scholarly journals The Generalized Transducing Salmonella Bacteriophage ES18: Complete Genome Sequence and DNA Packaging Strategy

2005 ◽  
Vol 187 (3) ◽  
pp. 1091-1104 ◽  
Author(s):  
Sherwood R. Casjens ◽  
Eddie B. Gilcrease ◽  
Danella A. Winn-Stapley ◽  
Petra Schicklmaier ◽  
Horst Schmieger ◽  
...  
Keyword(s):  
Shigella Flexneri ◽  
Bioinformatic Analysis ◽  
Dna Packaging ◽  
Phage Group ◽  
Double Stranded Dna ◽  
Functional Classes ◽  
Phage P22 ◽  
Genome Nucleotide Sequence ◽  
Group Members ◽  
Packaging Strategy

ABSTRACT The generalized transducing double-stranded DNA bacteriophage ES18 has an icosahedral head and a long noncontractile tail, and it infects both rough and smooth Salmonella enterica strains. We report here the complete 46,900-bp genome nucleotide sequence and provide an analysis of the sequence. Its 79 genes and their organization clearly show that ES18 is a member of the lambda-like (lambdoid) phage group; however, it contains a novel set of genes that program assembly of the virion head. Most of its integration-excision, immunity, Nin region, and lysis genes are nearly identical to those of the short-tailed Salmonella phage P22, while other early genes are nearly identical to Escherichia coli phages λ and HK97, S. enterica phage ST64T, or a Shigella flexneri prophage. Some of the ES18 late genes are novel, while others are most closely related to phages HK97, lambda, or N15. Thus, the ES18 genome is mosaically related to other lambdoid phages, as is typical for all group members. Analysis of virion DNA showed that it is circularly permuted and about 10% terminally redundant and that initiation of DNA packaging series occurs across an approximately 1-kbp region rather than at a precise location on the genome. This supports a model in which ES18 terminase can move substantial distances along the DNA between recognition and cleavage of DNA destined to be packaged. Bioinformatic analysis of large terminase subunits shows that the different functional classes of phage-encoded terminases can usually be predicted from their amino acid sequence.

scholarly journals Intravirion DNA Can Access the Space Occupied by the Bacteriophage P22 Ejection Proteins

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1504
Author(s):  
Justin C. Leavitt ◽  
Eddie B. Gilcrease ◽  
Brianna M. Woodbury ◽  
Carolyn M. Teschke ◽  
Sherwood R. Casjens
Keyword(s):  
Dna Packaging ◽  
Bacteriophage P22 ◽  
Portal Protein ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Phage P22

Tailed double-stranded DNA bacteriophages inject some proteins with their dsDNA during infection. Phage P22 injects about 12, 12, and 30 molecules of the proteins encoded by genes 7, 16 and 20, respectively. After their ejection from the virion, they assemble into a trans-periplasmic conduit through which the DNA passes to enter the cytoplasm. The location of these proteins in the virion before injection is not well understood, although we recently showed they reside near the portal protein barrel in DNA-filled heads. In this report we show that when these proteins are missing from the virion, a longer than normal DNA molecule is encapsidated by the P22 headful DNA packaging machinery. Thus, the ejection proteins occupy positions within the virion that can be occupied by packaged DNA when they are absent.

scholarly journals Phylogenetic evidence of headful packaging strategy in gene transfer agents

2020 ◽  
Author(s):  
Emma Esterman ◽  
Yuri I. Wolf ◽  
Roman Kogay ◽  
Eugene V. Koonin ◽  
Olga Zhaxybayeva
Keyword(s):  
Gene Transfer ◽  
Rhodobacter Capsulatus ◽  
Large Subunit ◽  
Dna Packaging ◽  
Host Genome ◽  
Bacterial And Archaeal Communities ◽  
History Of ◽  
Viral Dna Packaging ◽  
Packaging Strategy ◽  
Transfer Agents

AbstractGene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

scholarly journals Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus

2016 ◽  
Vol 82 (17) ◽  
pp. 5153-5165 ◽  
Author(s):  
Brian McDonnell ◽  
Jennifer Mahony ◽  
Horst Neve ◽  
Laurens Hanemaaijer ◽  
Jean-Paul Noben ◽  
...  
Keyword(s):  
Streptococcus Thermophilus ◽  
Control Measures ◽  
Phage Group ◽  
Content Type ◽  
Host Interaction ◽  
Adsorption Affinity ◽  
Group Members ◽  
Sequence Relatedness ◽  
Genome Information ◽  
Detrimental Impact

