scholarly journals Broad-Host-Range Yersinia Phage PY100: Genome Sequence, Proteome Analysis of Virions, and DNA Packaging Strategy

2007 ◽  
Vol 190 (1) ◽  
pp. 332-342 ◽  
Author(s):  
Dominik Schwudke ◽  
Asgar Ergin ◽  
Kathrin Michael ◽  
Sven Volkmar ◽  
Bernd Appel ◽  
...  
Keyword(s):  
Host Range ◽  
Proteome Analysis ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Lytic Bacteriophage ◽  
Coding Region ◽  
Putative Gene ◽  
Packaging Strategy ◽  
Virion Particles ◽  
Tail Proteins

ABSTRACT PY100 is a lytic bacteriophage with a broad host range within the genus Yersinia. The phage forms plaques on strains of the three human pathogenic species Yersinia enterocolitica, Y. pseudotuberculosis, and Y. pestis at 37°C. PY100 was isolated from farm manure and intended to be used in phage therapy trials. PY100 has an icosahedral capsid containing double-stranded DNA and a contractile tail. The genome consists of 50,291 bp and is predicted to contain 93 open reading frames (ORFs). PY100 gene products were found to be homologous to the capsid proteins and proteins involved in DNA metabolism of the enterobacterial phage T1; PY100 tail proteins possess homologies to putative tail proteins of phage AaΦ23 of Actinobacillus actinomycetemcomitans. In a proteome analysis of virion particles, 15 proteins of the head and tail structures were identified by mass spectrometry. The putative gene product of ORF2 of PY100 shows significant homology to the gene 3 product (small terminase subunit) of Salmonella phage P22 that is involved in packaging of the concatemeric phage DNA. The packaging mechanism of PY100 was analyzed by hybridization and sequence analysis of DNA isolated from virion particles. Newly replicated PY100 DNA is cut initially at a pac recognition site, which is located in the coding region of ORF2.

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 Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

2003 ◽  
Vol 185 (17) ◽  
pp. 5220-5233 ◽  
Author(s):  
Eric S. Miller ◽  
John F. Heidelberg ◽  
Jonathan A. Eisen ◽  
William C. Nelson ◽  
A. Scott Durkin ◽  
...  
Keyword(s):  
Host Range ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Group I Introns ◽  
Repair Enzymes ◽  
Group I

ABSTRACT The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.

scholarly journals The Terminally Redundant, Nonpermuted Genome of Listeria Bacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria

2008 ◽  
Vol 190 (17) ◽  
pp. 5753-5765 ◽  
Author(s):  
Jochen Klumpp ◽  
Julia Dorscht ◽  
Rudi Lurz ◽  
Regula Bielmann ◽  
Matthias Wieland ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Host Range ◽  
Genome Structure ◽  
High Resolution Electron Microscopy ◽  
Open Reading Frames ◽  
Trna Genes ◽  
Broad Host Range ◽  
Gram Positive ◽  
Terminal Repeats ◽  
Sequence Relatedness

ABSTRACT Only little information on a particular class of myoviruses, the SPO1-like bacteriophages infecting low-G+C-content, gram-positive host bacteria (Firmicutes), is available. We present the genome analysis and molecular characterization of the large, virulent, broad-host-range Listeria phage A511. A511 contains a unit (informational) genome of 134,494 bp, encompassing 190 putative open reading frames (ORFs) and 16 tRNA genes, organized in a modular fashion common among the Caudovirales. Electron microscopy, enzymatic fragmentation analyses, and sequencing revealed that the A511 DNA molecule contains linear terminal repeats of a total of 3,125 bp, encompassing nine small putative ORFs. This particular genome structure explains why A511 is unable to perform general transduction. A511 features significant sequence homologies to Listeria phage P100 and other morphologically related phages infecting Firmicutes such as Staphylococcus phage K and Lactobacillus phage LP65. Equivalent but more-extensive terminal repeats also exist in phages P100 (∼6 kb) and K (∼20 kb). High-resolution electron microscopy revealed, for the first time, the presence of long tail fibers organized in a sixfold symmetry in these viruses. Mass spectrometry-based peptide fingerprinting permitted assignment of individual proteins to A511 structural components. On the basis of the data available for A511 and relatives, we propose that SPO1-like myoviruses are characterized by (i) their infection of gram-positive, low-G+C-content bacteria; (ii) a wide host range within the host bacterial genus and a strictly virulent lifestyle; (iii) similar morphology, sequence relatedness, and collinearity of the phage genome organization; and (iv) large double-stranded DNA genomes featuring nonpermuted terminal repeats of various sizes.

scholarly journals Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 894
Author(s):  
Pasquale Marmo ◽  
Maria Cristina Thaller ◽  
Gustavo Di Lallo ◽  
Lucia Henrici De Angelis ◽  
Noemi Poerio ◽  
...  
Keyword(s):  
Burst Size ◽  
Latency Period ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Lytic Bacteriophage ◽  
Coding Region ◽  
Narrow Host Range ◽  
Physiological Characterization ◽  
Wide Range ◽  
Valuable Compounds

