The crystal structure of the double-stranded DNA bacteriophage HK97 mature empty capsid was determined at 3.6 angstrom resolution. The 660 angstrom diameter icosahedral particle contains 420 subunits ...with a new fold. The final capsid maturation step is an autocatalytic reaction that creates 420 isopeptide bonds between proteins. Each subunit is joined to two of its neighbors by ligation of the side-chain lysine 169 to asparagine 356. This generates 12 pentameric and 60 hexameric rings of covalently joined subunits that loop through each other, creating protein chainmail: topologically linked protein catenanes arranged with icosahedral symmetry. Catenanes have not been previously observed in proteins and provide a stabilization mechanism for the very thin HK97 capsid.
Jumbo Bacteriophages Hendrix, R. W.
Current topics in microbiology and immunology,
2009, Letnik:
328
Book Chapter, Journal Article
Recenzirano
There is currently a handful of genome sequences available for tailed bacteriophages with genomes of more than 200 kbp of DNA, designated here as giant or jumbo phages. The majority of the proteins ...predicted from the genome sequences of these phages have no matches in the current sequence databases, and the genomes themselves are diverse enough to preclude the sorts of detailed comparative analysis that has benefited study of the smaller phages, for which hundreds of genome sequences are available. However, it is informative to extrapolate the better known genome organizations and mechanisms of evolution seen in the smaller phages to the jumbo phages. In this way, we see that the jumbo phages encode the same functions as the smaller phages, supplemented with large numbers of mostly small genes of mostly undiscovered functions. A case can be made that the jumbo phages evolved from smaller tailed phages, possibly in a process mediated by the constraints imposed on genome size by capsid size.
Bacteriophages are the most abundant organisms in the biosphere and play major roles in the ecological balance of microbial life. The genomic sequences of ten newly isolated mycobacteriophages ...suggest that the bacteriophage population as a whole is amazingly diverse and may represent the largest unexplored reservoir of sequence information in the biosphere. Genomic comparison of these mycobacteriophages contributes to our understanding of the mechanisms of viral evolution and provides compelling evidence for the role of illegitimate recombination in horizontal genetic exchange. The promiscuity of these recombination events results in the inclusion of many unexpected genes including those implicated in mycobacterial latency, the cellular and immune responses to mycobacterial infections, and autoimmune diseases such as human lupus. While the role of phages as vehicles of toxin genes is well established, these observations suggest a much broader involvement of phages in bacterial virulence and the host response to bacterial infections.
Bacteriophage genomics Hendrix, Roger W
Current opinion in microbiology,
10/2003, Letnik:
6, Številka:
5
Journal Article
Recenzirano
Comparative genomic studies of bacteriophages, especially the tailed phages, together with environmental studies, give a dramatic new picture of the size, genetic structure and dynamics of this ...population. Sequence comparisons reveal some of the detailed mechanisms by which these viruses evolve and influence the evolution of their bacterial and archaeal hosts. We see rampant horizontal exchange of sequences among genomes, mediated by both homologous and nonhomologous recombination. High frequency exchange among phages occupying similar ecological niches leads to a high degree of mosaic diversity in local populations. Horizontal exchange also takes place at lower frequency across the entire span of phage sequence space.
Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage HK97 capsid, Head-II, was recently solved by crystallography, revealing a ...catenated cross-linked topology. We have visualized its precursor, Prohead-II, by cryoelectron microscopy and modeled the conformational change by appropriately adapting Head-II. Rigid-body rotations (∼40 degrees) cause switching to an entirely different set of interactions; in addition, two motifs undergo refolding. These changes stabilize the capsid by increasing the surface area buried at interfaces and bringing the cross-link-forming residues, initially ∼40 angstroms apart, close together. The inner surface of Prohead-II is negatively charged, suggesting that the transition is triggered electrostatically by DNA packaging.
Phage Genomics: Small Is Beautiful Brüssow, Harald; Hendrix, Roger W.
Cell,
01/2002, Letnik:
108, Številka:
1
Book Review, Journal Article
Recenzirano
Odprti dostop
The Age of Genomics dawned only gradually for bacteriophages. It was 1977 when the genome of phage φX174 was published and 1983 when the “large” genome of phage λ hit the streets. More recently, the ...pace has quickened, so that we now have over 100 complete phage genomes and can expect thousands in a very few years. These sequences have been marvelously informative for the biology of the individual phages, but with the advent of high volume sequencing technology, the real excitement for phage biology is that it is now possible to analyze the sequences together and thereby address—for the first time at whole genome resolution—a set of fundamental biological questions related to populations: What is the structure of the global phage population? What are its dynamics? How do phages evolve? This is Comparative Genomics with a capital “C”.
