanks to their wide host range and virulence, staphylococcal bacteriophages (phages) belonging to the genusTwortlikevirus(staphylococcal Twort-like phages) are regarded as ideal candidates for clinical application forStaphylococcus aureusinfections due to the emergence of antibiotic-resistant bacteria of this species. To increase the usability of these phages, it is necessary to understand the mechanism underlying host recognition, especially the receptor-binding proteins (RBPs) that determine host range. In this study, we found that the staphylococcal Twort-like phage ΦSA012 possesses at least two RBPs. Genomic analysis of five mutant phages of ΦSA012 revealed point mutations inorf103, in a region unique to staphylococcal Twort-like phages. Phages harboring mutated ORF103 could not infectS. aureusstrains in which wall teichoic acids (WTAs) are glycosylated with α-N-acetylglucosamine (α-GlcNAc). A polyclonal antibody against ORF103 also inhibited infection by ΦSA012 in the presence of α-GlcNAc, suggesting that ORF103 binds to α-GlcNAc. In contrast, a polyclonal antibody against ORF105, a short tail fiber component previously shown to be an RBP, inhibited phage infection irrespective of the presence of α-GlcNAc. Immunoelectron microscopy indicated that ORF103 is a tail fiber component localized at the bottom of the baseplate. From these results, we conclude that ORF103 binds α-GlcNAc in WTAs, whereas ORF105, the primary RBP, is likely to bind the WTA backbone. These findings provide insight into the infection mechanism of staphylococcal Twort-like phages.IMPORTANCEStaphylococcusphages belonging to the genusTwortlikevirus(called staphylococcal Twort-like phages) are considered promising agents for control ofStaphylococcus aureusdue to their wide host range and highly lytic capabilities. Although staphylococcal Twort-like phages have been studied widely for therapeutic purposes, the host recognition process of staphylococcal Twort-like phages remains unclear. This work provides new findings about the mechanisms of host recognition of the staphylococcal Twort-like phage ΦSA012. The details of the host recognition mechanism of ΦSA012 will allow us to analyze the mechanisms of infection and expand the utility of staphylococcal Twort-like phages for the control ofS. aureus.
15

Li, Lingling, Zhaofei Li, Weichun Chen, Chao Liu, Haili Huang, Kai Yang, and Yi Pang. "Characterization of Spodoptera exigua multicapsid nucleopolyhedrovirus ORF100 and ORF101, two homologues of E. coli ChaB." Virus Research 121, no. 1 (October 2006): 42–50. http://dx.doi.org/10.1016/j.virusres.2006.03.014.

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16

Schippers, Timo, Keith Jarosinski, and Nikolaus Osterrieder. "The ORF012 Gene of Marek's Disease Virus Type 1 Produces a Spliced Transcript and Encodes a Novel Nuclear Phosphoprotein Essential for Virus Growth." Journal of Virology 89, no. 2 (November 12, 2014): 1348–63. http://dx.doi.org/10.1128/jvi.02687-14.

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ABSTRACTMarek's disease virus (MDV), an alphaherpesvirus, is the causative agent of a lethal disease in chickens characterized by generalized nerve inflammation and rapid lymphoma development. The extensive colinearity of the MDV genome with those of related herpesviruses has eased functional characterization of many MDV genes. However, MDV carries a number of unique open reading frames (ORFs) that have not yet been investigated regarding their coding potentials and the functions of their products. Among these unique ORFs are two putative ORFs, ORF011 and ORF012, which are found at the extreme left end of the MDV unique long region. Using reverse transcriptase PCR, we showed that ORF011 and ORF012 are not individual genes but form a single gene through mRNA splicing of a small intron, resulting in the novel ORF012. We generated an ORF012-null virus using an infectious clone of MDV strain RB-1B. The deletion virus had a marked growth defectin vitroand could not be passaged in cultured cells, suggesting an essential role for the ORF012 product in virus replication. Further studies revealed that protein 012 (p012) localized to the nucleus in transfected and infected cells, and we identified by site-directed mutagenesis and green fluorescent protein (GFP) reporter fusion assays a nuclear localization signal (NLS) that was mapped to a 23-amino-acid sequence at the protein's C terminus. Nuclear export was blocked using leptomycin B, suggesting a potential role for p012 as a nuclear/cytoplasmic shuttling protein. Finally, p012 is phosphorylated at multiple residues, a modification that could possibly regulate its subcellular distribution.IMPORTANCEMarek's disease virus (MDV) causes a devastating oncogenic disease in chickens with high morbidity and mortality. The costs for disease prevention reach several billion dollars annually. The functional investigation of MDV genes is necessary to understand its complex replication cycle, which eventually could help us to interfere with MDV and herpesviral pathogenesis. We have identified a previously unidentified phosphoprotein encoded by MDV ORF012. We were able to show experimentally that predicted splicing of the gene based on bioinformatics data does indeed occur during replication. The newly identified p012 is essential for MDV replication and localizes to the nucleus due to the presence of a transferable nuclear localization signal at its C terminus. Our results also imply that p012 could constitute a nucleocytoplasmic shuttle protein, a feature that could prove interesting and important.
17

Horinouchi, Masae, Toshiaki Hayashi, Takako Yamamoto, and Toshiaki Kudo. "A New Bacterial Steroid Degradation Gene Cluster in Comamonas testosteroni TA441 Which Consists of Aromatic-Compound Degradation Genes for Seco-Steroids and 3-Ketosteroid Dehydrogenase Genes." Applied and Environmental Microbiology 69, no. 8 (August 2003): 4421–30. http://dx.doi.org/10.1128/aem.69.8.4421-4430.2003.

