Elucidation of the molecular mechanisms of retrons in anti-phage defense

• Applicant: Professor Dr. Jens Hör
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms ; Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology
• Term: from 2021 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 466645764

• Final Report Year: 2023

Final Report Abstract

Cell-autonomous immunity is the arsenal of intracellular defense strategies providing protection against invading pathogens. In bacteria, innate immunity is represented by an extremely diverse set of defense systems that confer protection against bacterial viruses (phages). Many of these bacterial defense systems are the evolutionary origin of eukaryotic innate immunity such as the cGAS-STING pathway, viperins or gasdermins. Additionally, bacteria encode for a plethora of defense systems that have not been conserved across the tree of life. However, since most bacterial anti-phage defense systems have only recently been discovered, the exact molecular mechanism of defense is unknown for the majority of them. Here, I studied the molecular mechanisms of two bacterial anti-phage defense systems: retrons and the bacterial ISG15-like (Bil) defense system. Retrons are defense systems that produce a unique RNA/DNA hybrid molecule called msDNA, which acts in concert with an effector protein to kill the infected cell after phage infection has been sensed in order to prevent further viral spread. By studying one retron in detail, I was able to show that the retron senses infection via direct binding of its msDNA to the single-stranded DNA-binding protein of the phage. This binding then leads to the activation of the effector protein and with it the death of the infected cell. The Bil system is a bacterial homolog of the eukaryotic ISG15 innate immune system and consists of a ubiquitin-like protein, ubiquitin-conjugating E1 and E2 enzymes as well as a deubiquitinase. I showed that the Bil system specifically conjugates its ubiquitin-like protein to the central tail fiber of the phage, which is an essential structural protein at the tip of the tail of the virion that is involved in tail assembly and binding to the host bacterium. This leads to the release of phage virions that are either tailless or are modified by the ubiquitin-like protein. Both of these types of virions have strongly reduced infectivity, which protects the surrounding bacteria from infection. Together, I identified how a retron senses phage infection and showed that conjugation of ubiquitin-like proteins is an antiviral strategy conserved across the tree of life.

Publications

• An expanded arsenal of immune systems that protect bacteria from phages. Cell Host & Microbe, 30(11), 1556-1569.e5.
  Millman, Adi; Melamed, Sarah; Leavitt, Azita; Doron, Shany; Bernheim, Aude; Hör, Jens; Garb, Jeremy; Bechon, Nathalie; Brandis, Alexander; Lopatina, Anna; Ofir, Gal; Hochhauser, Dina; Stokar-Avihail, Avigail; Tal, Nitzan; Sharir, Saar; Voichek, Maya; Erez, Zohar; Ferrer, Jose Lorenzo M.; Dar, Daniel ... & Sorek, Rotem
  
• Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly. Cold Spring Harbor Laboratory.
  Hör, Jens; Wolf, Sharon G. & Sorek, Rotem
  
• Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell, 186(9), 1863-1876.e16.
  Stokar-Avihail, Avigail; Fedorenko, Taya; Hör, Jens; Garb, Jeremy; Leavitt, Azita; Millman, Adi; Shulman, Gabriela; Wojtania, Nicole; Melamed, Sarah; Amitai, Gil & Sorek, Rotem