Members of Sphingomonas genus have gained a notable interest for their use in a wide range of biotechnological applications, ranging from bioremediation to the production of valuable compounds of industrial interest. To date, knowledge on phages targeting Sphingomonas spp. are still scarce. Here, we describe and characterize a lytic bacteriophage, named vB_StuS_MMDA13, able to infect the Sphingomonas turrisvirgatae MCT13 type strain. Physiological characterization demonstrated that vB_StuS_MMDA13 has a narrow host range, a long latency period, a low burst size, and it is overall stable to both temperature and pH variations. The phage has a double-stranded DNA genome of 63,743 bp, with 89 open reading frames arranged in two opposite arms separated by a 1186 bp non-coding region and shows a very low global similarity to any other known phages. Interestingly, vB_StuS_MMDA13 is endowed with an original nucleotide modification biosynthetic gene cluster, which greatly differs from those of its most closely related phages of the Nipunavirus genus. vB_StuS_MMDA13 is the first characterized lytic bacteriophage of the Siphoviridae family infecting members of the Sphingomonas genus.

scholarly journals Genomic and Functional Characterization of the Modular Broad-Host-Range RA3 Plasmid, the Archetype of the IncU Group

2008 ◽  
Vol 74 (13) ◽  
pp. 4119-4132 ◽  
Author(s):  
Anna Kulinska ◽  
Magdalena Czeredys ◽  
Finbarr Hayes ◽  
Grazyna Jagura-Burdzy
Keyword(s):  
Host Range ◽  
Antibiotic Resistance Gene ◽  
Functional Characterization ◽  
Repetitive Sequences ◽  
Replication Initiation ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Broad Host Range ◽  
Conjugative Transfer ◽  
Stable Maintenance

ABSTRACT IncU plasmids are a distinctive group of mobile elements with highly conserved backbone functions and variable antibiotic resistance gene cassettes. The IncU archetype is conjugative plasmid RA3, whose sequence (45,909 bp) shows it to be a mosaic, modular replicon with a class I integron different from that of other IncU replicons. Functional analysis demonstrated that RA3 possesses a broad host range and can efficiently self-transfer, replicate, and be maintained stably in alpha-, beta-, and gammaproteobacteria. RA3 contains 50 open reading frames clustered in distinct functional modules. The replication module encompasses the repA and repB genes embedded in long repetitive sequences. RepA, which is homologous to antitoxin proteins from alpha- and gammaproteobacteria, contains a Cro/cI-type DNA-binding domain present in the XRE family of transcriptional regulators. The repA promoter is repressed by RepA and RepB. The minireplicon encompasses repB and the downstream repetitive sequence r1/r2. RepB shows up to 80% similarity to putative replication initiation proteins from environmental plasmids of beta- and gammaproteobacteria, as well as similarity to replication proteins from alphaproteobacteria and Firmicutes. Stable maintenance functions of RA3 are most like those of IncP-1 broad-host-range plasmids and comprise the active partitioning apparatus formed by IncC (ParA) and KorB (ParB), the antirestriction protein KlcA, and accessory stability components KfrA and KfrC. The RA3 origin of transfer was localized experimentally between the maintenance and conjugative-transfer operons. The putative conjugative-transfer module is highly similar in organization and in its products to transfer regions of certain broad-host-range environmental plasmids.

scholarly journals Isolation and characterization of broad host-range of bacteriophages infecting Cronobacter sakazakii and its biocontrol potential in dairy products

2021 ◽  
Vol 13 (3) ◽  
pp. 21-44
Author(s):  
Huaxiang Li ◽  
Xiao-jun Yang ◽  
Xiao-yan Zhu ◽  
Lu Gao ◽  
Sheng-qi Rao ◽  
...  
Keyword(s):  
Host Range ◽  
Dairy Products ◽  
Antibacterial Properties ◽  
Antibiotic Resistance Genes ◽  
Good Alternative ◽  
Open Reading Frames ◽  
Phage Library ◽  
Broad Host Range ◽  
Cronobacter Sakazakii ◽  
Isolation And Characterization

Cronobacter sakazakii (C. sakazakii) is an important pathogen contaminating dairy products (e.g., milk pow-der) and causes high mortality in infants. Bacteriophage as a potential biocontrol agent is a good alternative method for the control of this pathogen in dairy production and its environment. Thus, it is important to complete the C. sakazakii phage library by isolating and characterizing the broad host range of bacteriophage against C. sakazakii for control use. In this study, C. sakazakii strains from different sources were used as hosts to isolate and purify phages from human stool and sewage samples by double-layer plates. The biological characteristics, antibacterial properties, and genomes of these phages were then studied. Finally, ten virulent phages (EspYZU01–EspYZU10) infecting C. sakazakii were isolated and identified as belonging to the Myoviridae, Podoviridae, Tectivirus, and Stylovinidae families. Phage EspYZU08 presented the broadest host range and could infect all the five host strains of C. sakazakii. All 10 phages retained their infectivity at 50°C and pH 5–9. Both genomes of EspYZU05 and EspYZU08 were double-stranded DNAs with sizes of 41723 bp and 145582 bp, G+C contents of 55.69% and 46.75%, and open reading frames of 47 and 103, respectively. No toxins and antibiotic resistance genes were detected in both EspYZU05 and EspYZU08. Phage EspYZU08 and phage cocktail-3 (EspYZU01 + EspYZU03 + EspYZU08 + EspYZU09 + EspYZU10) presented excellent antibacterial efficacy for C. sakazakii in liquid broth and milk at 4°C, 25°C, and 37°C, suggesting that the phages in this study have great potential for the development of biocontrol agents against C. sakazakii in dairy and its processing environment.

