BacterioFiles 360 - Fellow Phages Fight Fortifications

Bacteriophage
By Rolf Lood, Matthias Mörgelin,
Anna Holmberg, Magnus Rasmussen
and Mattias Collin
BMC Microbiology 2008,
8:139 doi:10.1186/1471-2180-8-139
CC BY 2.5

This episode: Bacteriophages with defenses against bacterial CRISPR defenses have to work together to succeed!

Thanks to Drs. Edze Westra and Stineke van Houte for their contributions, and to Calvin Cornell for suggesting this story!
Download Episode (9.6 MB, 10.5 minutes)

Show notes:
Microbe of the episode: Lactobacillus casei subsp. alactosus

News item 1/News item 2

Journal Papers:
Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J. 2018. Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell 174:917-925.e10.

Landsberger M, Gandon S, Meaden S, Rollie C, Chevallereau A, Chabas H, Buckling A, Westra ER, Houte S van. 2018. Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity. Cell 174:908-916.e12.

Other interesting stories:

• Aphids can see fluorescence from pathogenic bacteria to avoid them on leaves
• Fecal transplants from yourself before antibiotics could restore gut community after antibiotics
• Engineering E. coli to convert CO₂ and methanol into useful products (paper)
• Used panel of bioluminescent bacteria to test artificial sweetener toxicity

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook.

Episode outline:

• Background: Organisms evolve, always changing to adapt to new situations
• So nearly impossible to stop/kill/keep out of somewhere, for very long
• Find new ways to resist and survive
• Like hosts/parasites/pathogens
• New antibiotic/pesticide/etc meets resistance eventually, sometimes very quickly
• Amazing that some vaccines still effective, viruses don't evolve resistance (polio, measles)
• Others stop working pretty fast – flu
• And other organisms evolve resistance, then pathogens evolve to overcome
• CRISPR system in bacteria specifically targets phages, destroys genome
• Phages can change sequence to avoid targeting
• Then bacteria develop new target
• What’s new: But now, two groups publishing in Cell have described another way that phages can overcome CRISPR defenses, and discovered that these viruses have to work together to succeed!
• Anti-CRISPR proteins target specific proteins of bacterial defense
• Inhibit binding to target DNA or degradation
• But require certain concentration to work
• First is a team from UC San Francisco and Montana State University.
• Methods: Tried propagating 5 phages, each with different anti-CRISPR protein
• Infected Pseudomonas aeruginosa with CRISPR
• CRISPR protected bacteria somewhat, reducing some phages' infection efficiency
• Tried switching around proteins, some more protective to phages than others
• Depends on strength of CRISPR targeting too
• But all require certain concentration; determined how much it took to allow virus replication
• Needed certain amount of viruses per host cell, more for weaker anti-CRISPR proteins
• Made phage that could produce protein but not replicate, tested interaction with normal phages
• Assisted normal ones in replicating significantly
• Especially interesting paired with phages that replicate but don't produce protein
• Former kind get in, produce anti-CRISPR protein to shut off defenses, then stop
• Latter get in and replicate, taking advantage of situation
• Teamwork!
• Second is a team from University of Exeter and CNRS Universite de Montpellier: Mariann Landsberger, Sylvain Gandon, Sean Meaden, Clare Rollie, Anne Chevallereau, Helene Chabas, Angus Buckling, Edze Westra, and Stineke van Houte.
• Here are Drs. Westra and van Houte summarizing their work: statement
• Studies basically independent replications of each other
• Enhances reliability of findings
• Summary: Phages with anti-CRISPR genes infect a bacterial host one after another until the proteins they produce build up enough in the cell to allow their infection to succeed. So many sacrifice themselves for the cause!
• Applications and implications: Relevant to phage therapy – can overcome bacterial defenses
• Would require bigger dose though
• What do I think: Clonal behavior, not altruism
• If 100 bacteria, and takes 3 phages per cell for successful infection
• Need 300 phages to infect all, but 200 won't succeed, sacrifice themselves
• But all same genetics so doesn't matter, basically same entity
• Plus a lot more get created from infection than are lost

Author Transcript:
Parasites infect lots of organisms and are very good at suppressing the immune system of these hosts. For example, parasitic worms are very good at doing that, but also many viruses like HIV and human papillomavirus.

So bacteria also have immune systems that protect them against viruses, and these viruses can also immunosuppress. And we've studied how immunosuppression by these viruses can lead to successful infection. And what our work shows is that viruses, they need to work together. The first virus enters the host, but this is a kamikaze virus, so it will be destroyed by the immune system. But it still manages to immunosuppress its host, and now the next virus comes along, enters that host, and can now successfully replicate on that host.

And this teamwork means that viruses need to be at high density for them to amplify. If they are at low densities, they cannot work together, and therefore they will disappear. And initially, when we saw that, we got really confused because we saw viruses disappearing in our experimental treatments. But it turns out that this is a very reproducible result and probably also plays an important role in determining epidemics in the real world, where viruses and other pathogens need to be at high enough densities in order to cause these epidemics.