scholarly journals Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jian Zeng ◽  
Yan Wang ◽  
Ju Zhang ◽  
Shixing Yang ◽  
Wen Zhang
Keyword(s):  
Gc Content ◽  
Cloacal Swab ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Viral Metagenomics ◽  
Toxin Gene ◽  
Microbial Genomes ◽  
The Family ◽  
Zonula Occludens Toxin ◽  
Reference Strains

AbstractMembers of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.

scholarly journals Isolation and Characterization of a Bacteriophage Infecting Pseudomonas Aeruginosa and Its Application as a Potential Decontaminating Agent

2021 ◽  
Author(s):  
Sonika Sharma ◽  
Sibnarayan Datta ◽  
Soumya Chatterjee ◽  
Moumita Dutta ◽  
Jhuma Samanta ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Burst Size ◽  
Gc Content ◽  
Alginate Beads ◽  
Open Reading Frames ◽  
Isolation And Characterization ◽  
The Family ◽  
Infected Cells

Abstract To treat antibiotic resistance bacteria, bacteriophage (also called 'phage') application has recently drawn considerable attention from researchers globally. Bacteria like Pseudomonas aeruginosa are known to be associated with nosocomial infections especially in patients with compromised immune systems. In the present work, phage against P. aeruginosa (named 'DRLP1') was isolated from wastewater, enriched and characterized. Morphologically DRLP1 belongs to the family Myoviridae with a high lytic ability. DRLP1 has a burst size of approximately 100 PFU/infected cells, a rapid adsorption time when supplemented with MgCl2, and has viability in a wide temperature range and pH. Genomic sequencing and bioinformatics analysis showed that the phage genome is linear double-stranded, 66,243 bp in length and have a GC content of 54.9%. the genome encodes 93 phage related ORFs open reading frames (ORFs). Phage stability in lyophilized state, adsorption study on sodium alginate beads, and in-vitro pathogen reduction assays were also investigated. Study carried out with artificially contaminated fomites suggests that this phage has the potential for application as a biological decontaminant agent against P. aeruginosa in different conditions.

scholarly journals Characterization and complete genome sequences of two novel variants of the family Closteroviridae from Chinese kiwifruit

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242362
Author(s):  
Xin Feng ◽  
Rui-lian Lai ◽  
Min-xia Gao ◽  
Wen-guang Chen ◽  
Ru-jian Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Organization ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Viral Genomes ◽  
Relationship Analysis ◽  
The Family ◽  
Novel Variants ◽  
Rapid Amplification

Two distinct closterovirus-like genome sequences (termed AdV-1 v1 and v2) were identified in Actinidia chinensis var. deliciosa ‘Miliang-1’ that had no disease symptoms using high-throughput sequencing. Using overlapping reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends, the genomic sequences of AdV-1 v1 and v2 were confirmed as 17,646 and 18,578 nucleotides in length, respectively. The two complete genomes contained 9 and 15 open reading frames, respectively, coding for proteins having domains typical of Closteroviridae, such as RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homolog (HSP70h) and coat protein (CP). Sequence analysis showed that the amino acid sequences of RdRp, HSP70h, and CP of the two variants exhibited high similarity (> 80%), while their genomic organization was somewhat different. This suggested that the two viral genomes identified here are variants of the family Closteroviridae in a single kiwifruit host. Furthermore, phylogenetic relationship analysis revealed that the two variants had a closer relationship with the unclassified virus Persimmon virus B (PeVB) and Actinidia virus 1 (AcV-1) than with other members of the family Closteroviridae, as did their genomic organization. It is speculated that the two variants, together with PeVB and AcV-1 belong to a new subfamily of Closteroviridae.

A Novel Lytic Phage SZW_AS01 of Human Gut Bacteria Alistipes Shahii

2021 ◽  
Author(s):  
Yanchen Li ◽  
Juntao Shen ◽  
Junyu Chen ◽  
Luofei Mo ◽  
Jieqiong Zhang ◽  
...  
Keyword(s):  
Large Subunit ◽  
Gc Content ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
Transmission Electron ◽  
Wastewater Samples ◽  
Myoviridae Family ◽  
Distinct Branch ◽  
Siphoviridae Family

Abstract Alisitipes phage SZW_AS01, a novel lytic phage that specifically infects Alistipes shahii, was isolated from wastewater samples in Shenzhen, China. The phage's genome consists of 45,392 bp, with a GC content of 47%. The genome encodes 56 putative open reading frames (ORFs) and 1 tRNA gene. Direct terminal repeats with a length of 55 bp are present at both ends of the genome. Phylogenetic analysis of the amino acid sequences of terminase large subunit shows that phage SZW_AS01 forms a distinct branch from the Siphoviridae family phages, but is far from the Podoviridae and Myoviridae family phages. Transmission electron microscopy confirmed that SZW_AS01 belongs to the Siphoviridae family. To the best of our knowledge, this is the first report of a lytic phage infecting bacteria in the Alistipes genus.

