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 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.

Complete Genome of a Novel Lytic Vibrio parahaemolyticus Phage VPp1 and Characterization of Its Endolysin for Antibacterial Activities

2018 ◽  
Vol 81 (7) ◽  
pp. 1117-1125 ◽  
Author(s):  
MENGZHE LI ◽  
YANQIU JIN ◽  
HONG LIN ◽  
JINGXUE WANG ◽  
XIUPING JIANG
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Foodborne Pathogen ◽  
Antibacterial Activities ◽  
Nucleotide Metabolism ◽  
Open Reading Frames ◽  
Bacterial Cells ◽  
Control Groups ◽  
Double Stranded Dna ◽  
Reading Frames

ABSTRACT Vibrio parahaemolyticus is an important foodborne pathogen that is generally transmitted via raw or undercooked seafood. Endolysins originating from bacteriophages offer a new way to control bacterial pathogens. The objectives of this study were to sequence a novel lytic V. parahaemolyticus phage VPp1 and determine the antibacterial activities of the recombinant endolysin (LysVPp1) derived from this phage. The complete VPp1 genome contained a double-stranded DNA of 50,431 bp with a total G+C content of 41.35%. The genome was predicted to encode 67 open reading frames (ORFs), which were organized as nucleotide metabolism, replication, structure, packaging, lysis, and some additional functions. Two tRNAs were encoded to carry anticodons UGG and CCA. Among the functional proteins, ORF33 was deduced to encode endolysin, whereas no holin/antiholin or Rz/Rz1 lysis gene equivalents were found in the VPp1 genome. ORF33 was cloned and expressed. The endolysin LysVPp1 could lyse 9 of 12 V. parahaemolyticus strains, showing its relatively broader host spectrum than phage VPp1, which lysed only 3 of 12 V. parahaemolyticus strains. Furthermore, for EDTA-pretreated bacterial cells, the optical density of the LysVPp1 treatment group decreased by 0.4 at 450 nm, compared with less than 0.1 in control groups, demonstrating enhanced hydrolytic properties. These results contribute to the potential for development of novel enzybiotics for controlling V. parahaemolyticus.

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 Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

2020 ◽  
Author(s):  
Jacob B Jørgensen ◽  
Amaru M Djuurhus ◽  
Alexander B. Carstens ◽  
Witold Kot ◽  
Cindy E. Morris ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
New Genus ◽  
Open Reading Frames ◽  
Genomic Comparison ◽  
Double Stranded Dna ◽  
The Family ◽  
Genomic Characterization ◽  
Reading Frames

AbstractThree phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

scholarly journals Whole-Genome Sequence of Oryctes rhinoceros Nudivirus from Riau Province, Indonesia

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Yudistira Wahyu Kurnia ◽  
Zulfikar Achmad Tanjung ◽  
Condro Utomo ◽  
Mohammad Naim ◽  
Elizabeth Caroline Situmorang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Dna Virus ◽  
Content Type ◽  
Oryctes Rhinoceros ◽  
Double Stranded Dna ◽  
The Family ◽  
Total Dna ◽  
Reading Frames

A double-stranded DNA virus, Oryctes rhinoceros nudivirus (OrNV), was detected in the total DNA of diseased larvae of O. rhinoceros in Riau Province, Indonesia. The complete genome sequence was 124,926 bp long and encodes 123 open reading frames (ORFs). This strain belongs to the family Nudiviridae and was designated LiboV.

Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

2021 ◽  
Author(s):  
Yang Sun ◽  
Yan qiong Li ◽  
Wen han Dong ◽  
Ai li Sun ◽  
Ning wei Chen ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Rna Virus ◽  
Dsrna Virus ◽  
Open Reading Frames ◽  
The Family ◽  
Significant Amino Acid Sequence ◽  
Overlapping Open Reading Frames ◽  
Significant Amino Acid ◽  
Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

scholarly journals Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

2011 ◽  
Vol 77 (10) ◽  
pp. 3443-3450 ◽  
Author(s):  
Evelien M. Adriaenssens ◽  
Pieter-Jan Ceyssens ◽  
Vincent Dunon ◽  
Hans-Wolfgang Ackermann ◽  
Johan Van Vaerenbergh ◽  
...  
Keyword(s):  
Soil Samples ◽  
Pantoea Agglomerans ◽  
Open Reading Frames ◽  
Human Pathogen ◽  
Content Type ◽  
Host Diversity ◽  
Double Stranded Dna ◽  
Opportunistic Human Pathogen ◽  
Reading Frames

