Portal Stability Controls Dynamics of DNA Ejection from Phage

Bacteriophage Challenges in Industrial Processes: A Historical Unveiling and Future Outlook

Humans have used fermentation processes since the Neolithic period, mainly to produce beverages. The turning point occurred in the 1850s, when Louis Pasteur discovered that fermentation resulted from the metabolism of living microorganisms. This discovery led to the fast development of fermented food production. The importance of industrial processes based on fermentation significantly increased. Many branches of industry rely on the metabolisms of bacteria, for example, the dairy industry (cheese, milk, yogurts), pharmaceutical processes (insulin, vaccines, antibiotics), or the production of chemicals (acetone, butanol, acetic acid). These are the mass production processes involving a large financial outlay. That is why it is essential to minimize threats to production. One major threat affecting bacteria-based processes is bacteriophage infections, causing substantial economic losses. The first reported phage infections appeared in the 1930s, and companies still struggle to fight against phages. This review shows the cases of phage infections in industry and the most common methods used to prevent phage infections.

An Overview of Diverse Strategies To Inactivate Enterobacteriaceae-Targeting Bacteriophages

Bacteriophages are viruses that infect bacteria and thus threaten industrial processes relying on the production executed by bacterial cells. Industries bear huge economic losses due to such recurring and resilient infections. Depending on the specificity of the process, there is a need for appropriate methods of bacteriophage inactivation, with an emphasis on being inexpensive and high efficiency. In this review, we summarize the reports on antiphagents, i.e., antibacteriophage agents on inactivation of bacteriophages. We focused on bacteriophages targeting the representatives of the Enterobacteriaceae family, as its representative, Escherichia coli, is most commonly used in the bio-industry. The review is divided into sections dealing with bacteriophage inactivation by physical factors, chemical factors, and nanotechnology-based solutions.

Portal Protein: The Orchestrator of Capsid Assembly for the dsDNA Tailed Bacteriophages and Herpesviruses

Tailed, double-stranded DNA bacteriophages provide a well-characterized model system for the study of viral assembly, especially for herpesviruses and adenoviruses. A wealth of genetic, structural, and biochemical work has allowed for the development of assembly models and an understanding of the DNA packaging process. The portal complex is an essential player in all aspects of bacteriophage and herpesvirus assembly. Despite having low sequence similarity, portal structures across bacteriophages share the portal fold and maintain a conserved function. Due to their dynamic role, portal proteins are surprisingly plastic, and their conformations change for each stage of assembly. Because the maturation process is dependent on the portal protein, researchers have been working to validate this protein as a potential antiviral drug target. Here we review recent work on the role of portal complexes in capsid assembly, including DNA packaging, as well as portal ring assembly and incorporation and analysis of portal structures.

Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail

Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 Å resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an ϵ15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.

The mobility of packaged phage genome controls ejection dynamics

The cell decision between lytic and lysogenic infection is strongly influenced by dynamics of DNA injection into a cell from a phage population, as phages compete for limited resources and progeny. However, what controls the timing of viral DNA ejection events was not understood. This in vitro study reveals that DNA ejection dynamics for phages can be synchronized (occurring within seconds) or desynchronized (displaying minutes-long delays in initiation) based on mobility of encapsidated DNA, which in turn is regulated by environmental factors, such as temperature and extra-cellular ionic conditions. This mechano-regulation of ejection dynamics is suggested to influence viral replication where the cell’s decision between lytic and latent infection is associated with synchronized or desynchronized delayed ejection events from phage population adsorbed to a cell. Our findings are of significant importance for understanding regulatory mechanisms of latency in phage and Herpesviruses, where encapsidated DNA undergoes a similar mechanical transition.

Viruses are tiny ‘parasites’ that smuggle their genetic material inside a cell and then hijack its resources for their own benefit. A viral infection can either be lytic or latent. In a lytic cycle, viruses make their host produce many copies of themselves, ultimately killing the cell. In contrast, during a latent infection, the viruses go ‘dormant’: for instance, some of them can insert their genetic material into the DNA of their host, which then gets passed on as the cell divides.

Certain viruses are capable of both lytic and latent infections. One example is the lambda phage, which targets Escherichia coli bacteria. In the first stage of infection, the genetic material ‘shoots out’ of the virus and gets injected inside the bacterium. The dynamics of the ejection process determine the type of infection that will follow. If multiple phages release their genomes quickly and within seconds of each other into the same cell, the bacterium tends to incorporate the viral DNA into its own genome, leading to a latent cycle. If the infections take place more slowly and not all at the same time, the cell is more likely to go through a lytic phase. However, the mechanism behind the different injection behaviors is still unknown; in particular, it is unclear which factors control the specificities of the ejection process in the first place.

Here, Alex Evilevitch demonstrates that the mechanical state of the phage DNA just before ejection dictates how the genetic material will then be injected in the bacteria. The experiments measured the stiffness of the DNA and the amount of heat given off during infection. Like fluid toothpaste, if the DNA is more liquid and flexible, it gets ejected quickly and simultaneously from several phages. Then, the genetic information of these viruses can be incorporated in the genome of the bacteria. On the other hand, if the DNA is more solid, it is likely to ‘stick’ and take time before it can be squeezed out: the injections become unsynchronised, which leads to a lytic phase.

Evilevitch then shows that the environment can influence the properties of the phages’ genome. A little more heat, or certain chemicals, can make the DNA more fluid inside the viruses, and change the way it can be injected inside the bacteria.

Many viruses that cause diseases in humans – from cold sores to glandular fever – can switch between the lytic and latent cycles. For the first time, these results show that the mechanical properties of the DNA inside a virus influence the ‘decision’ between the two types of infection. This knowledge could help us prevent infections from becoming lytic and ultimately allow us to control the spread of disease.

In Vitro Studies of Lipopolysaccharide-Mediated DNA Release of Podovirus HK620

Gram-negative bacteria protect themselves with an outermost layer containing lipopolysaccharide (LPS). O-antigen-specific bacteriophages use tailspike proteins (TSP) to recognize and cleave the O-polysaccharide part of LPS. However, O-antigen composition and structure can be highly variable depending on the environmental conditions. It is important to understand how these changes may influence the early steps of the bacteriophage infection cycle because they can be linked to changes in host range or the occurrence of phage resistance. In this work, we have analyzed how LPS preparations in vitro trigger particle opening and DNA ejection from the E. coli podovirus HK620. Fluorescence-based monitoring of DNA release showed that HK620 phage particles in vitro ejected their genome at velocities comparable to those found for other podoviruses. Moreover, we found that HK620 irreversibly adsorbed to the LPS receptor via its TSP at restrictive low temperatures, without opening the particle but could eject its DNA at permissive temperatures. DNA ejection was solely stimulated by LPS, however, the composition of the O-antigen dictated whether the LPS receptor could start the DNA release from E. coli phage HK620 in vitro. This finding can be significant when optimizing bacteriophage mixtures for therapy, where in natural environments O-antigen structures may rapidly change.