ABSTRACTWe present the complete genome sequences of four members of a novel group of phages infectingStreptococcus thermophilus, designated here as the 987 group. Members of this phage group appear to have resulted from genetic exchange events, as evidenced by their “hybrid” genomic architecture, exhibiting DNA sequence relatedness to the morphogenesis modules of certain P335 groupLactococcus lactisphages and to the replication modules ofS. thermophilusphages. All four identified members of the 987 phage group were shown to elicit adsorption affinity to both their cognateS. thermophilushosts and a particularL. lactisstarter strain. The receptor binding protein of one of these phages (as a representative of this novel group) was defined using an adsorption inhibition assay. The emergence of a novel phage group infectingS. thermophilushighlights the continuous need for phage monitoring and development of new phage control measures.IMPORTANCEPhage predation ofS. thermophilusis an important issue for the dairy industry, where viral contamination can lead to fermentation inefficiency or complete fermentation failure. Genome information and phage-host interaction studies ofS. thermophilusphages, particularly those emerging in the marketplace, are an important part of limiting the detrimental impact of these viruses in the dairy environment.

DNA packaging by the double-stranded DNA bacteriophages

Cell ◽  
1980 ◽  
Vol 21 (2) ◽  
pp. 319-331 ◽  
Author(s):  
William C. Earnshaw ◽  
Sherwood R. Casjens
Keyword(s):  
Dna Packaging ◽  
Double Stranded Dna

scholarly journals Complete Genome Analysis of a Novel Shewanella Phage vB_Sb_QDWS

2021 ◽  
Author(s):  
Lin Tan ◽  
Guanhua Xuan ◽  
Hong Lin ◽  
Jingxue Wang
Keyword(s):  
Complete Genome ◽  
Bioinformatic Analysis ◽  
Lytic Bacteriophage ◽  
Protein Coding ◽  
Putative Protein ◽  
Protein Coding Genes ◽  
Double Stranded Dna ◽  
The Family ◽  
Wastewater Samples ◽  
Complete Genome Analysis

Abstract We present here the results of the analysis of the complete genome sequence of a lytic bacteriophage, vB_Sb_QDWS, which is isolated from wastewater samples collected in Qingdao, China. The genome of phage vB_Sb_QDWS is composed of circular double-stranded DNA that is 47,902 bp in length with a G + C content of 63.16%. It has been predicted to contain 69 putative protein-coding genes. Phage morphology and bioinformatic analysis indicated that vB_Sb_QDWS is a novel phage of the family Siphoviridae.

scholarly journals Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids

2019 ◽  
Vol 116 (9) ◽  
pp. 3556-3561 ◽  
Author(s):  
Oliver W. Bayfield ◽  
Evgeny Klimuk ◽  
Dennis C. Winkler ◽  
Emma L. Hesketh ◽  
Maria Chechik ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Integrity ◽  
Thermus Thermophilus ◽  
Dna Packaging ◽  
Dna Viruses ◽  
Portal Protein ◽  
Single Vertex ◽  
Double Stranded Dna ◽  
Β Sheets

Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Thermus thermophilus. Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.

scholarly journals Lactococcal 949 Group Phages Recognize a Carbohydrate Receptor on the Host Cell Surface

2015 ◽  
Vol 81 (10) ◽  
pp. 3299-3305 ◽  
Author(s):  
Jennifer Mahony ◽  
Walter Randazzo ◽  
Horst Neve ◽  
Luca Settanni ◽  
Douwe van Sinderen
Keyword(s):  
Cheese Whey ◽  
Phage Genome ◽  
Bioinformatic Analysis ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Host Recognition ◽  
Phage Group ◽  
Host Cell Surface ◽  
Reading Frames ◽  
Dairy Fermentation

ABSTRACTLactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly that for the receptor binding protein required for host recognition. Furthermore, we demonstrate that the 949 phages target cell wall phospho-polysaccharides as their receptors, accounting for the specificity of the interactions of these phages with their lactococcal hosts. Such information may ultimately aid in the identification of strains/strain blends that do not present the necessary saccharidic target for infection by these problematic phages.

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