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ABSTRACT In Comamonas testosteroni TA441, testosterone is degraded via aromatization of the A ring, which is cleaved by the meta-cleavage enzyme TesB, and further degraded by TesD, the hydrolase for the product of TesB. TesEFG, encoded downstream of TesD, are probably hydratase, aldolase, and dehydrogenase for degradation of 2-oxohex-4-enoicacid, one of the products of TesD. Here we present a new and unique steroid degradation gene cluster in TA441, which consists of ORF18, ORF17, tesI, tesH, ORF11, ORF12, and tesDEFG. TesH and TesI are 3-ketosteroid-Δ1-dehydrogenase and 3-ketosteroid-Δ4(5α)-dehydrogenase, respectively, which work in the early steps of steroid degradation. ORF17 probably encodes the reductase component of 9α-hydroxylase for 1,4-androstadiene-3,17-dione, which is the product of TesH in testosterone degradation. Gene disruption experiments showed that these genes are necessary for steroid degradation and do not have any isozymes in TA441. By Northern blot analysis, these genes were shown to be induced when TA441 was incubated with steroids (testosterone and cholic acid) but not with aromatic compounds [phenol, biphenyl, and 3-(3-hydroxyphenyl)propionic acid], indicating that these genes function exclusively in steroid degradation.
18

Yamaguchi, Tatsuo, Tadashi Watanabe, Yuki Iwaisako, and Masahiro Fujimuro. "Kaposi’s Sarcoma-Associated Herpesvirus ORF21 Enhances the Phosphorylation of MEK and the Infectivity of Progeny Virus." International Journal of Molecular Sciences 24, no. 2 (January 8, 2023): 1238. http://dx.doi.org/10.3390/ijms24021238.

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Kaposi’s sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus-8, is the causative agent of Kaposi’s sarcoma, Castleman’s disease, and primary effusion lymphoma. Although the functions of the viral thymidine kinases (vTK) of herpes simplex virus-1/2 are well understood, that of KSHV ORF21 (an ortholog of vTK) is largely unknown. Here, we investigated the role of ORF21 in lytic replication and infection by generating two ORF21-mutated KSHV BAC clones: ORF21-kinase activity deficient KSHV (21KD) and stop codon-induced ORF21-deleted KSHV (21del). The results showed that both ORF21 mutations did not affect viral genome replication, lytic gene transcription, or the production of viral genome-encapsidated particles. The ORF21 molecule-dependent function, other than the kinase function of ORF21, was involved in the infectivity of the progeny virus. ORF21 was expressed 36 h after the induction of lytic replication, and endogenously expressed ORF21 was localized in the whole cytoplasm. Moreover, ORF21 upregulated the MEK phosphorylation and anchorage-independent cell growth. The inhibition of MEK signaling by U0126 in recipient target cells suppressed the number of progeny virus-infected cells. These suggest that ORF21 transmitted as a tegument protein in the progeny virus enhances the new infection through MEK up-regulation in the recipient cell. Our findings indicate that ORF21 plays key roles in the infection of KSHV through the manipulation of the cellular function.
19

Makarenko, Maksim, Alexander Usatov, Tatiana Tatarinova, Kirill Azarin, Alexey Kovalevich, Vera Gavrilova, and Renate Horn. "The Investigation of Perennial Sunflower Species (Helianthus L.) Mitochondrial Genomes." Genes 11, no. 9 (August 24, 2020): 982. http://dx.doi.org/10.3390/genes11090982.

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The genus Helianthus is a diverse taxonomic group with approximately 50 species. Most sunflower genomic investigations are devoted to economically valuable species, e.g., H. annuus, while other Helianthus species, especially perennial, are predominantly a blind spot. In the current study, we have assembled the complete mitogenomes of two perennial species: H. grosseserratus (273,543 bp) and H. strumosus (281,055 bp). We analyzed their sequences and gene profiles in comparison to the available complete mitogenomes of H. annuus. Except for sdh4 and trnA-UGC, both perennial sunflower species had the same gene content and almost identical protein-coding sequences when compared with each other and with annual sunflowers (H. annuus). Common mitochondrial open reading frames (ORFs) (orf117, orf139, and orf334) in sunflowers and unique ORFs for H. grosseserratus (orf633) and H. strumosus (orf126, orf184, orf207) were identified. The maintenance of plastid-derived coding sequences in the mitogenomes of both annual and perennial sunflowers and the low frequency of nonsynonymous mutations point at an extremely low variability of mitochondrial DNA (mtDNA) coding sequences in the Helianthus genus.
20

Xia, Dongxiang, Shamala Srinivas, Hitoshi Sato, Lesley Pesnicak, Stephen E. Straus, and Jeffrey I. Cohen. "Varicella-Zoster Virus Open Reading Frame 21, Which Is Expressed during Latency, Is Essential for Virus Replication but Dispensable for Establishment of Latency." Journal of Virology 77, no. 2 (January 15, 2003): 1211–18. http://dx.doi.org/10.1128/jvi.77.2.1211-1218.2003.

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ABSTRACT Varicella-zoster virus (VZV) open reading frame 21 (ORF21) is one of at least five VZV genes expressed in latently infected human and rodent ganglia. To determine whether ORF21 is required for latent and lytic infection, we deleted 99% of ORF21 from the viral genome. The ORF21 deletion mutant virus could be propagated only in a cell line expressing the ORF21 protein. Insertion of the herpes simplex virus type 1 (HSV-1) homolog of VZV ORF21, HSV-1 UL37, into the ORF21 deletion mutant failed to complement the mutant for growth in cell culture. Inoculation of cotton rats with the ORF21 deletion virus resulted in latent infection in numbers of animals similar to those infected after inoculation with the parental virus. The mean numbers of latent VZV genomes were similar in animals infected with parental and ORF21 deletion viruses. Transcription of ORF63, another latency-associated gene, was detected in ganglia from similar numbers of animals infected with the mutant and parental viruses. Thus, ORF21 is the first VZV gene expressed during latency that has been shown to be dispensable for the establishment of latent infection.
21

Moonen, Mariëlle J. H., Nanne M. Kamerbeek, Adrie H. Westphal, Sjef A. Boeren, Dick B. Janssen, Marco W. Fraaije, and Willem J. H. van Berkel. "Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in Pseudomonas fluorescens ACB." Journal of Bacteriology 190, no. 15 (May 23, 2008): 5190–98. http://dx.doi.org/10.1128/jb.01944-07.

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ABSTRACT The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to β-ketoadipate. The P. fluorescens ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (hapCDEFGHIBA) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenyl acetate hydrolase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE), and maleylacetate reductase (hapF). In between hapF and hapB, three genes encoding a putative intradiol dioxygenase (hapG), a protein of the Yci1 family (hapH), and a [2Fe-2S] ferredoxin (hapI) were found. Downstream of the hap genes, five open reading frames are situated encoding three putative regulatory proteins (orf10, orf12, and orf13) and two proteins possibly involved in a membrane efflux pump (orf11 and orf14). Upstream of hapE, two genes (hapC and hapD) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the hapC and hapD gene products are involved in the ring cleavage of hydroquinone.
22

Siponen, Marina, Giuliano Sciara, Manuela Villion, Silvia Spinelli, Julie Lichière, Christian Cambillau, Sylvain Moineau, and Valérie Campanacci. "Crystal Structure of ORF12 from Lactococcus lactis Phage p2 Identifies a Tape Measure Protein Chaperone." Journal of Bacteriology 191, no. 3 (December 1, 2008): 728–34. http://dx.doi.org/10.1128/jb.01363-08.

