scholarly journals Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus

2021 ◽  
Vol 9 (3) ◽  
pp. 668
Author(s):  
Emilija Žukauskienė ◽  
Monika Šimoliūnienė ◽  
Lidija Truncaitė ◽  
Martynas Skapas ◽  
Algirdas Kaupinis ◽  
...  
Keyword(s):  
Single Species ◽  
Comparative Sequence Analysis ◽  
Open Reading Frames ◽  
Cold Adapted ◽  
Double Stranded Dna ◽  
Protein Encoding ◽  
The Family ◽  
Close Relationship ◽  
Phage Propagation ◽  
Encoding Genes

A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents.

scholarly journals Pantoea agglomerans-Infecting Bacteriophage vB_PagS_AAS21: A Cold-Adapted Virus Representing a Novel Genus within the Family Siphoviridae

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 479
Author(s):  
Monika Šimoliūnienė ◽  
Lidija Truncaitė ◽  
Emilija Petrauskaitė ◽  
Aurelija Zajančkauskaitė ◽  
Rolandas Meškys ◽  
...  
Keyword(s):  
Comparative Sequence Analysis ◽  
Pantoea Agglomerans ◽  
Open Reading Frames ◽  
Cold Adapted ◽  
Host Interactions ◽  
A Genome ◽  
Protein Encoding ◽  
The Family ◽  
Phage Propagation ◽  
Encoding Genes

A novel cold-adapted siphovirus, vB_PagS_AAS21 (AAS21), was isolated in Lithuania using Pantoea agglomerans as the host for phage propagation. AAS21 has an isometric head (~85 nm in diameter) and a non-contractile flexible tail (~174 × 10 nm). With a genome size of 116,649 bp, bacteriophage AAS21 is the largest Pantoea-infecting siphovirus sequenced to date. The genome of AAS21 has a G+C content of 39.0% and contains 213 putative protein-encoding genes and 29 genes for tRNAs. A comparative sequence analysis revealed that 89 AAS21 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 63 AAS21 ORFs were functionally annotated, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. Proteomic analysis led to the experimental identification of 19 virion proteins, including 11 that were predicted by bioinformatics approaches. Based on comparative phylogenetic analysis, AAS21 cannot be assigned to any genus currently recognized by ICTV and may represents a new branch of viruses within the family Siphoviridae.

scholarly journals Pantoea Bacteriophage vB_PagS_Vid5: A Low-Temperature Siphovirus That Harbors a Cluster of Genes Involved in the Biosynthesis of Archaeosine

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 583 ◽  
Author(s):  
Eugenijus Šimoliūnas ◽  
Monika Šimoliūnienė ◽  
Laura Kaliniene ◽  
Aurelija Zajančkauskaitė ◽  
Martynas Skapas ◽  
...  
Keyword(s):  
Low Temperature ◽  
Comparative Sequence Analysis ◽  
Open Reading Frames ◽  
Host Interactions ◽  
Protein Encoding ◽  
The Family ◽  
Virion Morphogenesis ◽  
Phage Propagation ◽  
Encoding Genes ◽  
Reading Frames

A novel low-temperature siphovirus, vB_PagS_Vid5 (Vid5), was isolated in Lithuania using Pantoea agglomerans isolate for the phage propagation. The 61,437 bp genome of Vid5 has a G–C content of 48.8% and contains 99 probable protein encoding genes and one gene for tRNASer. A comparative sequence analysis revealed that 46 out of 99 Vid5 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 33 Vid5 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a cluster of genes possibly involved in the biosynthesis of 7-deazaguanine derivatives was identified. Notably, one of these genes encodes a putative preQ0/preQ1 transporter, which has never been detected in bacteriophages to date. A proteomic analysis led to the experimental identification of 11 virion proteins, including nine that were predicted by bioinformatics approaches. Based on the phylogenetic analysis, Vid5 cannot be assigned to any genus currently recognized by ICTV, and may represent a new one within the family of Siphoviridae.

scholarly journals Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-deoxy-7-amido-7-deazaguanosine-Modified DNA

