Molecular architecture of bacteriophage T4

Mesyanzhinov, Vadim V.; Leiman, P.G.; Kostyuchenko, V.A.; Kurochkina, Lidia P.; Miroshnikov, Konstantin A.; Сыкилинда, Н. Н.; Shneider, Mikhail M.

doi:10.1007/s10541-005-0064-9

Cited by 24 publications

(28 citation statements)

References 126 publications

(141 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This assay targets a 163-bp region of the 1.97-kb gp18 tail protein gene, which forms the contractile sheath. 4,5 The 169-kb T4 bacteriophage genome contains approximately ten times more nucleotide base pairs than a typical plasmid DNA; thus, it should be efficiently extracted. The highly complex T4 bacteriophage capsid effectively protects the encapsulated DNA from nucleases present in biological fluids.…”

mentioning

confidence: 99%

Implementation of a T4 Extraction Control for Molecular Assays of Cerebrospinal Fluid and Stool Specimens

Gerriets

Greiner

Gebhart

2008

The Journal of Molecular Diagnostics

View full text Add to dashboard Cite

The use of appropriate extraction and amplification controls for acellular specimens is not standardized in the clinical laboratory community. Extraction controls and checks for inhibitors of amplification in cellular specimens are most often accomplished by amplification of an internal human genomic target. This approach is not feasible for acellular specimens, which may contain little or no amplifiable genomic material. Other specimen types , such as stool, frequently contain amplification inhibitors. Failure to test for these inhibitors can result in the reporting of false-negative results. The goal of this study was to evaluate the use of a T4 bacteriophage as an extraction and amplification control for acellular specimens. The T4 bacteriophage assay was evaluated for use as a control in 290 specimens , including cerebrospinal fluid , serum , and filtered stool. The use of appropriate extraction and amplification controls for acellular specimens is not standardized in the clinical laboratory community. Inhibitors present in some patient specimens decrease the efficiency of amplification and, if not controlled, can result in the reporting of false-negative results. False-negatives may also arise from undetected extraction failures. Accrediting agencies expect diagnostic laboratories to control for these variables. To meet quality assurance standards recommended by accrediting agencies, a method to detect the presence of inhibitors, while simultaneously providing a control for extraction in acellular specimens, is needed. Extraction controls and amplification inhibitor checks for cellular specimens are most often accomplished by amplification of an internal human genomic target. This approach is not feasible for acellular specimens, which may contain little or no amplifiable genomic material. In our experience, genomic DNA targets are successfully amplified in only approximately 40% of cerebrospinal fluid (CSF) specimens. Other acellular specimen types, such as stool, frequently contain amplification inhibitors.Several forms of internal controls have been evaluated, including plasmid DNA, ribosomal RNA, armored RNA, and Lambda phage. Plasmid-derived DNA may be degraded before extraction because it is unprotected and subjected to nucleases. 1 To protect the plasmid DNA, further packaging is required in a bacteriophage, which adds more time and expense to the control. Ribosomal 16 or 18S RNA is a convenient control for reverse transcription-polymerase chain reaction (PCR). Armored RNA is a nucleic acid packaged in bacteriophage coat proteins that protect the RNA from ribonucleases. The RNA is released from its protective coat during the extraction procedure and can be used as a control for reverse transcription-PCR. 2 The disadvantage of this technology is that it is proprietary and expensive, and the reverse transcription process adds unnecessary time and expense to DNA-targeted assays. Additionally, inhibitors of reverse transcription and of PCR cannot be distinguished. Specially engineered Lambda phage DNA fr...

show abstract

mentioning

confidence: 99%

Implementation of a T4 Extraction Control for Molecular Assays of Cerebrospinal Fluid and Stool Specimens

Gerriets

Greiner

Gebhart

2008

The Journal of Molecular Diagnostics

View full text Add to dashboard Cite

show abstract

“…Mostly they contain a sixfold symmetric baseplate composed of more than 16 different gene products. In total, myoviruses are the most complex phages [25][26][27]. Siphoviruses contain a long, flexible tail structure that is not contractile and a threefold symmetric baseplate [28].…”

