scholarly journals Analysis of the Choristoneura fumiferana nucleopolyhedrovirus genome

2005 ◽  
Vol 86 (4) ◽  
pp. 929-943 ◽  
Author(s):  
Jondavid G. de Jong ◽  
Hilary A. M. Lauzon ◽  
Cliff Dominy ◽  
Arkadi Poloumienko ◽  
Eric B. Carstens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Choristoneura Fumiferana ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Acid Identity ◽  
Orgyia Pseudotsugata ◽  
Double Stranded Dna ◽  
Enhancing Factor ◽  
Group I ◽  
Reading Frames

The double-stranded DNA genome of Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) was sequenced and analysed in the context of other group I nucleopolyhedroviruses (NPVs). The genome consists of 129 593 bp with a G+C content of 50·1 mol%. A total of 146 open reading frames (ORFs) of greater than 150 bp, and with no or minimal overlap were identified. In addition, five homologous regions were identified containing 7–10 repeats of a 36 bp imperfect palindromic core. Comparison with other completely sequenced baculovirus genomes revealed that 139 of the CfMNPV ORFs have homologues in at least one other baculovirus and seven ORFs are unique to CfMNPV. Of the 117 CfMNPV ORFs common to all group I NPVs, 12 are exclusive to group I NPVs. Overall, CfMNPV is most similar to Orgyia pseudotsugata MNPV based on gene content, arrangement and overall amino acid identity. Unlike other group I baculoviruses, however, CfMNPV encodes a viral enhancing factor (vef) and has two copies of p26.

scholarly journals Gene organization and sequencing of the Choristoneura fumiferana defective nucleopolyhedrovirus genome

2005 ◽  
Vol 86 (4) ◽  
pp. 945-961 ◽  
Author(s):  
Hilary A. M. Lauzon ◽  
Peter B. Jamieson ◽  
Peter J. Krell ◽  
Basil M. Arif
Keyword(s):  
Choristoneura Fumiferana ◽  
Amino Acid Identity ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Anticarsia Gemmatalis ◽  
Orgyia Pseudotsugata ◽  
Eastern Spruce Budworm ◽  
Group I ◽  
Average Amino Acid Identity ◽  
Late Expression

Two distinct nucleopolyhedrovirus species of the eastern spruce budworm, Choristoneura fumiferana, exist in a symbiont-like relationship. C. fumiferana defective nucleopolyhedrovirus (CfDEFNPV) only infects C. fumiferana larvae per os in the presence of C. fumiferana nucleopolyhedrovirus Ireland strain (CfMNPV), but is infective when injected into the haemolymph. CfDEFNPV synergizes CfMNPV in per os infections and CfMNPV is always the predominant progeny. This study was undertaken to report the genomic makeup and organization of CfDEFNPV in an attempt to identify its defect and understand its synergistic role. The genome was mapped, sequenced, characterized and compared to other baculoviruses. The CfDEFNPV genome was 131 160 nt long with 149 putative open reading frames (ORFs) and a G+C content of 45·8 mol%. Homologues of all 62 conserved lepidopteran baculovirus genes were found including those implicated in per os infectivity, p74, per os infectivity factor (pif) and pif-2. Although no obvious deletions were observed to explain the defect, two ORFs, Cfdef79 and Cfdef99 (inhibitor of apoptosis-4), contained potential deletions. Cfdef50 (late expression factor-10)/Cfdef51 (vp1054) and Cfdef76/Cfdef77 (telokin-like protein) had large overlaps and a potential homologue to ac105/he65 was split. Four baculovirus repeat ORFs were present, as were two unique genes, but no enhancins were identified. CfDEFNPV contained 13 homologous regions, each with one to five palindromes. Comparison with fully sequenced baculovirus genomes identified CfDEFNPV as a group I NPV with the closest average amino acid identity to Epiphyas postvittana NPV, followed by Orgyia pseudotsugata MNPV and CfMNPV, with its closest matches being to individual Anticarsia gemmatalis MNPV gene sequences.

Sequence and characterization of a novel chromosomal aminoglycoside phosphotransferase gene, aph (3')-IIb, in Pseudomonas aeruginosa.