2021 ◽  
Vol 22 (14) ◽  
pp. 7333
Author(s):  
Monika Šimoliūnienė ◽  
Emilija Žukauskienė ◽  
Lidija Truncaitė ◽  
Liang Cui ◽  
Geoffrey Hutinet ◽  
...  
Keyword(s):  
Comparative Sequence Analysis ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Host Interactions ◽  
Double Stranded Dna ◽  
New Information ◽  
Modified Dna ◽  
Phage Dna ◽  
Virion Morphogenesis ◽  
Phage Propagation

A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage–host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC–MS/MS analysis indicates 2′-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.

scholarly journals Microarray Analysis of Paramecium bursaria Chlorella Virus 1 Transcription

2009 ◽  
Vol 84 (1) ◽  
pp. 532-542 ◽  
Author(s):  
Giane M. Yanai-Balser ◽  
Garry A. Duncan ◽  
James D. Eudy ◽  
Dong Wang ◽  
Xiao Li ◽  
...  
Keyword(s):  
Life Cycle ◽  
Virus Infection ◽  
Dna Synthesis ◽  
Comprehensive Evaluation ◽  
Paramecium Bursaria ◽  
Chlorella Virus ◽  
Double Stranded Dna ◽  
Unicellular Green Alga ◽  
Protein Encoding ◽  
Encoding Genes

ABSTRACT Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large double-stranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: (i) the PBCV-1 replication cycle is temporally programmed and regulated; (ii) 360 (99%) of the arrayed PBCV-1 CDSs were expressed at some time in the virus life cycle in the laboratory; (iii) 227 (62%) of the CDSs were expressed before virus DNA synthesis begins; (iv) these 227 CDSs were grouped into two classes: 127 transcripts disappeared prior to initiation of virus DNA synthesis (considered early), and 100 transcripts were still detected after virus DNA synthesis begins (considered early/late); (v) 133 (36%) of the CDSs were expressed after virus DNA synthesis begins (considered late); and (vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor, aphidicolin, prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 life cycle.

scholarly journals Genome Sequence of the Broad-Host-Range Pseudomonas Phage Φ-S1

2012 ◽  
Vol 86 (18) ◽  
pp. 10239-10239 ◽  
Author(s):  
Sanna Sillankorva ◽  
Andrew M. Kropinski ◽  
Joana Azeredo
Keyword(s):  
Host Range ◽  
Genome Sequence ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Content Type ◽  
Double Stranded Dna ◽  
The Family ◽  
Reading Frames

The broad-host-range lyticPseudomonasphage Φ-S1 possess a 40,192 bp double-stranded DNA (dsDNA) genome of 47 open reading frames (ORFs) and belongs to the familyPodoviridae, subfamilyAutographivirinae, genusT7likevirus.

scholarly journals A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Thomas W. Allain ◽  
Grant D. Stentiford ◽  
David Bass ◽  
Donald C. Behringer ◽  
Jamie Bojko
Keyword(s):  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Open Reading Frames ◽  
The Novel ◽  
Dna Viruses ◽  
Gene Synteny ◽  
Double Stranded Dna ◽  
The Family ◽  
Novel Virus ◽  
Dikerogammarus Haemobaphes

Abstract The Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae).

scholarly journals The Characteristics and Genome Analysis of vB_AviM_AVP, the First Phage Infecting Aerococcus viridans

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 104 ◽  
Author(s):  
Hengyu Xi ◽  
Jiaxin Dai ◽  
Yigang Tong ◽  
Mengjun Cheng ◽  
Feiyang Zhao ◽  
...  
Keyword(s):  
Opportunistic Pathogen ◽  
Nucleotide Metabolism ◽  
Open Reading Frames ◽  
Gene Products ◽  
New Class ◽  
Aerococcus Viridans ◽  
Double Stranded Dna ◽  
The Family ◽  
Reading Frames ◽  
Human And Animal Diseases