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ABSTRACT We report here the characterization of the nonstructural protein ORF12 of the virulent lactococcal phage p2, which belongs to the Siphoviridae family. ORF12 was produced as a soluble protein, which forms large oligomers (6- to 15-mers) in solution. Using anti-ORF12 antibodies, we have confirmed that ORF12 is not found in the virion structure but is detected in the second half of the lytic cycle, indicating that it is a late-expressed protein. The structure of ORF12, solved by single anomalous diffraction and refined at 2.9-Å resolution, revealed a previously unknown fold as well as the presence of a hydrophobic patch at its surface. Furthermore, crystal packing of ORF12 formed long spirals in which a hydrophobic, continuous crevice was identified. This crevice exhibited a repeated motif of aromatic residues, which coincided with the same repeated motif usually found in tape measure protein (TMP), predicted to form helices. A model of a complex between ORF12 and a repeated motif of the TMP of phage p2 (ORF14) was generated, in which the TMP helix fitted exquisitely in the crevice and the aromatic patches of ORF12. We suggest, therefore, that ORF12 might act as a chaperone for TMP hydrophobic repeats, maintaining TMP in solution during the tail assembly of the lactococcal siphophage p2.
23

Shen, Yunwang, Haiping Wang, Weifan Xu, and Xiaofeng Wu. "Bombyx mori nucleopolyhedrovirus orf133 and orf134 are involved in the embedding of occlusion-derived viruses into polyhedra." Journal of General Virology 99, no. 5 (May 1, 2018): 717–29. http://dx.doi.org/10.1099/jgv.0.001058.

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24

Liu, XueQiao, and Jeffrey I. Cohen. "Varicella-Zoster Virus ORF12 Protein Activates the Phosphatidylinositol 3-Kinase/Akt Pathway To Regulate Cell Cycle Progression." Journal of Virology 87, no. 3 (November 28, 2012): 1842–48. http://dx.doi.org/10.1128/jvi.02395-12.

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ABSTRACTVaricella-zoster virus (VZV) activates the phosphatidylinositol 3-kinase (PI3K)/Akt pathway and alters cell cycle progression, but the viral protein(s) responsible for these activities is unknown. We previously reported that the VZV open reading frame 12 (ORF12) protein triggers phosphorylation of ERK. Here, we demonstrate that the VZV ORF12 protein also activates the PI3K/Akt pathway to regulate cell cycle progression. Transfection of cells with a plasmid expressing the ORF12 protein induced phosphorylation of Akt, which was dependent on PI3K. Infection of cells with wild-type VZV triggered phosphorylation of Akt, while infection with an ORF12 deletion mutant induced less phosphorylated Akt. The activation of Akt by ORF12 protein was associated with its binding to the p85 subunit of PI3K. Infection of cells with wild-type VZV resulted in increased levels of cyclin B1, cyclin D3, and phosphorylated glycogen synthase kinase 3β (GSK-3β), while infection with the ORF12 deletion mutant induced lower levels of these proteins. Wild-type VZV infection reduced the G1phase cell population and increased the M phase cell population, while infection with the ORF12 deletion mutant had a reduced effect on the G1and M phase populations. Inhibition of Akt activity with LY294002 reduced the G1and M phase differences observed in cells infected with wild-type and ORF12 mutant viruses. In conclusion, we have found that the VZV ORF12 protein activates the PI3K/Akt pathway to regulate cell cycle progression. Since VZV replicates in both dividing (e.g., keratinocytes) and nondividing (neurons) cells, the ability of the VZV ORF12 protein to regulate the cell cycle is likely important for VZV replication in various cell types in the body.
25

Dairi, Tohru, Yoshimitsu Hamano, Tomohisa Kuzuyama, Nobuya Itoh, Kazuo Furihata, and Haruo Seto. "Eubacterial Diterpene Cyclase Genes Essential for Production of the Isoprenoid Antibiotic Terpentecin." Journal of Bacteriology 183, no. 20 (October 15, 2001): 6085–94. http://dx.doi.org/10.1128/jb.183.20.6085-6094.2001.

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ABSTRACT A gene cluster containing the mevalonate pathway genes (open reading frame 2 [ORF2] to ORF7) for the formation of isopentenyl diphosphate and a geranylgeranyl diphosphate (GGDP) synthase gene (ORF1) had previously been cloned from Streptomyces griseolosporeus strain MF730-N6, a diterpenoid antibiotic, terpentecin (TP) producer (Y. Hamano, T. Dairi, M. Yamamoto, T. Kawasaki, K Kaneda, T. Kuzuyama, N. Itoh, and H. Seto, Biosci. Biotech. Biochem. 65:1627–1635, 2001). Sequence analysis in the upstream region of the cluster revealed seven new ORFs, ORF8 to ORF14, which were suggested to encode TP biosynthetic genes. We constructed two mutants, in which ORF11 and ORF12, which encode a protein showing similarities to eukaryotic diterpene cyclases (DCs) and a eubacterial pentalenene synthase, respectively, were inactivated by gene disruptions. The mutants produced no TP, confirming that these cyclase genes are essential for the production of TP. The two cyclase genes were also expressed in Streptomyces lividans together with the GGDP synthase gene under the control of theermE* constitutive promoter. The transformant produced a novel cyclic diterpenoid, ent-clerod-3,13(16),14-triene (terpentetriene), which has the same basic skeleton as TP. The two enzymes, each of which was overproduced in Escherichia coli and purified to homogeneity, converted GGDP into terpentetriene. To the best of our knowledge, this is the first report of a eubacterial DC.
26

Chen, Huiqing, Mei Li, Weijun Mai, Qi Tang, Guohui Li, Keping Chen, and Yajing Zhou. "Analysis of BmNPV orf101 disruption: orf101 is essential for mediating budded virus production." Cytotechnology 66, no. 6 (October 10, 2014): 1021–29. http://dx.doi.org/10.1007/s10616-014-9772-6.