1996 ◽  
Vol 40 (5) ◽  
pp. 1254-1256 ◽  
Author(s):  
H Hächler ◽  
P Santanam ◽  
F H Kayser
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Acid Identity ◽  
Aminoglycoside Phosphotransferase ◽  
Psti Fragment ◽  
Reading Frames

A novel, probably chromosomally encoded, aminoglycoside phosphotransferase gene was cloned on a 2,996-bp PstI fragment from Pseudomonas aeruginosa and designated aph (3')-IIb. It coded for a protein of 268 amino acids that showed 51.7% amino acid identity with APH (3')-II [APH(3') is aminoglycoside-3' phosphotransferase] from Tn5. Two other open reading frames on the cloned fragment showed homology to a signal-transducing system in P. aeruginosa.

scholarly journals Sequence analysis of the Choristoneura occidentalis granulovirus genome

2006 ◽  
Vol 87 (7) ◽  
pp. 1917-1933 ◽  
Author(s):  
Shannon R. Escasa ◽  
Hilary A. M. Lauzon ◽  
Amanda C. Mathur ◽  
Peter J. Krell ◽  
Basil M. Arif
Keyword(s):  
Amino Acid ◽  
Choristoneura Fumiferana ◽  
Cydia Pomonella ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Homologous Region ◽  
Choristoneura Occidentalis ◽  
Homologous Proteins ◽  
Group I ◽  
Apoptosis Inhibitor

The genome of the Choristoneura occidentalis granulovirus (ChocGV) isolated from the western spruce budworm, Choristoneura occidentalis, was sequenced completely. It was 104 710 bp long, with a 67.3 % A+T content and contained 116 potential open reading frames (ORFs) covering 88.4 % of the genome. Of these, 29 ORFs were conserved in all fully sequenced baculovirus genomes, 30 were GV-specific, 53 were present in some nucleopolyhedroviruses (NPVs) and/or GVs, three were common to ChocGV and Choristoneura fumiferana GV (ChfuGV) and one was so far unique. To date, ChocGV is the only GV identified that contains a homologue of the apoptosis inhibitor protein P35/P49, present in some group I NPVs. It is also the first GV without a Xestia c-nigrum GV ORF 26 homologue. Five homologous regions (hrs)/repeat regions, lacking typical NPV hr palindromes were identified. ChocGV hrs were similar to each other but not to other GV hrs. A 1.8 kb repeat region with a high A+T content (81 %) and multiple repeats of 21–210 bp was found between choc36 and 37. This area resembled the non-homologous region origin of DNA replication (non-hr ori) identified in Cryptophlebia leucotreta GV (CrleGV) and Cydia pomonella GV (CpGV). Based on the mean amino acid identities of homologous proteins, ChocGV was closest to fully sequenced genomes CpGV (52.3 %) and CrleGV (52.1 %). The closest amino acid identity was to individual ORFs from the partially sequenced ChfuGV genome (97.2 % in 38 ORFs). Phylogenetic analysis placed ChocGV in a clade with CrleGV and CpGV.

scholarly journals Characterization of the hrpC and hrpRSOperons of Pseudomonas syringae Pathovars Syringae, Tomato, and Glycinea and Analysis of the Ability of hrpF,hrpG, hrcC, hrpT, and hrpVMutants To Elicit the Hypersensitive Response and Disease in Plants

1998 ◽  
Vol 180 (17) ◽  
pp. 4523-4531 ◽  
Author(s):  
Wen-Ling Deng ◽  
Gail Preston ◽  
Alan Collmer ◽  
Chun-Jung Chang ◽  
Hsiou-Chen Huang
Keyword(s):  
Amino Acid ◽  
Outer Membrane ◽  
Pseudomonas Syringae ◽  
Hypersensitive Response ◽  
Amino Acid Identity ◽  
The Other ◽  
Wild Type ◽  
Acid Identity ◽  
Type Iii ◽  
Group I