scholarly journals Isolation of a New Broad-Host-Range IncQ-Like Plasmid, pTC-F14, from the Acidophilic Bacterium Acidithiobacillus caldus and Analysis of the Plasmid Replicon

2001 ◽  
Vol 183 (11) ◽  
pp. 3303-3309 ◽  
Author(s):  
Murray N. Gardner ◽  
Shelly M. Deane ◽  
Douglas E. Rawlings
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Host Range ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Autonomous Replication ◽  
Acidithiobacillus Caldus ◽  
Plasmid Replicon ◽  
High Amino Acid ◽  
Reading Frames

ABSTRACT A moderately thermophilic (45 to 50°C), highly acidophilic (pH 1.5 to 2.5), chemolithotrophic Acidithiobacillus caldusstrain, f, was isolated from a biooxidation process used to treat nickel ore. Trans-alternating field electrophoresis analysis of total DNA from the A. caldus cells revealed two plasmids of approximately 14 and 45 kb. The 14-kb plasmid, designated pTC-F14, was cloned and shown by replacement of the cloning vector with a kanamycin resistance gene to be capable of autonomous replication inEscherichia coli. Autonomous replication was also demonstrated in Pseudomonas putida andAgrobacterium tumefaciens LBA 4404, which suggested that pTC-F14 is a broad-host-range plasmid. Sequence analysis of the pTC-F14 replicon region revealed five open reading frames and a replicon organization like that of the broad-host-range IncQ plasmids. Three of the open reading frames encoded replication proteins which were most closely related to those of IncQ-like plasmid pTF-FC2 (amino acid sequence identities: RepA, 81%; RepB, 78%; RepC, 74%). However, the two plasmids were fully compatible and pTC-F14 represents a new IncQ-like plasmid replicon. Surprisingly, asymmetrical incompatibility was found with the less closely related IncQ plasmid R300B derivative pKE462 and the IncQ-like plasmid derivative pIE1108. Analysis of the pTC-F14 oriV region revealed five direct repeats consisting of three perfectly conserved 22-bp iterons flanked by iterons of 23 and 21 bp. Plasmid pTC-F14 had a copy number of 12 to 16 copies per chromosome in both E. coli, and A. caldus. The rep gene products of pTC-F14 and pTF-FC2 were unable to functionally complement each other'soriV regions, but replication occurred when the genes for each plasmid's own RepA, RepB, and RepC proteins were provided intrans. Two smaller open reading frames were found between the repB and repA genes of pTC-F14, which encode proteins with high amino acid sequence identity (PasA, 81%; PasB, 72%) to the plasmid addiction system of pTF-FC2. This is the second time a plasmid stability system of this type has been found on an IncQ-like plasmid.

scholarly journals Efficacy of a Broad Host Range Lytic Bacteriophage Against E. coli Adhered to Urothelium

2010 ◽  
Vol 62 (4) ◽  
pp. 1128-1132 ◽  
Author(s):  
Sanna Sillankorva ◽  
Dulce Oliveira ◽  
Alexandra Moura ◽  
Mariana Henriques ◽  
Alberta Faustino ◽  
...  
Keyword(s):  
Host Range ◽  
Broad Host Range ◽  
Lytic Bacteriophage ◽  
E Coli

Isolation and properties of a bacteriophage lytic for a wide range of pseudomonads

1971 ◽  
Vol 17 (5) ◽  
pp. 677-682 ◽  
Author(s):  
R. A. Kelln ◽  
R. A. J. Warren
Keyword(s):  
Latent Period ◽  
Pseudomonas Fluorescens ◽  
Host Range ◽  
Burst Size ◽  
Broad Host Range ◽  
Lytic Bacteriophage ◽  
Bacterial Strains ◽  
Short Tail ◽  
Wide Range ◽  
Different Strains

The lytic bacteriophage ø-S1 was isolated from sewage using a strain of Pseudomonas fluorescens as host. It had a hexagonal head 60 nm in diameter and a short tail 30 nm long. ø-S1 had a broad host range, lysing strains from 10 biotypes of Pseudomonads. Although the latent period was fairly constant for the bacterial strains tested, the burst size varied considerably. The rate of adsorption of the phage to different strains also varied considerably.

Sign in / Sign up

Export Citation Format

Share Document