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 Sequence analysis and genomic organization of Aphid lethal paralysis virus: a new member of the family Dicistroviridae

2002 ◽  
Vol 83 (12) ◽  
pp. 3131-3138 ◽  
Author(s):  
M. van Munster ◽  
A. M. Dullemans ◽  
M. Verbeek ◽  
J. F. J. M. van den Heuvel ◽  
A. Clérivet ◽  
...  
Keyword(s):  
Rhopalosiphum Padi ◽  
Trialeurodes Vaporariorum ◽  
Aphid Species ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
The Family ◽  
Orf 5 ◽  
Sequence Similarities ◽  
Paralysis Virus ◽  
Reading Frames

The complete nucleotide sequence of the genomic RNA of an aphid-infecting virus, Aphid lethal paralysis virus (ALPV), has been determined. The genome is 9812 nt in length and contains two long open reading frames (ORFs), which are separated by an intergenic region of 163 nt. The first ORF (5′ ORF) is preceded by an untranslated leader sequence of 506 nt, while an untranslated region of 571 nt follows the second ORF (3′ ORF). The deduced amino acid sequences of the 5′ ORF and 3′ ORF products respectively showed similarity to the non-structural and structural proteins of members of the newly recognized genus Cripavirus (family Dicistroviridae). On the basis of the observed sequence similarities and identical genome organization, it is proposed that ALPV belongs to this genus. Phylogenetic analysis showed that ALPV is most closely related to Rhopalosiphum padi virus, and groups in a cluster with Drosophila C virus and Cricket paralysis virus, while the other members of this genus are more distantly related. Infectivity experiments showed that ALPV can not only infect aphid species but is also able to infect the whitefly Trialeurodes vaporariorum, extending its host range to another family of the order Hemiptera.

scholarly journals An Additional Regulatory Gene for Actinorhodin Production in Streptomyces lividans Involves a LysR-Type Transcriptional Regulator

1999 ◽  
Vol 181 (14) ◽  
pp. 4353-4364 ◽  
Author(s):  
Oscar H. Martínez-Costa ◽  
Angel J. Martín-Triana ◽  
Eduardo Martínez ◽  
Miguel A. Fernández-Moreno ◽  
Francisco Malpartida
Keyword(s):  
Streptomyces Coelicolor ◽  
Regulatory Gene ◽  
Streptomyces Lividans ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
The Family ◽  
The Right ◽  
Different Sources ◽  
Transcription Expression

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.

scholarly journals Complete Genome Sequence of a Phapecoctavirus Isolated from a Pigeon Cloacal Swab Sample

2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Anthony Khalifeh ◽  
Simona Kraberger ◽  
Daria Dziewulska ◽  
Tomasz Stenzel ◽  
Arvind Varsani
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Gc Content ◽  
Columba Livia ◽  
Cloacal Swab ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Reading Frames

ABSTRACT The complete genome sequence of a bacteriophage in the genus Phapecoctavirus (family Myoviridae) isolated from a cloacal swab specimen from a domestic pigeon (Columba livia f. domestica) was identified using a high-throughput sequencing approach. The genome is 150,892 bp with a GC content of 39.1%, containing 269 open reading frames and 11 tRNA genes.

scholarly journals Morphological and molecular evidence that Culex nigripalpus baculovirus is an unusual member of the family Baculoviridae

2001 ◽  
Vol 82 (2) ◽  
pp. 283-297 ◽  
Author(s):  
Bettina A. Moser ◽  
James J. Becnel ◽  
Susan E. White ◽  
Claudio Afonso ◽  
Gerald Kutish ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Gc Content ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Molecular Evidence ◽  
Culex Nigripalpus ◽  
Double Stranded Dna ◽  
The Family ◽  
Occlusion Bodies ◽  
Infected Cells

We present evidence that a newly discovered mosquito virus from Culex nigripalpus is an unusual member of the family Baculoviridae. Development of this virus was restricted to nuclei of midgut epithelial cells in the gastric caeca and posterior stomach. The globular occlusion bodies were not enveloped, measured around 400 nm in diameter, occurred exclusively in nuclei of infected cells and typically contained four, sometimes up to eight, virions. The developmental sequence involved two virion phenotypes: an occluded form (ODV) that initiated infection in the midgut epithelial cells, and a budded form that spread the infection in the midgut. Each ODV contained one rod-shaped enveloped nucleocapsid (40×200 nm). The double-stranded DNA genome was approximately 105–110 kbp with an estimated GC content of 52%. We have sequenced approximately one-third of the genome and detected 96 putative ORFs of 50 amino acids or more including several genes considered to be unique to baculoviruses. Phylogenetic analysis of the amino acid sequences of DNApol and p74 placed this virus in a separate clade from the genera Nucleopolyhedrovirus and Granulovirus. We provisionally assign this virus in the genus Nucleopolyhedrovirus, henceforth abbreviated as CuniNPV (for Culex nigripalpus nucleopolyhedrovirus), and suggest that, awaiting additional data to clarify its taxonomic status, it may be a member of a new genus within the family Baculoviridae.