The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster ofhrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. DNA sequence analysis of the hrpC and hrpRSoperons of P. syringae pv. syringae 61 (brown spot of beans), P. syringae pv. glycinea U1 (bacterial blight of soybeans), and P. syringae pv. tomato DC3000 (bacterial speck of tomatos) revealed that the 13 genes comprising the right half of the hrp cluster (including those in the previously sequenced hrpZ operon) are conserved and identically arranged. The hrpC operon is comprised of hrpF,hrpG, hrcC, hrpT, and hrpV. hrcC encodes a putative outer membrane protein that is conserved in all type III secretion systems. The other four genes appear to be characteristic of group I Hrp systems, such as those possessed byP. syringae and Erwinia amylovora. The predicted products of these four genes in P. syringae pv. syringae 61 are HrpF (8 kDa), HrpG (15.4 kDa), HrpT (7.5 kDa), and HrpV (13.4 kDa). HrpT is a putative outer membrane lipoprotein. HrpF, HrpG, and HrpV are all hydrophilic proteins lacking N-terminal signal peptides. The HrpG, HrcC, HrpT, and HrpV proteins of P. syringae pathovars syringae and tomato (the two most divergent pathovars) had at least 76% amino acid identity with each other, whereas the HrpF proteins of these two pathovars had only 36% amino acid identity. The HrpF proteins of P. syringae pathovars syringae and glycinea also showed significant similarity to the HrpA pilin protein of P. syringae pathovar tomato. Functionally nonpolar mutations were introduced into each of the genes in thehrpC operon of P. syringae pv. syringae 61 by insertion of an nptII cartridge lacking a transcription terminator. The mutants were assayed for their ability to elicit the HR in nonhost tobacco leaves or to multiply and cause disease in host bean leaves. Mutations in hrpF, hrcC, andhrpT abolished or greatly reduced the ability of P. syringae pv. syringae 61 to elicit the HR in tobacco. ThehrpG mutant had only weakly reduced HR activity, and the activity of the hrpV mutant was indistinguishable from that of the wild type. Each of the mutations could be complemented, but surprisingly, the hrpV subclone caused a reduction in the HR elicitation ability of the ΔhrpV::nptIImutant. The hrpF and hrcC mutants caused no disease in beans, whereas the hrpG, hrpT, and hrpV mutants had reduced virulence. Similarly, thehrcC mutant grew little in beans, whereas the other mutants grew to intermediate levels in comparison with the wild type. These results indicate that HrpC and HrpF have essential functions in the Hrp system, that HrpG and HrpT contribute quantitatively but are not essential, and that HrpV is a candidate negative regulator of the Hrp system.

scholarly journals Genome of the most widely used viral biopesticide: Anticarsia gemmatalis multiple nucleopolyhedrovirus

2006 ◽  
Vol 87 (11) ◽  
pp. 3233-3250 ◽  
Author(s):  
Juliana Velasco de Castro Oliveira ◽  
José Luiz Caldas Wolff ◽  
Alejandra Garcia-Maruniak ◽  
Bergmann Morais Ribeiro ◽  
Maria Elita Batista de Castro ◽  
...  
Keyword(s):  
Choristoneura Fumiferana ◽  
Heliothis Zea ◽  
Control Programme ◽  
Open Reading Frames ◽  
Anticarsia Gemmatalis ◽  
Coding Regions ◽  
Orgyia Pseudotsugata ◽  
Multiple Nucleopolyhedrovirus ◽  
Group I ◽  
Overlapping Open Reading Frames

The genome of Anticarsia gemmatalis multiple nucleopolyhedrovirus isolate 2D (AgMNPV-2D), which is the most extensively used virus pesticide in the world, was completely sequenced and shown to have 132 239 bp (G+C content 44.5 mol%) and to be capable of encoding 152 non-overlapping open reading frames (ORFs). Three ORFs were unique to AgMNPV-2D, one of which (ag31) had similarity to eukaryotic poly(ADP-ribose) polymerases. The lack of chiA and v-cath may explain some of the success and growth of the AgMNPV biological control programme, as it may explain the high recovery of polyhedra sequestered inside dead larvae in the field, which are collected and used for further application as biological pesticides in soybean fields. The genome organization was similar to that of the Choristoneura fumiferana defective MNPV (CfDefNPV). Most of the variation between the two genomes took place near highly repetitive regions, which were also closely associated with bro-coding regions. The separation of the NPVs into groups I and II was supported by: (i) a phenogram of the complete genomes of 28 baculovirus and Heliothis zea virus 1, (ii) the most parsimonious reconstruction of gene content along the phenograms and (iii) comparisons of genomic features. Moreover, these data also reinforced the notion that group I of the NPVs can be split further into the AgMNPV lineage (AgMNPV, CfDefNPV, Epiphyas postvittana NPV, Orgyia pseudotsugata MNPV and C. fumiferana MNPV), sharing eight defining genes, and the Autographa californica MNPV (AcMNPV) lineage (AcMNPV, Rachiplusia ou NPV and Bombyx mori NPV), sharing nine defining genes.