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27

Tomita, Haruyoshi, Elizabeth Kamei, and Yasuyoshi Ike. "Cloning and Genetic Analyses of the Bacteriocin 41 Determinant Encoded on the Enterococcus faecalis Pheromone-Responsive Conjugative Plasmid pYI14: a Novel Bacteriocin Complemented by Two Extracellular Components (Lysin and Activator)." Journal of Bacteriology 190, no. 6 (January 18, 2008): 2075–85. http://dx.doi.org/10.1128/jb.01056-07.

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ABSTRACT The conjugative plasmid pYI14 (61 kbp) was isolated from Enterococcus faecalis YI714, a clinical isolate. pYI14 conferred a pheromone response on its host and encoded bacteriocin 41 (bac41). Bacteriocin 41 (Bac41) only showed activity against E. faecalis. Physical mapping of pYI14 showed that it consisted of EcoRI fragments A to P. The clone pHT1100, containing EcoRI fragments A (12.6 kbp) and H (3.5 kbp), conferred the bacteriocin activity on E. faecalis strains. Genetic analysis showed that the determinant was located in a 6.6-kbp region within the EcoRI AH fragments. Six open reading frames (ORFs) were identified in this region and designated ORF7 (bacL1 ) ORF8 (bacL2 ), ORF9, ORF10, ORF11 (bacA), and ORF12 (bacI). They were aligned in this order and oriented in the same direction. ORFs bacL1 , bacL2 , bacA, and bacI were essential for expression of the bacteriocin in E. faecalis. Extracellular complementation of bacteriocin expression was possible for bacL1 and -L2 and bacA mutants. bacL1 and -L2 and bacA encoded bacteriocin component L and activator component A, respectively. The products of these genes are secreted into the culture medium and extracellularly complement bacteriocin expression. bacI encoded immunity, providing the host with resistance to its own bacteriocin activity. The bacL1 -encoded protein had significant homology with lytic enzymes that attack the gram-positive bacterial cell wall. Sequence data for the deduced bacL1 -encoded protein suggested that it has a domain structure consisting of an N-terminal signal peptide, a second domain with the enzymatic activity, and a third domain with a three-repeat structure directing the proenzyme to its cell surface receptor.
28

Deák, Veronika, Rita Lukács, Zsuzsanna Buzás, Adrienn Pálvölgyi, Péter P. Papp, László Orosz, and Péter Putnoky. "Identification of Tail Genes in the Temperate Phage 16-3 of Sinorhizobium meliloti 41." Journal of Bacteriology 192, no. 6 (January 14, 2010): 1617–23. http://dx.doi.org/10.1128/jb.01335-09.

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ABSTRACT Genes encoding the tail proteins of the temperate phage 16-3 of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti 41 have been identified. First, a new host range gene, designated hII, was localized by using missense mutations. The corresponding protein was shown to be identical to the 85-kDa tail protein by determining its N-terminal sequence. Electron microscopic analysis showed that phage 16-3 possesses an icosahedral head and a long, noncontractile tail characteristic of the Siphoviridae. By using a lysogenic S. meliloti 41 strain, mutants with insertions in the putative tail region of the genome were constructed and virion morphology was examined after induction of the lytic cycle. Insertions in ORF017, ORF018a, ORF020, ORF021, the previously described h gene, and hII resulted in uninfectious head particles lacking tail structures, suggesting that the majority of the genes in this region are essential for tail formation. By using different bacterial mutants, it was also shown that not only the RkpM and RkpY proteins but also the RkpZ protein of the host takes part in the formation of the phage receptor. Results for the host range phage mutants and the receptor mutant bacteria suggest that the HII tail protein interacts with the capsular polysaccharide of the host and that the tail protein encoded by the original h gene recognizes a proteinaceous receptor.
29

Boname, Jessica M., Janet S. May, and Philip G. Stevenson. "Murine Gammaherpesvirus 68 Open Reading Frame 11 Encodes a Nonessential Virion Component." Journal of Virology 79, no. 5 (March 1, 2005): 3163–68. http://dx.doi.org/10.1128/jvi.79.5.3163-3168.2005.

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ABSTRACT Open reading frame 11 (ORF11) is a conserved gammaherpesvirus gene that remains undefined. We identified the product of murine gammaherpesvirus 68 (MHV-68) ORF11, p43, as a virion component with a predominantly perinuclear distribution in infected cells. MHV-68 lacking p43 grew normally in vitro but showed reduced lytic replication in vivo and a delay in seeding to the spleen. Subsequent latency amplification was normal. Thus, MHV-68 ORF11 encoded a virion component that was important for in vivo lytic replication but dispensable for the establishment of latency.
30

Rozen, Ramona, Narayanan Sathish, Yong Li, and Yan Yuan. "Virion-Wide Protein Interactions of Kaposi's Sarcoma-Associated Herpesvirus." Journal of Virology 82, no. 10 (March 5, 2008): 4742–50. http://dx.doi.org/10.1128/jvi.02745-07.

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ABSTRACT Herpesvirus virions are highly organized structures built through specific protein-protein interactions. Thus, revelation of the protein interactions among virion proteins will shed light on the processes and the mechanisms of virion formation. Recently, we identified 24 virion proteins of Kaposi's sarcoma-associated herpesvirus (KSHV), using a proteomic approach (F. X. Zhu et al., J. Virol. 79:800-811, 2005). In the current study, a comprehensive analysis of protein-protein interaction between KSHV virion proteins was carried out using yeast two-hybrid (Y2H) and coimmunoprecipitation (co-IP) approaches. Every pairwise combination between KSHV tegument and capsid proteins, between tegument and envelope proteins, and among tegument proteins was tested for possible binary interaction. Thirty-seven protein-protein interactions were identified by both Y2H and co-IP analyses. The results revealed interactions between tegument and capsid proteins such as that of open reading frame 64 (ORF64) with ORF25 (major capsid protein [MCP]), ORF62 (triplex-1 [TRI-1]), and ORF26 (TRI-2). Many interactions were detected among the tegument proteins. ORF64 was found to interact with several tegument proteins including ORF11, ORF21, ORF33, ORF45, ORF63, ORF75, and ORF64 itself, suggesting that ORF64 may serve as a hub protein and play a role in recruiting tegument proteins during tegumentation and virion assembly. Our investigation also revealed redundant interactions between tegument proteins and envelope glycoproteins. These interactions are believed to contribute to final envelopment in virion assembly. Overall, this study allows us to establish a virion-wide protein interaction map, which provides insight into the architecture of the KSHV virion and sets up a foundation for exploring the functions of these proteins in viral particle assembly.
31

Johnson, Glenn R., Rakesh K. Jain, and Jim C. Spain. "Origins of the 2,4-Dinitrotoluene Pathway." Journal of Bacteriology 184, no. 15 (August 1, 2002): 4219–32. http://dx.doi.org/10.1128/jb.184.15.4219-4232.2002.