Section: Bacteriophagesmentioning

confidence: 99%

Endosialidases: Versatile Tools for the Study of Polysialic Acid

Jakobsson

Schwarzer

Jokilammi

et al. 2012

Topics in Current Chemistry

View full text Add to dashboard Cite

Polysialic acid is an α2,8-linked N-acetylneuraminic acid polymer found on the surface of both bacterial and eukaryotic cells. Endosialidases are bacteriophage-borne glycosyl hydrolases that specifically cleave polysialic acid. The crystal structure of an endosialidase reveals a trimeric mushroom-shaped molecule which, in addition to the active site, harbors two additional polysialic acid binding sites. Folding of the protein crucially depends on an intramolecular C-terminal chaperone domain that is proteolytically released in an intramolecular reaction. Based on structural data and previous considerations, an updated catalytic mechanism is discussed. Endosialidases degrade polysialic acid in a processive mode of action, and a model for its mechanism is suggested. The review summarizes the structural and biochemical elucidations of the last decade and the importance of endosialidases in biochemical and medical applications. Active endosialidases are important tools in studies on the biological roles of polysialic acid, such as the pathogenesis of septicemia and meningitis by polysialic acid-encapsulated bacteria, or its role as a modulator of the adhesion and interactions of neural and other cells. Endosialidase mutants that have lost their polysialic acid cleaving activity while retaining their polysialic acid binding capability have been fused to green fluorescent protein to provide an efficient tool for the specific detection of polysialic acid.

show abstract

“…It can also be easily grown in large quantities. T4 is one of the most complex viruses, but its structure was investigated and very well described using X-ray crystallography, cryo-EM, and three-dimensional (3D) image reconstruction (Fokine et al 2004;Mesyanzhinov et al 2004;Olson et al 2001).…”

Section: Introductionmentioning

confidence: 99%

“…The genome, which is dsDNA, is tightly packed in the protein capsid. Considering that some viruses have genomes containing only 5 × 10 3 bp (bacteriophage φX174), T4 seems to be a giant (Mesyanzhinov et al 2004). Its DNA consists of 1.69 × 10 5 bp constituting 289 open reading frames, eight tRNA genes, and at least two genes whose products are small RNAs of unknown function.…”

Section: Introductionmentioning

confidence: 99%

“…More than 150 genes of this virus have been characterized, 62 of which have been described as "essential". The virion consists of about 50 different kinds of proteins (Mesyanzhinov et al 2004), of which at least 12 build the T4 head (Leiman et al 2003). Except for nucleic acid, there are only a few non-protein constituents in the virion: polyamines associated with DNA (putrescine, spermidine, cadaverine), ATP and Ca 2+ associated with the tail sheath, and dihydropteroylhexaglutamate associated with the baseplate (Birge 2006).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular modification of T4 bacteriophage proteins and its potential application — Review

et al. 2009

View full text Add to dashboard Cite

Bacteriophage T4 is a virus with well-known genetics, structure, and biology. Such techniques as X-ray crystallography, cryo-EM, and three-dimensional (3D) image reconstruction allowed describing its structure very precisely. The genome of this bacteriophage was completely sequenced, which opens the way for the use of many molecular techniques, such as site-specific mutagenesis, which was widely applied, e.g., in investigating the functions of some essential T4 proteins. The phage-display method, which is commonly applied in bacteriophage modifications, was successfully used to display antigens (PorA protein, VP2 protein of vvIBDV, and antigens of anthrax and HIV) on T4's capsid platform. As first studies showed, the phage-display system as well as site-specific mutagenesis may also be used to modify interactions between phage particles and mammalian cells or to obtain phages infecting species other than the host bacteria. These may be used, among others, in the constantly developing bacteriophage therapy. All manipulations of this popular bacteriophage may enable the development of vaccine technology, phage therapy, and other branches of biological and medical science.

show abstract

Molecular architecture of bacteriophage T4

Cited by 24 publications

References 126 publications

Implementation of a T4 Extraction Control for Molecular Assays of Cerebrospinal Fluid and Stool Specimens

Implementation of a T4 Extraction Control for Molecular Assays of Cerebrospinal Fluid and Stool Specimens

Endosialidases: Versatile Tools for the Study of Polysialic Acid

Molecular modification of T4 bacteriophage proteins and its potential application — Review

Contact Info

Product

Resources

About