scholarly journals Sequence and Binding Activity of the Autolysin-Adhesin Ami from Epidemic Listeria monocytogenes 4b

2004 ◽  
Vol 72 (8) ◽  
pp. 4401-4409 ◽  
Author(s):  
Eliane Milohanic ◽  
Renaud Jonquières ◽  
Philippe Glaser ◽  
Pierre Dehoux ◽  
Christine Jacquet ◽  
...  
Keyword(s):  
Amino Acids ◽  
Listeria Monocytogenes ◽  
Amino Acid ◽  
Mammalian Cells ◽  
Amino Acid Identity ◽  
Allelic Polymorphism ◽  
Bacterial Cells ◽  
Phylogenic Tree ◽  
Acid Identity ◽  
Group I

ABSTRACT Ami is an autolytic amidase from Listeria monocytogenes that is targeted to the bacterial surface via its C-terminal cell wall anchoring (CWA) domain. We recently showed that the CWA domain from Ami of L. monocytogenes EGD (serovar 1/2a) (Ami 1/2a) mediated bacterial binding to mammalian cells. Here we studied the sequence and binding properties of Ami from CHUT 82337 (serovar 4b) (Ami 4b). The Ami 4b polypeptide is predicted to be 770 amino acids long (compared with the 917 amino acids of Ami 1/2a from EGD). Ami 1/2a and Ami 4b are almost identical in the N-terminal enzymatic domain (∼98% amino acid identity), but the sequence is poorly conserved in the C-terminal CWA domain, with only ∼54% amino acid identity and eight GW modules in Ami 1/2a compared with six GW modules in Ami 4b. The purified Ami 4b CWA domain efficiently bound serovar 4b bacterial cells and only poorly bound serovar 1/2a bacterial cells. The Ami 4b CWA domain was also significantly less able to bind Hep-G2 human hepatocytic cells than the Ami 1/2a CWA domain. We sequenced the ami regions encoding CWA domains of reference strains belonging to the 12 L. monocytogenes serovars. The phylogenic tree constructed from the sequences yielded a binary division into group I (serovars 1/2a, 1/2b, 1/2c, 3a, 3b, 3c, and 7) and group II (serovars 4a, 4b, 4c, 4d, and 4e). This is the first direct evidence of divergence between serovars 1/2a and 4b in a gene involved in the adhesion of L. monocytogenes to mammalian cells, as well as the first demonstration of allelic polymorphism correlated with the somatic antigen in this species.

scholarly journals Quaranfil, Johnston Atoll, and Lake Chad Viruses Are Novel Members of the Family Orthomyxoviridae

2009 ◽  
Vol 83 (22) ◽  
pp. 11599-11606 ◽  
Author(s):  
Rachel M. Presti ◽  
Guoyan Zhao ◽  
Wandy L. Beatty ◽  
Kathie A. Mihindukulasuriya ◽  
Amelia P. A. Travassos da Rosa ◽  
...  
Keyword(s):  
Amino Acid ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Febrile Illness ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Emerging Infections ◽  
Lake Chad ◽  
Acid Identity ◽  
The Family

ABSTRACT Arboviral infections are an important cause of emerging infections due to the movements of humans, animals, and hematophagous arthropods. Quaranfil virus (QRFV) is an unclassified arbovirus originally isolated from children with mild febrile illness in Quaranfil, Egypt, in 1953. It has subsequently been isolated in multiple geographic areas from ticks and birds. We used high-throughput sequencing to classify QRFV as a novel orthomyxovirus. The genome of this virus is comprised of multiple RNA segments; five were completely sequenced. Proteins with limited amino acid similarity to conserved domains in polymerase (PA, PB1, and PB2) and hemagglutinin (HA) genes from known orthomyxoviruses were predicted to be present in four of the segments. The fifth sequenced segment shared no detectable similarity to any protein and is of uncertain function. The end-terminal sequences of QRFV are conserved between segments and are different from those of the known orthomyxovirus genera. QRFV is known to cross-react serologically with two other unclassified viruses, Johnston Atoll virus (JAV) and Lake Chad virus (LKCV). The complete open reading frames of PB1 and HA were sequenced for JAV, while a fragment of PB1 of LKCV was identified by mass sequencing. QRFV and JAV PB1 and HA shared 80% and 70% amino acid identity to each other, respectively; the LKCV PB1 fragment shared 83% amino acid identity with the corresponding region of QRFV PB1. Based on phylogenetic analyses, virion ultrastructural features, and the unique end-terminal sequences identified, we propose that QRFV, JAV, and LKCV comprise a novel genus of the family Orthomyxoviridae.