ABSTRACTPantoea agglomeransis a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight ofP. agglomeransare lytic phages, isolated from soil samples, belonging to thePodoviridaeand are the firstPantoeaphages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,032 bp and 44,546 bp, respectively) encode 57 and 55 open reading frames (ORFs). Based on the presence of an RNA polymerase in their genomes and their overall genome architecture, these phages should be classified in the subfamily of theAutographivirinae, within the genus of the “phiKMV-like viruses.” Phylogenetic analysis of all the sequenced members of theAutographivirinaesupports the classification of phages LIMElight and LIMEzero as members of the “phiKMV-like viruses” and corroborates the subdivision into the different genera. These data expand the knowledge ofPantoeaphages and illustrate the wide host diversity of phages within the “phiKMV-like viruses.”

scholarly journals Characterization of Two Virulent Phages of Lactobacillus plantarum

2012 ◽  
Vol 78 (24) ◽  
pp. 8719-8734 ◽  
Author(s):  
Mariángeles Briggiler Marcó ◽  
Josiane E. Garneau ◽  
Denise Tremblay ◽  
Andrea Quiberoni ◽  
Sylvain Moineau
Keyword(s):  
Lactobacillus Plantarum ◽  
Corn Silage ◽  
Open Reading Frames ◽  
High Identity ◽  
Content Type ◽  
Defense Systems ◽  
Double Stranded Dna ◽  
Type Phage ◽  
Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

scholarly journals The First Complete Papillomavirus Genome Characterized from a Marsupial Host: a Novel Isolate from Bettongia penicillata

2010 ◽  
Vol 84 (10) ◽  
pp. 5448-5453 ◽  
Author(s):  
Mark D. Bennett ◽  
Andrea Reiss ◽  
Hans Stevens ◽  
Elisabeth Heylen ◽  
Marc Van Ranst ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Double Stranded Dna ◽  
Bettongia Penicillata ◽  
European Hedgehog ◽  
Reading Frames

ABSTRACT The first fully sequenced papillomavirus (PV) of marsupials, tentatively named Bettongia penicillata papillomavirus type 1 (BpPV1), was detected in papillomas from a woylie (Bettongia penicillata ogilbyi). The circular, double-stranded DNA genome contains 7,737 bp and encodes 7 open reading frames (ORFs), E6, E7, E1, E2, E4, L2, and L1, in typical PV conformation. BpPV1 is a close-to-root PV with L1 and L2 ORFs most similar to European hedgehog PV and bandicoot papillomatosis carcinomatosis virus types 1 and 2 (BPCV1 and -2). It appears that the BPCVs arose by recombination between an ancient PV and an ancient polyomavirus more than 10 million years ago.

scholarly journals Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses

2004 ◽  
Vol 32 (2) ◽  
pp. 204-208 ◽  
Author(s):  
D. Prangishvili ◽  
R.A. Garrett
Keyword(s):  
Aquatic Ecosystems ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Open Reading Frames ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Sequence Patterns ◽  
Hydrothermal Environments ◽  
Homologous Orfs ◽  
Reading Frames

The remarkable diversity of the morphologies of viruses found in terrestrial hydrothermal environments with temperatures >80°C is unprecedented for aquatic ecosystems. The best-studied viruses from these habitats have been assigned to novel viral families: Fuselloviridae, Lipothrixviridae and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine fever virus and Chlorella viruses. Sequence patterns at the ends of the linear genome of the lipothrixvirus AFV1 are reminiscent of the telomeric ends of linear eukaryal chromosomes and suggest that a primitive telomeric mechanism operates in this virus.

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