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ABSTRACT The degradation of synthetic compounds requires bacteria to recruit and adapt enzymes from pathways for naturally occurring compounds. Previous work defined the steps in 2,4-dinitrotoluene (2,4-DNT) metabolism through the ring fission reaction. The results presented here characterize subsequent steps in the pathway that yield the central metabolic intermediates pyruvate and propionyl coenzyme A (CoA). The genes encoding the degradative pathway were identified within a 27-kb region of DNA cloned from Burkholderia cepacia R34, a strain that grows using 2,4-DNT as a sole carbon, energy, and nitrogen source. Genes for the lower pathway in 2,4-DNT degradation were found downstream from dntD, the gene encoding the extradiol ring fission enzyme of the pathway. The region includes genes encoding a CoA-dependent methylmalonate semialdehyde dehydrogenase (dntE), a putative NADH-dependent dehydrogenase (ORF13), and a bifunctional isomerase/hydrolase (dntG). Results from analysis of the gene sequence, reverse transcriptase PCR, and enzyme assays indicated that dntD dntE ORF13 dntG composes an operon that encodes the lower pathway. Additional genes that were uncovered encode the 2,4-DNT dioxygenase (dntAaAbAcAd), methylnitrocatechol monooxygenase (dntB), a putative LysR-type transcriptional (ORF12) regulator, an intradiol ring cleavage enzyme (ORF3), a maleylacetate reductase (ORF10), a complete ABC transport complex (ORF5 to ORF8), a putative methyl-accepting chemoreceptor protein (ORF11), and remnants from two transposable elements. Some of the additional gene products might play as-yet-undefined roles in 2,4-DNT degradation; others appear to remain from recruitment of the neighboring genes. The presence of the transposon remnants and vestigial genes suggests that the pathway for 2,4-DNT degradation evolved relatively recently because the extraneous elements have not been eliminated from the region.
32

Patiño, Luisa F., Vanessa Aguirre-Hoyos, Laura I. Pinilla, León F. Toro, and Rigoberto Ríos-Estepa. "Environmental Factors Modulate the Role of orf21 Sigma Factor in Clavulanic Acid Production in Streptomyces Clavuligerus ATCC27064." Bioengineering 9, no. 2 (February 16, 2022): 78. http://dx.doi.org/10.3390/bioengineering9020078.

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Sigma factors and sigma factor-related mechanisms control antibiotic production in Streptomyces. In this contribution, the orf21 gene was overexpressed in the wild-type strain of Streptomyces clavuligerus ATCC2764, yielding S. clavuligerus/pIORF21, to further evaluate its regulatory effect on clavulanic acid (CA) biosynthesis under different culture medium conditions. The orf21 overexpression, regulated under the constitutive promoter ermE*, led to 2.6-fold increase in CA production in GSPG medium, and a 1.8-fold decrease using ISP medium. As for GYM and MYM media, S. clavuligerus/pIORF21 strain showed higher aerial mycelium production compared to control. Glycerol uptake rate profile was affected by orf21 overexpression. Furthermore, in GSPG, S. clavuligerus/pIORF21 slightly increased the expression of adpA and gcas genes, whilst, in ISP, the claR gene expression was drastically reduced, which is consistent with a decreased CA production, observed in this medium. These findings suggest the protein encoded by the orf21 gene plays a role in the regulation of CA biosynthesis as a response to the nutritional composition of the medium.
33

Guo, Z., L. Qiu, M. Du, and S. An. "Characterization of ORF127 of Helicoverpa armigera nucleopolyhedrovirus." Acta Virologica 53, no. 4 (December 2009): 247–53. http://dx.doi.org/10.4149/av_2009_04_247.

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34

Terzano, Susanna, Ilaria Oliva, Francesca Forti, Claudia Sala, Francesca Magnoni, Gianni Dehò, and Daniela Ghisotti. "Bacteriophage P4 sut1: a mutation suppressing transcription termination." Journal of General Virology 88, no. 3 (March 1, 2007): 1041–47. http://dx.doi.org/10.1099/vir.0.82605-0.

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In the Escherichia coli satellite phage P4, transcription starting from PLE is prevalently controlled via premature termination at several termination sites. We identified a spontaneous mutation, P4 sut1 (suppression of termination), in the natural stop codon of P4 orf151 that, by elongating translation, suppresses transcription termination at the downstream t151 site. Both the translational and the transcriptional profile of P4 sut1 differed from those of P4 wild-type. First of all, P4 sut1 did not express Orf151, but a higher molecular mass protein, compatible with the 303 codon open reading frame generated by the fusion of orf151, cnr and the intervening 138 nt. Moreover, after infection of E. coli, the mutant expressed a very low amount of the 1.3 and 1.7 kb transcripts originating at PLE and PLL promoters, respectively, and terminating at the intracistronic t151 site, whereas correspondingly higher amounts of the 4.1 and 4.5 kb RNAs arising from the same promoters and covering the entire operon were detected. Thus the sut1 mutation converts a natural stop codon into a sense codon, suppresses a natural intracistronic termination site and leads to overexpression of the downstream cnr and α genes. This correlates with the inability of P4 sut1 to propagate in the plasmid state. By cloning different P4 DNA fragments, we mapped the t151 transcription termination site within the 7633–7361 region between orf151 and gene cnr. A potential stem–loop structure, resembling the structure of a Rho-independent termination site, was predicted by mfold sequence analysis at 7414–7385.
35

Truong, Jia Quyen, Santosh Panjikar, Linda Shearwin-Whyatt, John B. Bruning, and Keith E. Shearwin. "Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68." Acta Crystallographica Section D Structural Biology 75, no. 7 (July 1, 2019): 670–81. http://dx.doi.org/10.1107/s2059798319009008.

