scholarly journals Analysis of the genome of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV-19) and of the high genomic heterogeneity in group II nucleopolyhedroviruses

2008 ◽  
Vol 89 (5) ◽  
pp. 1202-1211 ◽  
Author(s):  
José Luiz Caldas Wolff ◽  
Fernando Hercos Valicente ◽  
Renata Martins ◽  
Juliana Velasco de Castro Oliveira ◽  
Paolo Marinho de Andrade Zanotto
Keyword(s):  
Spodoptera Frugiperda ◽  
Point Mutations ◽  
Open Reading Frames ◽  
Temporal Organization ◽  
Agrotis Segetum ◽  
Gene Gain ◽  
Physical Maps ◽  
Polyadenylation Sites ◽  
Group Ii ◽  
Reading Frames

The genome of the most virulent among 22 Brazilian geographical isolates of Spodoptera frugiperda nucleopolyhedrovirus, isolate 19 (SfMNPV-19), was completely sequenced and shown to comprise 132 565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-19 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-19 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-19 were conserved in the closely related Spodoptera exigua NPV (SeMNPV) and Agrotis segetum NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group II NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group II had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60 % of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

scholarly journals The Moraxella catarrhalis Immunoglobulin D-Binding Protein MID Has Conserved Sequences and Is Regulated by a Mechanism Corresponding to Phase Variation

2003 ◽  
Vol 185 (7) ◽  
pp. 2285-2295 ◽  
Author(s):  
Andrea Möllenkvist ◽  
Therése Nordström ◽  
Christer Halldén ◽  
Jens Jørgen Christensen ◽  
Arne Forsgren ◽  
...  
Keyword(s):  
Moraxella Catarrhalis ◽  
Point Mutations ◽  
Phase Variation ◽  
The United States ◽  
Open Reading Frames ◽  
Peptide Sequence ◽  
Transcriptional Level ◽  
Signal Peptide Sequence ◽  
Immunoglobulin D ◽  
Reading Frames

ABSTRACT The prevalence of the Moraxella catarrhalis immunoglobulin D (IgD)-binding outer membrane protein MID and its gene was determined in 91 clinical isolates and in 7 culture collection strains. Eighty-four percent of the clinical Moraxella strains expressed MID-dependent IgD binding. The mid gene was detected in all strains as revealed by homology of the signal peptide sequence and a conserved area in the 3′ end of the gene. When MID proteins from five different strains were compared, an identity of 65.3 to 85.0% and a similarity of 71.2 to 89.1% were detected. Gene analyses showed several amino acid repeat motifs in the open reading frames, and MID could be called a putative autotransport protein. Interestingly, homopolymeric {polyguanine [poly(G)]} tracts were detected at the 5′ ends within the open reading frames. By flow cytometry, using human IgD and fluorescein isothiocyanate-conjugated anti-IgD polyclonal antibodies, most strains showed two peaks: one high- and one low-intensity peak. All isolates expressing high levels of MID had 1, 2, or 3 triplets of G's in their poly(G) tracts, while strains not expressing MID had 4, 7, 8, or 10 G’s in their poly(G) tracts or point mutations causing a putative preterminated translation. Northern blot analysis revealed that the mid gene was regulated at the transcriptional level. Experiments with nonclumping variants of M. catarrhalis proved that bacteria lost their MID expression by removing a G in their poly(G) tracts. Moraxella strains isolated from the nasopharynx or from blood and sputum specimens expressed MID at approximately the same frequency. In addition, no variation was observed between strains of different geographical origins (Australia, Europe, Japan, or the United States). MID and the mid gene were found solely in M. catarrhalis, whereas related Neisseria and Moraxella species did not express MID. Taken together, MID appears to be a conserved protein that can be found in essentially all M. catarrhalis strains. Furthermore, MID is governed by poly(G) tracts when bacteria undergo phase variation.

scholarly journals Functional Importance of Deletion Mutant Genotypes in an Insect Nucleopolyhedrovirus Population

