Archaeal Virus as Cat Toy

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

This post is/was inspired by Stedman, K. M., M. DeYoung, M. Saha, M. B. Sherman, and M. C. Morais. 2015. Structural insights into the architecture of the hyperthermophilic fusellovirus SSV1. Virology 474:105-109. (ncbi.nlm.nih.gov/pubmed/25463608)

Turns out this spindle-shaped virus of Sulfolobus, potentially resembling “two fused fullerene cones”, is an almost perfect prolate spheroid, which (apparently) is the shape of a pig’s bladder, which in turn is the shape of the American football.

The virus itself, however, possesses a “hexameric tail”, which sort of looks like streamers emanating from one end of the “football”. And that, in turn, sure looks an awful lot like this, particularly were the tail trimmed:

http://www.entirelypets.com/jw-pet-cataction-football-streamers.html

“Art” imitates life belongs to cats!

For my renderings on this subject – archaeal virus as football – see:

https://www.facebook.com/pages/Bacteriophage-Ecology-Group/111721928901953

 

 

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The ecology of viruses that infect eukaryotic algae

The world of algal viruses has only gotten more interesting in recent years as it has become increasingly clear just the sheer quantity of mortality they cause and how much that drives global nutrient cycling in ways we’ve been largely blind to.

Chlorovirus

The ecology of viruses that infect eukaryotic algae

Because viruses of eukaryotic algae are incredibly diverse, sweeping generalizations about their ecology are rare. These obligate parasites infect a range of algae and their diversity can be illustrated by considering that isolates range from small particles with ssRNA genomes to much larger particles with 560 kb dsDNA genomes. Molecular research has also provided clues about the extent of their diversity especially considering that genetic signatures of algal viruses in the environment rarely match cultivated viruses. One general concept in algal virus ecology that has emerged is that algal viruses are very host specific and most infect only certain strains of their hosts; with the exception of viruses of brown algae, evidence for interspecies infectivity is lacking. Although some host–virus systems behave with boom-bust oscillations, complex patterns of intraspecies infectivity can lead to host–virus coexistence obfuscating the role of viruses in host population dynamics. Within the framework of population dynamics, host density dependence is an important phenomenon that influences virus abundances in nature. Variable burst sizes of different viruses also influence their abundances and permit speculations about different life strategies, but as exceptions are common in algal virus ecology, life strategy generalizations may not be broadly applicable. Gaps in knowledge of virus seasonality and persistence are beginning to close and investigations of environmental reservoirs and virus resilience may answer questions about virus inter-annual recurrences. Studies of algal mortality have shown that viruses are often important agents of mortality reinforcing notions about their ecological relevance, while observations of the surprising ways viruses interact with their hosts highlight the immaturity of our understanding. Considering that just two decades ago algal viruses were hardly acknowledged, recent progress affords the optimistic perspective that future studies will provide keys to unlocking our understanding of algal virus ecology specifically, and aquatic ecosystems generally.

Data Storage and Standard Parts

Genetic data storage, scaleable cell-cell communication, and still-better gene expression, all thanks to phage!

Cross-talk between Diverse Serine Integrases

Abstract
Phage-encoded serine integrases are large serine recombinases that mediate integrative and excisive site-specific recombination of temperate phage genomes. They are well suited for use in heterologous systems and for synthetic genetic circuits as the attP and attB attachment sites are small (< 50 bp), there are no host factor or DNA supercoiling requirements, and they are strongly directional, doing only excisive recombination in the presence of a recombination directionality factor. Combining different recombinases that function independently and without cross-talk to construct complex synthetic circuits is desirable, and several different serine integrases are available. However, we show here that these functions are not reliably predictable, and we describe a pair of serine integrases encoded by mycobacteriophages Bxz2 and Peaches with unusual and unpredictable specificities. The integrases share only 59% amino acid sequence identity and the attP sites have fewer than 50% shared bases, but they use the same attB site and there is non-reciprocal cross-talk between the two systems. The DNA binding specificities do not result from differences in specific DNA contacts but from the constraints imposed by the configuration of the component half-sites within each of the attachment site DNAs.

New Applications for Phage Integrases

Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line.

21st Biennial Evergreen International Phage Meeting!

the-evergreen-state-college

You can register for the 21st Biennial Evergreen International Phage Meeting Aug. 2-7 on the Evergreen web site: www.evergreen.edu/phage.  If you register by April 30, you will qualify for the “Early Registration” rate: $600 for academics, $700 for Corporate Rate, $450 for graduate and undergraduate students and guests.  This covers all meeting costs, including room and board.  (If you choose to stay off campus, it will be $150 less, but still include meals.)  Some registration assistance is potentially available.

You will then have until May 24 to at least pay a $100 nonrefundable deposit, apply for assistance, or tell us that you are waiting for a visa.  If you register after May 1, the rates will be $100 more in each category.  Further meeting information is on the web site and will be regularly updated there.