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Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin.
36

Falero, Alina, Andy Caballero, Beatriz Ferrán, Yovanny Izquierdo, Rafael Fando та Javier Campos. "DNA Binding Proteins of the Filamentous Phages CTXφ and VGJφ of Vibrio cholerae". Journal of Bacteriology 191, № 18 (17 липня 2009): 5873–76. http://dx.doi.org/10.1128/jb.01206-08.

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ABSTRACT The native product of open reading frame 112 (orf112) and a recombinant variant of the RstB protein, encoded by Vibrio cholerae pathogen-specific bacteriophages VGJφ and CTXφ, respectively, were purified to more than 90% homogeneity. Orf112 protein was shown to specifically bind single-stranded genomic DNA of VGJφ; however, RstB protein unexpectedly bound double-stranded DNA in addition to the single-stranded genomic DNA. The DNA binding properties of these proteins may explain their requirement for the rolling circle replication of the respective phages and RstB's requirement for single-stranded-DNA chromosomal integration of CTXφ phage dependent on XerCD recombinases.
37

Bifang, Hao, Guo XiaoFang, Wang Meng, and Shen Xingjia. "Subcelluar localization of orf126 of Bombyx mori nucleopolyhedrovirus." African Journal of Biotechnology 10, no. 44 (August 15, 2011): 8877–80. http://dx.doi.org/10.5897/ajb11.1213.

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38

Bibi, Shabana, Dong Wang, Yuanbing Wang, Ghazala Mustafa, and Hong Yu. "Mitogenomic and Phylogenetic Analysis of the Entomopathogenic Fungus Ophiocordyceps lanpingensis and Comparative Analysis with Other Ophiocordyceps Species." Genes 14, no. 3 (March 14, 2023): 710. http://dx.doi.org/10.3390/genes14030710.

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Ophiocordyceps lanpingensis (O. lanpingensis) belongs to the genus Ophiocordyceps, which is often found in Yunnan Province, China. This species is pharmacologically important for the treatment of renal disorders induced by oxidative stress and an inadequate immune response. In the present study, the mitogenome of O. lanpingensis was determined to be a circular molecule 117,560 bp in length, and to have 31% G + C content and 69% A + T content. This mitogenome comprised 82% of the whole genome that codes for significant genes. The protein-coding regions of the O. lanpingensis mitogenome, containing 24 protein-coding genes, were associated with respiratory chain complexes, such as 3 ATP-synthase complex F0 subunits (atp6, atp8, and atp9), 2 complex IV subunits/cytochrome c oxidases (cox2 and cox3), 1 complex III subunit (cob), 4 electron transport complex I subunits/NADH dehydrogenase complex subunits (nad1, nad4, nad5, and nad6), 2 ribosomal RNAs (rns, rnl), and 11 hypothetical/predicted proteins, i.e., orf609, orf495, orf815, orf47, orf150, orf147, orf292, orf127, orf349, orf452, and orf100. It was noted that all genes were positioned on the same strand. Further, 13 mitochondrial genes with respiratory chain complexes, which presented maximum similarity with other fungal species of Ophiocordyceps, were investigated. O. lanpingensis was compared with previously sequenced species within Ophiocordycepitaceae. Comparative analysis indicated that O. lanpingensis was more closely related to O. sinensis, which is one of the most remarkable and expensive herbs due to its limited availability and the fact that it is difficult to culture. Therefore, O. lanpingensis is an important medicinal resource that can be effectively used for medicinal purposes. More extensive metabolomics research is recommended for O. lanpingensis.
39

Kumar, Naveen, Yogesh Chander, Ram Kumar, Nitin Khandelwal, Thachamvally Riyesh, Khushboo Chaudhary, Karuppusamy Shanmugasundaram, et al. "Isolation and characterization of lumpy skin disease virus from cattle in India." PLOS ONE 16, no. 1 (January 11, 2021): e0241022. http://dx.doi.org/10.1371/journal.pone.0241022.

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Lumpy skin disease (LSD) has devastating economic impact. During the last decade, LSD had spread to climatically new and previously disease-free countries, which also includes its recent emergence in the Indian subcontinent (2019). This study deals with the LSD outbreak(s) from cattle in Ranchi (India). Virus was isolated from the scabs (skin lesions) in the primary goat kidney cells. Phylogenetic analysis based on nucleotide sequencing of LSD virus (LSDV) ORF011, ORF012 and ORF036 suggested that the isolated virus (LSDV/Bos taurus-tc/India/2019/Ranchi) is closely related to Kenyan LSDV strains. Further, we adapted the isolated virus in Vero cells. Infection of the isolated LSDV to Vero cells did not produce cytopathic effect (CPE) until the 4th blind passage, but upon adaptation, it produced high viral titres in the cultured cells. The kinetics of viral DNA synthesis and one-step growth curve analysis suggested that Vero cell-adapted LSDV initiates synthesizing its genome at ~24 hours post-infection (hpi) with a peak level at ~96 hpi whereas evidence of progeny virus particles was observed at 36–48 hours (h) with a peak titre at ~120 h. To the best of our knowledge, this study describes the first successful isolation of LSDV in India, besides providing insights into the life cycle Vero cell-adapted LSDV.
40

Yamagishi, Hiroshi, Megumi Jikuya, Kanako Okushiro, Ayako Hashimoto, Asumi Fukunaga, Mizuki Takenaka, and Toru Terachi. "A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish." Molecular Genetics and Genomics 296, no. 3 (March 26, 2021): 705–17. http://dx.doi.org/10.1007/s00438-021-01777-y.