scholarly journals A Nymphalid-Infecting Group I Alphabaculovirus Isolated from the Major Passion Fruit Caterpillar Pest Dione juno juno (Lepidoptera: Nymphalidae)

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 602 ◽  
Author(s):  
Bergmann Morais Ribeiro ◽  
Ethiane Rozo dos Santos ◽  
Luana Beló Trentin ◽  
Leonardo Assis da Silva ◽  
Fernando Lucas de Melo ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Insect Pests ◽  
Open Reading Frames ◽  
Thymidylate Kinase ◽  
Orgyia Pseudotsugata ◽  
Group I ◽  
Reading Frames ◽  
Core Genes

Baculoviruses are capable of infecting a wide diversity of insect pests. In the 1990s, the Dione juno nucleopolyhedrovirus (DijuNPV) was isolated from larvae of the major passionfruit defoliator pest Dione juno juno (Nymphalidae) and described at ultrastructural and pathological levels. In this study, the complete genome sequence of DijuNPV was determined and analyzed. The circular genome presents 122,075 bp with a G + C content of 50.9%. DijuNPV is the first alphabaculovirus completely sequenced that was isolated from a nymphalid host and may represent a divergent species. It appeared closely related to Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) and other Choristoneura-isolated group I alphabaculoviruses. We annotated 153 open reading frames (ORFs), including a set of 38 core genes, 26 ORFs identified as present in lepidopteran baculoviruses, 17 ORFs unique in baculovirus, and several auxiliary genes (e.g., bro, cathepsin, chitinase, iap-1, iap-2, and thymidylate kinase). The thymidylate kinase (tmk) gene was present fused to a dUTPase (dut) gene in other baculovirus genomes. DijuNPV likely lost the dut portion together with the iap-3 homolog. Overall, the genome sequencing of novel alphabaculoviruses enables a wide understanding of baculovirus evolution.

scholarly journals Gene organization and complete sequence of the Hyphantria cunea nucleopolyhedrovirus genome

2006 ◽  
Vol 87 (9) ◽  
pp. 2549-2562 ◽  
Author(s):  
Motoko Ikeda ◽  
Masamitsu Shikata ◽  
Noriko Shirata ◽  
Sudawan Chaeychomsri ◽  
Michihiro Kobayashi
Keyword(s):  
Choristoneura Fumiferana ◽  
Complete Sequence ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Hyphantria Cunea ◽  
Orgyia Pseudotsugata ◽  
Group I ◽  
Close Phylogenetic Relationship ◽  
Autographa Californica Mnpv

The whole-genome sequence of the Hyphantria cunea nucleopolyhedrovirus (HycuNPV) was analysed. The entire nucleotide sequence of the HycuNPV genome was 132 959 bp long, with a G+C content of 45.1 mol%. A total of 148 open reading frames (ORFs) consisting of more than 50 aa were encoded by the genome. HycuNPV shares more than 122 ORFs with other lepidopteran group I NPVs, including Autographa californica MNPV, Bombyx mori NPV, Choristoneura fumiferana MNPV (CfMNPV), Choristoneura fumiferana defective NPV, Epiphyas postvittana MNPV and Orgyia pseudotsugata MNPV (OpMNPV). Six ORFs are identified as being unique to HycuNPV. Most of the HycuNPV ORFs showed higher similarity to CfMNPV and OpMNPV ORFs than to those of the other group I NPVs. HycuNPV encodes two conotoxin-like homologues (ctls), which are observed only in OpMNPV in group I NPVs. HycuNPV encodes three inhibitors of apoptosis (iaps), hycu-iap-1, hycu-iap-2 and hycu-iap-3, a feature that it shares only with CfMNPV. In addition, six homologous regions (hrs) are identified in the HycuNPV genome. These hrs are located in regions similar to those of the OpMNPV hrs, but different from most of the CfMNPV hrs. Based on the close phylogenetic relationship and conservation of group I NPV-specific genes, such as gp64, ie-2 and ptp-1, it is concluded that HycuNPV belongs to the group I NPVs and is most similar to CfMNPV or OpMNPV.

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