Aerococcus viridans is an opportunistic pathogen that is clinically associated with various human and animal diseases. In this study, the first identified A. viridans phage, vB_AviM_AVP (abbreviated as AVP), was isolated and studied. AVP belongs to the family Myoviridae. AVP harbors a double-stranded DNA genome with a length of 133,806 bp and a G + C content of 34.51%. The genome sequence of AVP showed low similarity (<1% identity) to those of other phages, bacteria, or other organisms in the database. Among 165 predicted open reading frames (ORFs), there were only 69 gene products exhibiting similarity (≤65% identity) to proteins of known functions in the database. In addition, the other 36 gene products did not match any viral or prokaryotic sequences in any publicly available database. On the basis of the putative functions of the ORFs, the genome of AVP was divided into three modules: nucleotide metabolism and replication, structural components, and lysis. A phylogenetic analysis of the terminase large subunits and capsid proteins indicated that AVP represents a novel branch of phages. The observed characteristics of AVP indicate that it represents a new class of phages.

scholarly journals Complete Genome Analysis of a Novel Alcaligenes Faecalis Phage vB_Af_QDWS595

2021 ◽  
Author(s):  
Yujie Jing ◽  
Hong Lin ◽  
Houqi Ning ◽  
Jingxue Wang
Keyword(s):  
Genome Analysis ◽  
Gc Content ◽  
Alcaligenes Faecalis ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
Double Stranded Dna ◽  
Phylogeny Analysis ◽  
The Family ◽  
Complete Genome Analysis ◽  
Reading Frames

Abstract A novel lytic phage named vB_Af_QDWS595 against Alcaligenes faecalis was isolated and characterized in this study. The genome of phage vB_Af_QDWS595 was sequenced and analyzed, and the result revealed that the phage contained a 88,795 bp of circular double-stranded DNA with 41.12% of GC content. There were 74 putative open reading frames (ORFs) and 11 tRNAs predicted in genome of phage vB_Af_QDWS595. Phenotype and phylogeny analysis indicated that this phage might be a new member within the family Schitoviridae. Phage vB_Af_QDWS595 is the first sequenced phage against Alcaligenes faecalis to the best of our knowledge.

scholarly journals Characterization and Complete Genome Analysis of a Novel Escherichia Phage, vB_EcoM-RPN242

2022 ◽  
Author(s):  
Napakhwan Imklin ◽  
Pattaraporn Sripras ◽  
Narut Thanantong ◽  
Porntippa Lekcharoensuk ◽  
Rujikan Nasanit
Keyword(s):  
Escherichia Coli ◽  
Nucleotide Sequence ◽  
Sequence Comparison ◽  
The Novel ◽  
Base Pairs ◽  
E Coli ◽  
Double Stranded Dna ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Complete Genome Analysis

Abstract The novel Escherichia phage vB_EcoM-RPN242 was isolated using a strain of Escherichia coli host originated from a diarrheal piglet. The phage was able to form plaques on the E. coli lawn at 15−45ºC. Moreover, it was stable over a wide pH (4−10) and temperature (4−70ºC) range. The vB_EcoM-RPN242 genome was found to be a linear, double-stranded DNA consisting of 154,840 base pairs. There were 195 protein-encoding genes and 2 tRNAs detected in the genome, however no unfavorable gene was found. According to the overall nucleotide sequence comparison, the vB_EcoM-RPN242 possibly represents a new phage species in the genus Agtrevirus.

scholarly journals Contribution of Penicillin-Binding Protein Homologs to Antibiotic Resistance, Cell Morphology, and Virulence of Listeria monocytogenes EGDe

2006 ◽  
Vol 50 (8) ◽  
pp. 2824-2828 ◽  
Author(s):  
Caitriona M. Guinane ◽  
Paul D. Cotter ◽  
R. Paul Ross ◽  
Colin Hill
Keyword(s):  
Listeria Monocytogenes ◽  
Cell Morphology ◽  
Insertional Mutagenesis ◽  
Binding Protein ◽  
Open Reading Frames ◽  
Penicillin Binding Protein ◽  
Virulence Potential ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Reading Frames

ABSTRACT Seven open reading frames, annotated as potential penicillin-binding-protein-encoding genes (lmo0441, lmo0540, lmo1438, lmo1892, lmo2039, lmo2229, and lmo2754), were targeted for insertional mutagenesis in Listeria monocytogenes EGDe. These genes were found to contribute in various degrees to β-lactam resistance, cell morphology, or the virulence potential of this organism.

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