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AbstractCytoplasmic male sterility (CMS) observed in many plants leads defect in the production of functional pollen, while the expression of CMS is suppressed by a fertility restorer gene in the nuclear genome. Ogura CMS of radish is induced by a mitochondrial orf138, and a fertility restorer gene, Rfo, encodes a P-type PPR protein, ORF687, acting at the translational level. But, the exact function of ORF687 is still unclear. We found a Japanese variety showing male sterility even in the presence of Rfo. We examined the pollen fertility, Rfo expression, and orf138 mRNA in progenies of this variety. The progeny with Type H orf138 and Rfo showed male sterility when their orf138 mRNA was unprocessed within the coding region. By contrast, all progeny with Type A orf138 were fertile though orf138 mRNA remained unprocessed in the coding region, demonstrating that ORF687 functions on Type A but not on Type H. In silico analysis suggested a specific binding site of ORF687 in the coding region, not the 5′ untranslated region estimated previously, of Type A. A single nucleotide substitution in the putative binding site diminishes affinity of ORF687 in Type H and is most likely the cause of the ineffectiveness of ORF687. Furthermore, fertility restoration by RNA processing at a novel site in some progeny plants indicated a new and the third fertility restorer gene, Rfs, for orf138. This study clarified that direct ORF687 binding to the coding region of orf138 is essential for fertility restoration by Rfo.
41

Phan, Kim, Maurice Bessman, Juan Rodríguez, and Sandra Gabelli. "Structural basis of inhibition of the NUDIX family ORF141." Acta Crystallographica Section A Foundations and Advances 77, a1 (July 30, 2021): a281. http://dx.doi.org/10.1107/s010876732109718x.

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42

Maruyama, Chitose, Haruka Niikura, Miho Izumikawa, Junko Hashimoto, Kazuo Shin-ya, Mamoru Komatsu, Haruo Ikeda, et al. "tRNA-Dependent Aminoacylation of an Amino Sugar Intermediate in the Biosynthesis of a Streptothricin-Related Antibiotic." Applied and Environmental Microbiology 82, no. 12 (April 15, 2016): 3640–48. http://dx.doi.org/10.1128/aem.00725-16.

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ABSTRACTThe antibiotic streptothricin (ST) possesses an amino sugar bound to anl-β-lysine (β-Lys) residue via a peptide bond. The peptide bond formation has been shown to be catalyzed by a nonribosomal peptide synthetase (NRPS) during ST biosynthesis. The focus of this study is the closely related ST analogue BD-12, which carries a glycine-derived side chain rather than a β-Lys residue. Here, inStreptomyces luteocolorNBRC13826, we describe our biosynthetic studies of BD-12, which revealed that the peptide bond between the amino sugar and the glycine residue is catalyzed by a Fem-like enzyme (Orf11) in a tRNA-dependent manner rather than by an NRPS. Although there have been several reports of peptide bond-forming tRNA-dependent enzymes, to our knowledge, Orf11 is the first enzyme that can accept an amino sugar as a substrate. Our findings clearly demonstrate that the structural diversity of the side chains of ST-type compounds in nature is generated in an unusual manner via two distinct peptide bond-forming mechanisms. Moreover, the identification and functional analysis of Orf11 resulted in not only the production of new ST-related compounds, but also the provision of new insights into the structure-activity relationship of the ST-related antibiotics.IMPORTANCEThe antibiotic streptothricin (ST) possesses an amino sugar bound to anl-β-lysine (β-Lys) side chain via a peptide bond formed by a nonribosomal peptide synthetase (NRPS). BD-12, an analogue of ST, carries a glycine-derived side chain rather than β-Lys, and here, we describe the BD-12-biosynthetic gene cluster fromStreptomycesluteocolorNBRC13826, which contains theorf11gene encoding a novel tRNA-dependent peptide bond-forming enzyme. The unique Fem-like enzyme (Orf11) accepts the amino sugar as a substrate and mediates the peptide formation between the amino sugar intermediate and glycine. Our studies demonstrate that the structural diversity of the side chains of ST-related compounds in nature is generated via two distinct peptide bond-forming mechanisms.
43

Braunagel, Sharon C., Paula A. Guidry, German Rosas-Acosta, Luke Engelking, and Max D. Summers. "Identification of BV/ODV-C42, an Autographa californica Nucleopolyhedrovirus orf101-Encoded Structural Protein Detected in Infected-Cell Complexes with ODV-EC27 and p78/83." Journal of Virology 75, no. 24 (December 15, 2001): 12331–38. http://dx.doi.org/10.1128/jvi.75.24.12331-12338.2001.

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ABSTRACT orf101 is a late gene of Autographa californica nucleopolyhedrovirus (AcMNPV). It encodes a protein of 42 kDa which is a component of the nucleocapsid of budded virus (BV) and occlusion-derived virus (ODV). To reflect this viral localization, the product of orf101 was named BV/ODV-C42 (C42). C42 is predominantly detected within the infected-cell nucleus: at 24 h postinfection (p.i.), it is coincident with the virogenic stroma, but by 72 h p.i., the stroma is minimally labeled while C42 is more uniformly located throughout the nucleus. Yeast two-hybrid screens indicate that C42 is capable of directly interacting with the viral proteins p78/83 (1629K) and ODV-EC27 (orf144). These interactions were confirmed using blue native gels and Western blot analyses. At 28 h p.i., C42 and p78/83 are detected in two complexes: one at approximately 180 kDa and a high-molecular-mass complex (500 to 600 kDa) which also contains EC27.
44

Ge, Jun-Qing, Jin-Fang Zhao, Ya-Ming Shao, Cai-Hong Tian, and Chuan-Xi Zhang. "Characterization of an early gene orf122 from Bombyx mori nucleopolyhedrovirus." Molecular Biology Reports 36, no. 3 (February 2, 2008): 543–48. http://dx.doi.org/10.1007/s11033-008-9212-9.

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45

Zhao, Ying, Huan Yu, Ni Li, and GuoHua Huang. "Characterization of Heliothis Virescens Ascovirus 3h orf21 that Encodes a Virion Protein." Journal of Applied Virology 8, no. 4 (March 19, 2020): 59–70. http://dx.doi.org/10.21092/jav.v8i4.114.

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Homologues of Heliothis virescens ascovirus 3h (HvAV-3h) orf21 are found in 9 completely sequenced members of the ascoviruses, but so far their functions are unknown. Here, orf21 (3h-21) was cloned in-frame into a pET-28a bacterial expression vector. The fusion protein produced by this construct was used for the preparation of a polyclonal antiserum. RT-PCR analysis showed a single transcript of 3h-21 of approximately 0.7kb was transcribed beginning at 24h post-infection in infected Helicoverpa armigera larvae. Western blot analysis of extracts from HvAv-3h-infected Helicoverpa armigera larvae detected a 25.6 kDa protein late in infection. This antiserum also reacted with a 25.6 kDa protein in purified virions of HvAv-3h. The protein was not extensively modified post-translation. Immunoelectron microscopy confirmed that the 3H-21 is associated with the structure of HvAV-3h virions.
46

Takamatsu, Daisuke, Makoto Osaki, and Tsutomu Sekizaki. "Evidence for Lateral Transfer of the Suilysin Gene Region of Streptococcus suis." Journal of Bacteriology 184, no. 7 (April 1, 2002): 2050–57. http://dx.doi.org/10.1128/jb.184.7.2050-2057.2002.