2005 ◽  
Vol 71 (8) ◽  
pp. 4254-4262 ◽  
Author(s):  
Oihane Simón ◽  
Trevor Williams ◽  
Miguel López-Ferber ◽  
Primitivo Caballero
Keyword(s):  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
Genotypic Diversity ◽  
Open Reading Frames ◽  
Median Lethal Concentration ◽  
Functional Importance ◽  
Positive Interaction ◽  
Reading Frame ◽  
Genomic Deletions ◽  
Reading Frames

ABSTRACT A Nicaraguan isolate of a nucleopolyhedrovirus (SfNIC) that attacks the fall armyworm, Spodoptera frugiperda, survives as a mixture of nine genotypes (SfNIC A to I) that all present genomic deletions, except variant B (complete genotype). Sequencing of cloned restriction fragments revealed that genotypic variants lack between 5 and 16 of the open reading frames present in a contiguous sequence of 18 kb of the SfNIC genome. The absence of oral infectivity of SfNIC-C and -D variants is related to the deletion of the pif and/or pif-2 gene, while that of SfNIC-G remains unexplained. The presence of open reading frame 10, homolog of Se030, also appeared to influence pathogenicity in certain variants. Previous studies demonstrated a significant positive interaction between genotypes B and C. We compared the median lethal concentration of single genotypes (A, B, C, D, and F) and co-occluded genotype mixtures (B+A, B+D, B+F, A+C, and F+C in a 3:1 ratio). Mixtures B+A and B+D showed increased pathogenicity, although only B+D restored the activity of the mixture to that of the natural population. Mixtures of two deletion variants (A+C and F+C) did not show interactions in pathogenicity. We conclude that minority genotypes have an important influence on the overall pathogenicity of the population. These results clearly demonstrate the value of retaining genotypic diversity in virus-based bioinsecticides.

scholarly journals Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment

2009 ◽  
Vol 75 (24) ◽  
pp. 7663-7673 ◽  
Author(s):  
Pilar García ◽  
Beatriz Martínez ◽  
José María Obeso ◽  
Rob Lavigne ◽  
Rudi Lurz ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Recombination ◽  
Point Mutations ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Functional Genomic Analysis ◽  
Replication Point ◽  
Terminal Amino ◽  
Functional Analyses ◽  
Reading Frames

ABSTRACT The genomes of the two lytic mutant Staphylococcus aureus bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (cos) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the S. aureus-infecting phages.

scholarly journals Genome sequence of an enhancin gene-rich nucleopolyhedrovirus (NPV) from Agrotis segetum: collinearity with Spodoptera exigua multiple NPV

2006 ◽  
Vol 87 (3) ◽  
pp. 537-551 ◽  
Author(s):  
Agata K. Jakubowska ◽  
Sander A. Peters ◽  
Jadwiga Ziemnicka ◽  
Just M. Vlak ◽  
Monique M. van Oers
Keyword(s):  
Genome Sequence ◽  
Spodoptera Exigua ◽  
Open Reading Frames ◽  
Agrotis Segetum ◽  
Coding Regions ◽  
Baculovirus Gene ◽  
Homologous Genes ◽  
A Genome ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

The genome sequence of a Polish isolate of Agrotis segetum nucleopolyhedrovirus (AgseNPV-A) was determined and analysed. The circular genome is composed of 147 544 bp and has a G+C content of 45·7 mol%. It contains 153 putative, non-overlapping open reading frames (ORFs) encoding predicted proteins of more than 50 aa, together making up 89·8 % of the genome. The remaining 10·2 % of the DNA constitutes non-coding regions and homologous-repeat regions. One hundred and forty-three AgseNPV-A ORFs are homologues of previously reported baculovirus gene sequences. There are ten unique ORFs and they account for 3 % of the genome in total. All 62 lepidopteran baculovirus genes, including the 29 core baculovirus genes, were found in the AgseNPV-A genome. The gene content and gene order of AgseNPV-A are most similar to those of Spodoptera exigua (Se) multiple NPV and their shared homologous genes are 100 % collinear. Three putative enhancin genes were identified in the AgseNPV-A genome. In phylogenetic analysis, the AgseNPV-A enhancins form a cluster separated from enhancins of the Mamestra species NPVs.