AMD3100 is a CXCR4 receptor inhibitor with anti–HIV-1 activity in vitro. We tested the safety, pharmacokinetics, and antiviral effect of AMD3100 administered for 10 days by continuous intravenous ...infusion in an open-label dose escalation study from 2.5 to 160 μg/kg/h. Forty HIV-infected patients with an HIV RNA level >5000 copies/mL on stable antiretroviral (ARV) regimens or off therapy were enrolled. Syncytium-inducing (SI) phenotype in an MT-2 cell assay was required in higher dose cohorts. Most subjects were black (55%), male (98%), and off ARV therapy. HIV phenotype was SI (30%), non–SI (45%), or not tested (25%). One patient (5 μg/kg/h) had serious and possibly drug-related thrombocytopenia. Two patients (40 and 160 μg/kg/h) had unexpected, although not serious, premature ventricular contractions. Most patients in the 80- and 160-μg/kg/h cohorts had paresthesias. Steady-state blood concentration and area under the concentration-time curve were dose proportional across all dose levels; the median terminal elimination half-life was 8.6 hours (range8.1–11.1 hours). Leukocytosis was observed in all patients, with an estimated maximum effect of 3.4 times baseline (95% confidence interval2.9–3.9). Only 1 patient, the patient whose virus was confirmed to use purely CXCR4 and who also received the highest dose (160 μg/kg/h), had a significant 0.9-log10 copies/mL HIV RNA drop at day 11. Overall, however, the average change in viral load across all patients was +0.03 log10 HIV RNA. Given these results, AMD3100 is not being further developed for ARV therapy, but development continues for stem cell mobilization.
The dsDNA-tailed bacteriophages are probably the largest evolving group in the Biosphere and they are arguably very ancient. Comparative examination of genomes indicates that the hallmark of phage ...evolution is horizontal exchange of sequences. This is accomplished, first, by rampant non-homologous recombination between different genomes and, second, by reassortment of the variant sequences so created through homologous recombination. The comparative analysis suggests mechanisms by which new genes can be added to phage genomes and by which genes with novel functions may be assembled from parts. Horizontal exchange of sequences occurs most frequently among closely related phages, but it also extends across the entire global population at lower frequency. Bacteriophages also have probable ancestral connections with viruses of eukaryotes and archaea.
Occurrence of Resveratrol in Edible Peanuts Sanders, Timothy H; McMichael, Robert W; Hendrix, Keith W
Journal of agricultural and food chemistry,
04/2000, Letnik:
48, Številka:
4
Journal Article
Recenzirano
Resveratrol has been associated with reduced cardiovascular disease and reduced cancer risk. This phytoalexin has been reported in a number of plant species, including grapes, and may be one of the ...compounds responsible for the health benefits of red wine. Analytical methods for measuring resveratrol in wine and peanuts were adapted to isolate, identify, and quantify resveratrol in several cultivars of peanuts. Aqueous ethanol (80% v/v) extracts from peanuts without seed coats were purified over alumina/silica gel columns and analyzed by reversed phase HPLC using a C-18 column. Peanuts from each market type, Virginia, runner, and Spanish, produced in four different locations contained from 0.03 to 0.14 μg of resveratrol/g. Seed coats from runner and Virginia types contained ∼0.65 μg/g of seed coat, which is equivalent to <0.04 μg/seed. Quantitative analysis of 15 cultivars representing 3 peanut market types, which had been cold stored for up to 3 years, indicated a range of 0.02−1.79 μg/g of peanut compared to 0.6−8.0 μg/mL in red wines. Keywords: Peanuts; resveratrol; 3,5,4‘-trihydroxystilbene; Arachis hypogaea L.
A programmed translational frameshift similar to frameshifts in retroviral
gag-pol genes and bacterial insertion elements was found to be strongly conserved in tail assembly genes of dsDNA phages and ...to be independent of sequence similarities. In bacteriophage λ, this frameshift controls production of two proteins with overlapping sequences, gpG and gpGT, that are required for tail assembly. We developed bioinformatic approaches to identify analogous −1 frameshifting sites and experimentally confirmed our predictions for five additional phages. Clear evidence was also found for an unusual but analogous −2 frameshift in phage Mu. Frameshifting sites could be identified for most phages with contractile or noncontractile tails whose length is controlled by a tape measure protein. Phages from a broad spectrum of hosts spanning Eubacteria and Archaea appear to conserve this frameshift as a fundamental component of their tail assembly mechanisms, supporting the idea that their tail genes share a common, distant ancestry.
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