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ABSTRACT Suilysin is a cholesterol-binding cytolysin encoded by sly in Streptococcus suis. DNA sequence determination of the sly locus in a strain lacking sly revealed the presence of another gene, designated orf102, in the place of sly. No transposable element or long-repeat sequence was found in the close vicinity. Except for six strains whose corresponding loci have been rearranged, all of the remaining 62 strains examined had either sly or orf102 at the same locus and their flanking regions were conserved. The genetic organizations having either sly or orf102 were found in the strains whose 16S rRNA sequences were identical. These results suggest that S. suis acquired sly or orf102 from a foreign source and that these genes subsequently spread among S. suis strains by homologous recombination.
47

Wang, Licong, Maoxia Yang, Sheng Luo, Guanjun Yang, Xinjiang Lu, Jianfei Lu, and Jiong Chen. "Oral Vaccination of Recombinant Saccharomyces cerevisiae Expressing ORF132 Induces Protective Immunity against Cyprinid Herpesvirus-2." Vaccines 11, no. 1 (January 16, 2023): 186. http://dx.doi.org/10.3390/vaccines11010186.

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Cyprinid herpesvirus 2 (CyHV-2) is the etiological agent of herpesviral hematopoietic necrosis (HVHN) disease, which causes serious economic losses in the crucian carp culture industry. In this study, by displaying ORF132 on the surface of Saccharomyces cerevisiae cells (named EBY100/pYD1-ORF132), we evaluated the protective efficacy of oral administration against CyHV-2 infection. Intense innate and adaptive immune responses were evoked in both mucosal and systemic tissues after oral vaccination with EBY100/pYD1-ORF132. Importantly, oral vaccination provided significant protection for crucian carp post CyHV-2 infection, resulting in a relative percent survival (RPS) of 64%. In addition, oral administration suppressed the virus load and relieved histological damage in selected tissues. Our results indicated that surface-displayed ORF132 on S. cerevisiae could be used as potential oral vaccine against CyHV-2 infection.
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Guo, Chang-Jun, Wei-Jian Chen, Li-Qun Yuan, Li-Shi Yang, Shao-Ping Weng, Xiao-Qiang Yu та Jian-Guo He. "The viral ankyrin repeat protein (ORF124L) from infectious spleen and kidney necrosis virus attenuates nuclear factor-κB activation and interacts with IκB kinase β". Journal of General Virology 92, № 7 (1 липня 2011): 1561–70. http://dx.doi.org/10.1099/vir.0.031120-0.

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The ankyrin (ANK) repeat is one of the most common protein–protein interaction motifs, found predominantly in eukaryotes and bacteria, but the functions of the ANK repeat are rarely researched in animal viruses, with the exception of poxviruses. Infectious spleen and kidney necrosis virus (ISKNV) is a typical member of the genus Megalocytivirus in the family Iridoviridae and is a causative agent of epizootics in fish. The genome of ISKNV contains four putative viral ANK (vANK) repeat proteins and their functions remain largely unknown. In the present study, it was found that ORF124L, a vANK repeat protein in ISKNV, encodes a protein of 274 aa with three ANK repeats. Transcription of ORF124L was detected at 12 h post-infection (p.i.) and reached a peak at 40 h p.i. ORF124L was found to localize to both the nucleus and the cytoplasm in mandarin fish fry cells. ISKNV ORF124L interacted with the mandarin fish IκB kinase β protein (scIKKβ), and attenuated tumour necrosis factor alpha (TNF-α)- or phorbol myristate acetate (PMA)-induced activity of a nuclear factor κB (NF-κB)–luciferase reporter but did not interfere with the activity of an activator protein 1 (AP-1)–luciferase reporter. Phosphorylation of IκBα and nuclear translocation of NF-κB were also impaired by ISKNV ORF124L. In summary, ORF124L was identified as a vANK repeat protein and its role in inhibition of TNF-α-induced NF-κB signalling was investigated through interaction with the mandarin fish IKKβ. This work may help to improve our understanding of the function of fish iridovirus ANK repeat proteins.
49

Tang, Hoang V., Ruying Chang, and Daryl R. Pring. "Cosegregation of Single Genes Associated with Fertility Restoration and Transcript Processing of Sorghum Mitochondrial orf107 and urf209." Genetics 150, no. 1 (September 1, 1998): 383–91. http://dx.doi.org/10.1093/genetics/150.1.383.

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Abstract Defective nuclear-cytoplasmic interactions leading to aberrant microgametogenesis in sorghum carrying the IS1112C male-sterile cytoplasm occur very late in pollen maturation. Amelioration of this condition, the restoration of pollen viability, involves a novel two-gene gametophytic system, wherein genes designated Rf3 and Rf4 are required for viability of individual gametes. Rf3 is tightly linked to, or represents, a single gene that regulates a transcript processing activity that cleaves transcriptsof orf107, a chimeric mitochondrial open reading frame specific to IS1112C. The mitochondrial gene urf 209 is also subject to nucleus-specific enhanced transcript processing, 5′ to the gene, conferred by a single dominant gene designated Mmt1. Examinations of transcript patterns in F2 and two backcross populations indicated cosegregation of the augmented orf107 and urf209 processing activities in IS1112C. Several sorghum lines that do not restore fertility or confer orf107 transcript processing do exhibit urf209 transcript processing, indicating that the activities are distinguishable. We conclude that the nuclear gene(s) conferring enhanced orf107 and urf209 processing activities are tightly linked in IS1112C. Alternatively, the similarity in apparent regulatory action of the genes may indicate allelic differences wherein the IS1112C Rf3 allele may differ from alleles of maintainer lines by the capability to regulate both orf107 and urf209 processing activities.
50

Chen, Huiqing, Mei Li, Guoping Huang, Weijun Mai, Keping Chen, and Yajing Zhou. "Bombyx mori Nucleopolyhedrovirus ORF101 Encodes a Budded Virus Envelope Associated Protein." Current Microbiology 69, no. 2 (March 28, 2014): 158–63. http://dx.doi.org/10.1007/s00284-014-0570-3.

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