scholarly journals Soluble Methane Monooxygenase Gene Clusters from Trichloroethylene-Degrading Methylomonas sp. Strains and Detection of Methanotrophs during In Situ Bioremediation

1999 ◽  
Vol 65 (12) ◽  
pp. 5198-5206 ◽  
Author(s):  
Toru Shigematsu ◽  
Satoshi Hanada ◽  
Masahiro Eguchi ◽  
Yoichi Kamagata ◽  
Takahiro Kanagawa ◽  
...  
Keyword(s):  
Sequence Data ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Soluble Methane Monooxygenase ◽  
Group I ◽  
Monooxygenase Gene ◽  
Group Ii ◽  
Reading Frames

ABSTRACT The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment fromMethylomonas sp. strain KSWIII and a 7.5-kbSalI fragment from Methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporiumOB3b and Methylocystis sp. strain M in the group II methanotrophs. Based on the sequence data of sMMO genes of our strains and other methanotrophs, we designed a new PCR primer to amplify sMMO gene fragments of all the known methanotrophs harboring themmoX gene. The primer set was successfully used for detecting methanotrophs in the groundwater of trichloroethylene-contaminated sites during in situ-biostimulation treatments.

scholarly journals Transcription termination signals in the nin region of bacteriophage lambda: identification of Rho-dependent termination regions.

Genetics ◽  
1995 ◽  
Vol 140 (3) ◽  
pp. 875-887 ◽  
Author(s):  
S W Cheng ◽  
D L Court ◽  
D I Friedman
Keyword(s):  
Transcription Termination ◽  
Bacteriophage Lambda ◽  
Point Mutations ◽  
Open Reading Frames ◽  
Deletion Analysis ◽  
Testing System ◽  
Transcription Antitermination ◽  
Termination Activity ◽  
Phage Growth ◽  
Reading Frames

Abstract The approximately 3-kb nin region of bacteriophage lambda, located between genes P and Q contains transcription termination signals as well as 10 open reading frames. Deletions in the nin region frees phage growth from dependence on the lambda-encoded N-transcription antitermination system, conferring a Nin phenotype (N-independence). A subregion of nin, roc, is defined by a 1.9-kb deletion (delta roc) which partially frees lambda growth from the requirement for N antitermination. The roc region has strong transcription termination activity as assayed by a plasmid-based terminator testing system. We report the following features of the roc region: the biologically significant terminators in the roc region are Rho dependent, deletion analysis located the biologically significant termination signals to a 1.2 kb-segment of roc, and analysis of other deletions and point mutations in the roc region suggested at least two biologically significant regions of termination, tR3 (extending from bp 42020 to 42231) and tR4 (extending from bp 42630 to 42825).

scholarly journals Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts

2019 ◽  
Author(s):  
Alexander M. Price ◽  
Katharina E. Hayer ◽  
Daniel P. Depledge ◽  
Angus C. Wilson ◽  
Matthew D. Weitzman
Keyword(s):  
Rna Sequencing ◽  
Open Reading Frames ◽  
Short Read ◽  
Sequencing Technologies ◽  
Protein Functions ◽  
Long Read ◽  
Cleavage And Polyadenylation ◽  
Polyadenylation Sites ◽  
Splice Junctions ◽  
Reading Frames

AbstractAdenovirus is a common human pathogen that relies on host cell processes for production and processing of viral RNA. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. The canonical viral early and late RNA cassettes were confirmed, but analysis of splice junctions within long RNA reads revealed an additional 20 novel viral transcripts. These RNAs include seven new splice junctions which lead to expression of canonical open reading frames (ORF), as well as 13 transcripts encoding for messages that potentially alter protein functions through truncations or the fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.

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