scholarly journals Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail

2017 ◽  
Vol 91 (8) ◽  
Author(s):  
Laura Kaliniene ◽  
Eugenijus Šimoliūnas ◽  
Lidija Truncaitė ◽  
Aurelija Zajančkauskaitė ◽  
Juozas Nainys ◽  
...  
Keyword(s):  
Gc Content ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Tail Fiber ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Transmission Electron ◽  
The Family ◽  
Contractile Tail ◽  
Phage Propagation

ABSTRACTThis is the first report on a myophage that infectsArthrobacter. A novel virus, vB_ArtM-ArV1 (ArV1), was isolated from soil usingArthrobactersp. strain 68b for phage propagation. Transmission electron microscopy showed its resemblance to members of the familyMyoviridae: ArV1 has an isometric head (∼74 nm in diameter) and a contractile, nonflexible tail (∼192 nm). Phylogenetic and comparative sequence analyses, however, revealed that ArV1 has more genes in common with phages from the familySiphoviridaethan it does with any myovirus characterized to date. The genome of ArV1 is a linear, circularly permuted, double-stranded DNA molecule (71,200 bp) with a GC content of 61.6%. The genome includes 101 open reading frames (ORFs) yet contains no tRNA genes. More than 50% of ArV1 genes encode unique proteins that either have no reliable identity to database entries or have homologues only inArthrobacterphages, both sipho- and myoviruses. Using bioinformatics approaches, 13 ArV1 structural genes were identified, including those coding for head, tail, tail fiber, and baseplate proteins. A further 6 ArV1 ORFs were annotated as encoding putative structural proteins based on the results of proteomic analysis. Phylogenetic analysis based on the alignment of four conserved virion proteins revealed thatArthrobactermyophages form a discrete clade that seems to occupy a position somewhat intermediate between myo- and siphoviruses. Thus, the data presented here will help to advance our understanding of genetic diversity and evolution of phages that constitute the orderCaudovirales.IMPORTANCEBacteriophages, which likely originated in the early Precambrian Era, represent the most numerous population on the planet. Approximately 95% of known phages are tailed viruses that comprise three families:Podoviridae(with short tails),Siphoviridae(with long noncontractile tails), andMyoviridae(with contractile tails). Based on the current hypothesis, myophages, which may have evolved from siphophages, are thought to have first emerged among Gram-negative bacteria, whereas they emerged only later among Gram-positive bacteria. The results of the molecular characterization of myophage vB_ArtM-ArV1 presented here conform to the aforementioned hypothesis, since, at a glance, bacteriophage vB_ArtM-ArV1 appears to be a siphovirus that possesses a seemingly functional contractile tail. Our work demonstrates that such “chimeric” myophages are of cosmopolitan nature and are likely characteristic of the ecologically important soil bacterial genusArthrobacter.

scholarly journals The Bacteriophage pEp_SNUABM_08 Is a Novel Singleton Siphovirus with High Host Specificity for Erwinia pyrifoliae

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1231
Author(s):  
Sang Guen Kim ◽  
Eunjung Roh ◽  
Jungkum Park ◽  
Sib Sankar Giri ◽  
Jun Kwon ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Gc Content ◽  
Apple Orchard ◽  
Open Reading Frames ◽  
Plant Diseases ◽  
Lytic Bacteriophage ◽  
Limited Information ◽  
The Family ◽  
Public Repositories ◽  
Genome Information

Species belonging to the genus Erwinia are predominantly plant pathogens. A number of bacteriophages capable of infecting Erwinia have been used for the control of plant diseases such as fire blight. Public repositories provide the complete genome information for such phages, which includes genomes ranging from 30 kb to 350 kb in size. However, limited information is available regarding bacteriophages belonging to the family Siphoviridae. A novel lytic siphophage, pEp_SNUABM_08, which specifically infects Erwinia pyrifoliae, was isolated from the soil of an affected apple orchard in South Korea. A comprehensive genome analysis was performed using the Erwinia-infecting siphophage. The whole genome of pEp_SNUABM_08 comprised 62,784 bp (GC content, 57.24%) with 79 open reading frames. The genomic characteristics confirmed that pEp_SNUABM_08 is a singleton lytic bacteriophage belonging to the family Siphoviridae, and no closely related phages have been reported thus far. Our study not only characterized a unique phage, but also provides insight into the genetic diversity of Erwinia bacteriophages.

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